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Conserved domains on  [gi|766615769|ref|WP_044792604|]
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MULTISPECIES: sigma-70 family RNA polymerase sigma factor [Bacillus]

Protein Classification

PRK12543 family protein( domain architecture ID 11485987)

PRK12543 family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 14-192 1.90e-92

RNA polymerase sigma factor; Provisional


:

Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 267.37  E-value: 1.90e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  14 TLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKRWMR 93
Cdd:PRK12543   1 MLSGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKRWRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  94 LRIIKKAEEQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKK 173
Cdd:PRK12543  81 FRIFEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKK 160

                        170
                 ....*....|....*....
gi 766615769 174 LRQKEQVEEIFLGEVGNVK 192
Cdd:PRK12543 161 LRQKEQIEEIFLGEVGNVK 179
 
Name Accession Description Interval E-value
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 14-192 1.90e-92

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 267.37  E-value: 1.90e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  14 TLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKRWMR 93
Cdd:PRK12543   1 MLSGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKRWRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  94 LRIIKKAEEQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKK 173
Cdd:PRK12543  81 FRIFEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKK 160

                        170
                 ....*....|....*....
gi 766615769 174 LRQKEQVEEIFLGEVGNVK 192
Cdd:PRK12543 161 LRQKEQIEEIFLGEVGNVK 179
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-177 1.36e-43

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: 143.21  E-value: 1.36e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   1 MKDETvytDLIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAI 80
Cdd:COG1595    1 MSSDE---ELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIAR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  81 KQIHSYRRKRWMRLRIIKKAEEQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPI 160
Cdd:COG1595   78 NLAIDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                        170
                 ....*....|....*..
gi 766615769 161 GTVKSRIHAALKKLRQK 177
Cdd:COG1595  158 GTVKSRLSRARKKLREA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 20-177 7.50e-32

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: 112.44  E-value: 7.50e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   20 EAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKRwMRLRIIKK 99
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRK-RRLRRELD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 766615769  100 AEEQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQK 177
Cdd:TIGR02937  80 LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 121-175 6.13e-15

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: 65.97  E-value: 6.13e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 766615769 121 NQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLR 175
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 ...
 122-174 2.62e-13

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 61.70  E-value: 2.62e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 766615769  122 QKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKL 174
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
 
Name Accession Description Interval E-value
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 14-192 1.90e-92

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 267.37  E-value: 1.90e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  14 TLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKRWMR 93
Cdd:PRK12543   1 MLSGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKRWRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  94 LRIIKKAEEQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKK 173
Cdd:PRK12543  81 FRIFEKAEEQRKPVSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKK 160

                        170
                 ....*....|....*....
gi 766615769 174 LRQKEQVEEIFLGEVGNVK 192
Cdd:PRK12543 161 LRQKEQIEEIFLGEVGNVK 179
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-177 1.36e-43

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: 143.21  E-value: 1.36e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   1 MKDETvytDLIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAI 80
Cdd:COG1595    1 MSSDE---ELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIAR 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  81 KQIHSYRRKRWMRLRIIKKAEEQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPI 160
Cdd:COG1595   78 NLAIDHLRKRRRRRELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                        170
                 ....*....|....*..
gi 766615769 161 GTVKSRIHAALKKLRQK 177
Cdd:COG1595  158 GTVKSRLSRARKKLREA 174
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 20-177 7.50e-32

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: 112.44  E-value: 7.50e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   20 EAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKRwMRLRIIKK 99
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRK-RRLRRELD 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 766615769  100 AEEQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQK 177
Cdd:TIGR02937  80 LLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 16-176 1.17e-28

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 105.05  E-value: 1.17e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  16 SGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKRWMRLR 95
Cdd:PRK11924   9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKA 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  96 IIKKAEEQrkPVQIDFSND----VISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAAL 171
Cdd:PRK11924  89 VLSDDALE--PEFAETAETpeaaLLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRAR 166


                 ....*
gi 766615769 172 KKLRQ 176
Cdd:PRK11924 167 QLLRE 171
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 8-175 4.73e-26

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 98.17  E-value: 4.73e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   8 TDLIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYR 87
Cdd:PRK09638   6 KELIQKAKKGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  88 RKR---WMRLRIIKKAEEQRKPVQIDFSNdviskISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVK 164
Cdd:PRK09638  86 RKQkreKLRLQRAKEETLRKEKWEAAIKG-----AEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVK 160

                        170
                 ....*....|.
gi 766615769 165 SRIHAALKKLR 175
Cdd:PRK09638 161 SRVHHGIKQLR 171
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 16-177 3.67e-23

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 91.02  E-value: 3.67e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  16 SGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWL----IGLAIKqihSYRR-KR 90
Cdd:PRK09652   6 RGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLyriaRNTAIN---YLRKqGR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  91 WMR---LRIIKKAEEQRKPVQIDFS---NDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVK 164
Cdd:PRK09652  83 RPPasdVDAEEAEDFDLADALRDIStpeNELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVR 162

                        170
                 ....*....|...
gi 766615769 165 SRIHAALKKLRQK 177
Cdd:PRK09652 163 SRIFRAREALRAK 175
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 10-176 2.24e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 83.61  E-value: 2.24e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  10 LIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIeDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRK 89
Cdd:PRK12518   1 LILRCQRGDRQSFRQLYRRYQQKVRSTLYQLC-GRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQ 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  90 RWMRLRIIKKAEEQRKPVQIDFSNDvISKISNQKLIEL-IHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIH 168
Cdd:PRK12518  80 FAQRPSRIQDDSLNDQPSRPSDTPD-LMQLHYQDLVQQgLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLF 158


                 ....*...
gi 766615769 169 AALKKLRQ 176
Cdd:PRK12518 159 YARRQLRK 166
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 10-176 2.78e-20

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: 83.22  E-value: 2.78e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   10 LIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRK 89
Cdd:TIGR02954   6 LVKKAKRGNKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECIDLLKK 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   90 RwmrlriiKKAEEQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHA 169
Cdd:TIGR02954  86 K-------KKVIPFDPNTSIEKGECETHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHR 158


                  ....*..
gi 766615769  170 ALKKLRQ 176
Cdd:TIGR02954 159 ALKKLKK 165
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 19-181 2.32e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 80.68  E-value: 2.32e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  19 KEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKRWMRLRIIK 98
Cdd:PRK12522   2 EEKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKKKRWKDRIL 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  99 KAEEQRKPVQIDFSNDV------ISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALK 172
Cdd:PRK12522  82 DLFHKEDGGEIEFADDVniseefIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKK 161


                 ....*....
gi 766615769 173 KLRQKEQVE 181
Cdd:PRK12522 162 QMREHLEGF 170
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 16-182 2.41e-19

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


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 80.51  E-value: 2.41e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   16 SGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKY-DSEKPfRPWLIGLAIKQIHSYRRKRWMRL 94
Cdd:TIGR02983   2 SATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIrDPDAP-DAYVRRVLVNLARSRWRRRRLLE 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   95 RIIKKAEEQRKPvqiDFSNDVISKISnqkLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKL 174
Cdd:TIGR02983  81 LPTRELPDAAAP---DPAPDVALRAA---LARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARL 154


                  ....*...
gi 766615769  175 RqkEQVEE 182
Cdd:TIGR02983 155 R--ELLEE 160
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 9-183 4.78e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 78.47  E-value: 4.78e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   9 DLIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRR 88
Cdd:PRK11922  19 ELVARVLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLR 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  89 KRWmrlRIIKKAEEQRKPVQIDFSNDVISKISN-----------QKLIE-LIHKLPYKLKKVIILRYLHDYSQEEVAQIL 156
Cdd:PRK11922  99 RRR---RLVNLAEMVMASTIAGGERTPLADPAEdperaaarreiRALLErAIDALPDAFRAVFVLRVVEELSVEETAQAL 175

                        170       180
                 ....*....|....*....|....*..
gi 766615769 157 HIPIGTVKSRIHAALKKLRqkEQVEEI 183
Cdd:PRK11922 176 GLPEETVKTRLHRARRLLR--ESLARE 200
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 4-177 7.14e-18

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 77.04  E-value: 7.14e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   4 ETVYTDLIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWL----IGLA 79
Cdd:PRK09641   2 DLLIKRLIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLyriaTNLT 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  80 IKQIHsyRRKRWMRLRI-IKKAEEQRKPVQIDFSND-----VISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVA 153
Cdd:PRK09641  82 IDRLR--KRKPDYYLDAeVAGTEGLTMYSQLAADDAlpeeqVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEIS 159

                        170       180
                 ....*....|....*....|....
gi 766615769 154 QILHIPIGTVKSRIHAALKKLRQK 177
Cdd:PRK09641 160 EILDLPVGTVKTRIHRGREALRKQ 183
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 23-177 3.25e-16

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 72.47  E-value: 3.25e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  23 SELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKRWMRLRIIKKAEE 102
Cdd:PRK09415  19 DEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSWHNKKVIVTEDIF 98

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 766615769 103 QRKPVQIDFSND-VISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQK 177
Cdd:PRK09415  99 TYMESQKESVEEeVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKG 174
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 20-182 1.50e-15

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 70.36  E-value: 1.50e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  20 EAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPfrPWLIGLAIKQIHSYRRK-RWMRLRIIK 98
Cdd:PRK09639   3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFKGIENEK--GWLIKSARNVAYNYLRSeKRRRARILG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  99 KAEEQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYlHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQK- 177
Cdd:PRK09639  81 EFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIy 159


                 ....*
gi 766615769 178 EQVEE 182
Cdd:PRK09639 160 EQMEE 164
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 121-175 6.13e-15

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: 65.97  E-value: 6.13e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 766615769 121 NQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLR 175
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 20-177 1.22e-14

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 67.97  E-value: 1.22e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   20 EAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKRWMRLRIikK 99
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKY--Q 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  100 AEEQRKPVQIDFSNDVISKISNQKLIELIH----KLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLR 175
Cdd:TIGR02985  79 EELAEIEERELSEADPEEELEAKELEEIIEeaieKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLR 158


                  ..
gi 766615769  176 QK 177
Cdd:TIGR02985 159 KE 160
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 16-176 3.19e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 67.78  E-value: 3.19e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  16 SGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYeslRK--YDSEK-PFRPWLIGL----AIKQIHSYRR 88
Cdd:PRK12519  25 AGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLW---RKssYDPKRgSLSSYLLTLtrsrAIDRLRSRRS 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  89 krwmRLRIIKKAEEQRK---PVQIDFSNDVISKISnQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKS 165
Cdd:PRK12519 102 ----RQRLLERWQQELLgeaSEDTPLEQASLAERS-QRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKA 176

                        170
                 ....*....|.
gi 766615769 166 RIHAALKKLRQ 176
Cdd:PRK12519 177 RARQGLLKLRE 187
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 40-177 5.41e-14

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: 66.19  E-value: 5.41e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   40 LIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKRWMRLRIIKK------AEEQRKPVQIDFSN 113
Cdd:TIGR02989  21 LVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRDRLVFDDdllealAAEAEPTEAERLSD 100

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 766615769  114 DViskisnQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILhipiGTVKSRIHAALKKLRQK 177
Cdd:TIGR02989 101 DR------QALEGCLEKLPERQRELLDLRYQRGQKATALAEQT----GRTVNAVYKALQRIRVS 154
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 122-174 2.62e-13

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 61.70  E-value: 2.62e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 766615769  122 QKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKL 174
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 10-182 2.75e-13

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 64.94  E-value: 2.75e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  10 LIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEK-PFRPWLIGLAIKQIHSYRR 88
Cdd:PRK13919  13 LLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRgSARAWLLALAHHAAVDHVR 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  89 KRWMRLRIIKKAEEQrkPVQIDFSN---DVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKS 165
Cdd:PRK13919  93 RRAARPQPLEPDERE--PEAFDLPGpglDEEGHLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKT 170

                        170
                 ....*....|....*..
gi 766615769 166 RIHAALKKLrqKEQVEE 182
Cdd:PRK13919 171 RARRALSRL--KEVLRE 185
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
8-176 3.78e-12

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 61.99  E-value: 3.78e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   8 TDLIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPfRP--WLIGLAIKQ-IH 84
Cdd:PRK09646  18 DALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SAlaWLLTLAHRRaVD 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  85 SYRRKRWMRLRIIKKAEEQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVK 164
Cdd:PRK09646  97 RVRSEQAASQREVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVK 176

                        170
                 ....*....|..
gi 766615769 165 SRIHAALKKLRQ 176
Cdd:PRK09646 177 TRMRDGLIRLRD 188
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 17-175 5.01e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 61.63  E-value: 5.01e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  17 GNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKRWMRLRI 96
Cdd:PRK12513  23 GDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRRHGARQAP 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  97 IKKAEEQRKpVQIDFSNDVISKISNQKLIELIHK----LPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALK 172
Cdd:PRK12513 103 SLDADEQLH-ALADDGAAPEQQLSLFRDRRRLQAaletLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQ 181


                 ...
gi 766615769 173 KLR 175
Cdd:PRK12513 182 KLR 184
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 9-174 1.63e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 60.13  E-value: 1.63e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   9 DLIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLA-IKQIHSYR 87
Cdd:PRK12515  11 MLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIArFKALSALR 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  88 RKRWMRLriikkaeEQRKPVQIDFSND-----VISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGT 162
Cdd:PRK12515  91 RRKHEEI-------DDEAAAAIEDGADtpevaLQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPEST 163

                        170
                 ....*....|..
gi 766615769 163 VKSRIHAALKKL 174
Cdd:PRK12515 164 VKTRMFYARKKL 175
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 127-176 2.45e-11

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: 56.28  E-value: 2.45e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 766615769  127 LIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQ 176
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 41-176 4.25e-11

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 58.84  E-value: 4.25e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  41 IEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKrwmrlriiKKAEEQRKPVQIDFSNDVISKIs 120
Cdd:PRK09637  22 VSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRK--------KNRSEELPDDLLFEDEEREENA- 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769 121 NQKLIE----LIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQ 176
Cdd:PRK09637  93 KKELAPclrpFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 24-182 7.88e-11

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 57.97  E-value: 7.88e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  24 ELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKpFRPWLIGLAIKQIHSYRRKRwmRLRIIKKAEEQ 103
Cdd:PRK09644   5 EIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQK-VKPWLFKVAYHTFIDFVRKE--KKVSFVGTDEI 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 766615769 104 RKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQKEQVEE 182
Cdd:PRK09644  82 EAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKEEK 160
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 34-174 9.50e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 58.59  E-value: 9.50e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  34 YKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPfRPWLigLAIkqihsYRRKRWMRLRIIKKAEEQRKPVQID--- 110
Cdd:PRK12533  32 YNLARWLCGNASDADDVVQEACMRALRFFDSFRGDNA-RPWL--LAI-----VRHTWYSEWRRRANAHEVAAPDTLDdad 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 766615769 111 -------FSNDVISKISNQKLIELIH----KLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKL 174
Cdd:PRK12533 104 slddwqpAGEDPLALLLRAEDVRLVNaalaKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRL 178
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 10-177 9.92e-11

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 58.03  E-value: 9.92e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  10 LIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQ-IHSYRR 88
Cdd:PRK09640  16 RVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNEcITQYRK 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  89 KRWMRLRI-------IKKAEEQRKPvQIDFSNDVISKISNQKLIElihklpyklKKVIILRYLHDYSQEEVAQILHIPIG 161
Cdd:PRK09640  96 ERRKRRLMdalsldpLEEASEEKAP-KPEERGGLDRWLVHVNPID---------REILVLRFVAELEFQEIADIMHMGLS 165

                        170
                 ....*....|....*.
gi 766615769 162 TVKSRIHAALKKLRQK 177
Cdd:PRK09640 166 ATKMRYKRALDKLREK 181
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 17-188 2.34e-10

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 56.87  E-value: 2.34e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  17 GNKEAYSELYDKTIQEVYKTAH---FLIEDKTDVDDVVQEIYIQLYESLRKYDSEK-PFRPWLIGLA-IKQIHSYRRKRw 91
Cdd:PRK06811  15 KNEKALEFIVDTYGNLVKKIVHkvlGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKgSFKKWIAAISkYKAIDYKRKLT- 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  92 mRLRIIKKAEEQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAAL 171
Cdd:PRK06811  94 -KNNEIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGR 172

                        170
                 ....*....|....*..
gi 766615769 172 KKLrQKEQVEEIFLGEV 188
Cdd:PRK06811 173 KKL-QKNKLNISLGGEV 188
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 10-170 3.35e-10

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 56.73  E-value: 3.35e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  10 LIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRK 89
Cdd:PRK11923  10 LVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLVS 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  90 RwmrlriikkaeeQRKPVQIDFS---------NDVISKISN----------QKLI-ELIHKLPYKLKKVIILRYLHDYSQ 149
Cdd:PRK11923  90 R------------GRRPPDSDVSsedaefydgDHALKDIESperallrdeiEGTVhRTIQQLPEDLRTALTLREFDGLSY 157

                        170       180
                 ....*....|....*....|.
gi 766615769 150 EEVAQILHIPIGTVKSRIHAA 170
Cdd:PRK11923 158 EDIASVMQCPVGTVRSRIFRA 178
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 25-91 7.83e-10

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: 52.98  E-value: 7.83e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 766615769   25 LYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKP--FRPWLIGLAIKQIHSYRRKRW 91
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGvsFSTWLYTIIRNAIIDYLRKQR 69
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 97-177 1.72e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 54.81  E-value: 1.72e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  97 IKKAEEQRKPVQIDFSNDVISKisnqKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQ 176
Cdd:PRK12526 124 IEQALAESQSESEEFSDHLMDK----QILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199


                 .
gi 766615769 177 K 177
Cdd:PRK12526 200 Q 200
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 3-174 5.61e-09

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 53.12  E-value: 5.61e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   3 DETVyTDLIQLTLSGNKEAYSELYDKTIQEVYKTAHFLiEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQ 82
Cdd:PRK09649   8 DEAV-TALALSAAKGNGRALEAFIKATQQDVWRFVAYL-SDVGSADDLTQETFLRAIGAIPRFSARSSARTWLLAIARHV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  83 IHSYRRKRWMRLRIIKKAEEQRKpvqidFSNDVISKiSNQKLIE---LIHKLPYKLKKVIILRYLHDYSQEEVAQILHIP 159
Cdd:PRK09649  86 VADHIRHVRSRPRTTRGARPEHL-----IDGDRHAR-GFEDLVEvttMIADLTTDQREALLLTQLLGLSYADAAAVCGCP 159

                        170
                 ....*....|....*
gi 766615769 160 IGTVKSRIHAALKKL 174
Cdd:PRK09649 160 VGTIRSRVARARDAL 174
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 2-174 8.07e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 52.98  E-value: 8.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   2 KDETVYTDLIQLTLSGNKEAYSELYDKTIQEVYKT-AHflIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAi 80
Cdd:PRK12535   7 RDDAHVTDLALAAGRGDRAALTEFIRETQDDVWRLlAH--LGGHDIADDLTQETYLRVMSALPRFAARSSARTWLLSLA- 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  81 kqihsyrRKRWMRLRIIKKAEEQRKPVQI-DFSNDVISKISNQKLIE------LIHKLPYKLKKVIILRYLHDYSQEEVA 153
Cdd:PRK12535  84 -------RRVWVDNIRHDMARPRKSATEYeDAAATTASNETTGSWSEwidvrtLIDALPPERREALILTQVLGYTYEEAA 156

                        170       180
                 ....*....|....*....|.
gi 766615769 154 QILHIPIGTVKSRIHAALKKL 174
Cdd:PRK12535 157 KIADVRVGTIRSRVARARADL 177
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
25-175 2.11e-08

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 51.23  E-value: 2.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  25 LYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLY---ESLRkyDSEKPFRPWLIGLAIKQIHSYRRKRwmRLRIIKKAE 101
Cdd:PRK09645  14 LYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWqhpEVLA--DTGRSARAWLFTVARNLVIDERRSA--RARPVEGGD 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 766615769 102 EQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLR 175
Cdd:PRK09645  90 DVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALR 163
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
45-176 2.13e-08

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 51.51  E-value: 2.13e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  45 TDVDDVVQEIYIQLYESLRKY-DSEKPFRPWLIGLAIKQIHSYRRkRWMRLRIIKKAEeqrKPVQIDFSND----VISKI 119
Cdd:PRK09648  53 LSADDVAQEVCLAVITALPRYrDQGRPFLAFVYGIAAHKVADAHR-AAGRDKAVPTEE---VPERPSDDAGpeerALRSE 128

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 766615769 120 SNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQ 176
Cdd:PRK09648 129 SSNRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARLRA 185
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 8-176 3.15e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 50.98  E-value: 3.15e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   8 TDLIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYD-SEKPFRPWLIGLAikQIHSY 86
Cdd:PRK12514   7 EKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAvSGLSPMTWLITIA--RNHAI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  87 RRKRwmrlriikkaeeQRKPVQIDFSN-------------DVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVA 153
Cdd:PRK12514  85 DRLR------------ARKAVAVDIDEahdladpspgpeaEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELA 152

                        170       180
                 ....*....|....*....|...
gi 766615769 154 QILHIPIGTVKSRIHAALKKLRQ 176
Cdd:PRK12514 153 ERHDVPLNTMRTWLRRSLLKLRE 175
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 17-176 1.41e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 49.39  E-value: 1.41e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  17 GNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEK-PFRPWLIGLAIKQIHSYRRKRWMRLR 95
Cdd:PRK12537  20 GDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARgSARGWIYSVTRHLALNVLRDTRREVV 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  96 IIKKAEEQRKpVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLR 175
Cdd:PRK12537 100 LDDDAEETAQ-TLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178


                 .
gi 766615769 176 Q 176
Cdd:PRK12537 179 E 179
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 122-177 1.66e-07

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: 49.44  E-value: 1.66e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 766615769 122 QKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVkSRIHA-ALKKLRQK 177
Cdd:COG1191  178 EALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRV-SRLHKkALARLREY 233
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 122-183 2.24e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 48.77  E-value: 2.24e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 766615769 122 QKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQKEQVEEI 183
Cdd:PRK12531 133 EQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMDAESL 194
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 37-178 2.33e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 48.63  E-value: 2.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  37 AHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLigLAIkqIHSYRRKRWMRlriiKKAEEQRKPVQIDFSNDVI 116
Cdd:PRK12511  21 ARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWL--MSI--LHNAFIDELRR----RRVEARRADELAVLADASL 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 766615769 117 -----SKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQKE 178
Cdd:PRK12511  93 paaqeHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 31-181 6.87e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 47.37  E-value: 6.87e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  31 QEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLaikqihsYRRKRWMRLriikkaeeQRKpvQID 110
Cdd:PRK12517  34 ADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITI-------LRRENARRF--------ERK--QFD 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769 111 FSN-------DVIS-----KISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAA---LKKLR 175
Cdd:PRK12517  97 LVDieddsieDDAShsseeEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRArnqLKEAL 176


                 ....*.
gi 766615769 176 QKEQVE 181
Cdd:PRK12517 177 EKPDVQ 182
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 32-175 7.76e-07

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 47.47  E-value: 7.76e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  32 EVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYdseKP--FRPWL----IGLAIKQIhsyRRKRwmRLRIIKKAEEQRK 105
Cdd:PRK09647  40 RVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNY---QPgtFEGWLhritTNLFLDMV---RRRA--RIRMEALPEDYDR 111

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 766615769 106 PVQIDFSNDVISKISN--QKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLR 175
Cdd:PRK09647 112 VPGDEPNPEQIYHDARldPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLR 183
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 3-175 1.06e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 46.97  E-value: 1.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   3 DETvyTDLIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDsekPFRP----WLIGL 78
Cdd:PRK12534  10 DET--GRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFD---PSRArgltWLAMI 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  79 AIKQIHSYRRKRwmrlriikkaEEQRKPVQIDFSNDVIS-----------KISNQKLIELIHKLPYKLKKVIILRYLHDY 147
Cdd:PRK12534  85 ARNKAIDHLRAN----------APQRRNVALDDAGELRAadasplerterASTRRRIDHCLAELEPPRSELIRTAFFEGI 154

                        170       180
                 ....*....|....*....|....*...
gi 766615769 148 SQEEVAQILHIPIGTVKSRIHAALKKLR 175
Cdd:PRK12534 155 TYEELAARTDTPIGTVKSWIRRGLAKLK 182
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 19-179 1.18e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 46.47  E-value: 1.18e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  19 KEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKpFRPWLIGLAIKQIHSYRRKRwmRLRIIK 98
Cdd:PRK12541   4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEE-IRPWLFTIAYNAFIDWYRKE--KKYKTT 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  99 KAEEQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQKE 178
Cdd:PRK12541  81 TIEEFHLPNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160


                 .
gi 766615769 179 Q 179
Cdd:PRK12541 161 E 161
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 40-182 2.06e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 45.99  E-value: 2.06e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  40 LIEDKTDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKRW---------MRLRIIKKAEEQRKPVQID 110
Cdd:PRK12546  27 LTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKrevpdpegvHAASLAVKPAHDGRLAMSD 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 766615769 111 FSndviskisnqkliELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQKEQVEE 182
Cdd:PRK12546 107 FR-------------AAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQLEE 165
PRK09642 PRK09642
RNA polymerase sigma factor;
33-184 1.44e-05

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 43.55  E-value: 1.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  33 VYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSeKPFRPWLIGLAIKQIHSYRRKRWMR---LRIIKKAEEQRKPVQi 109
Cdd:PRK09642   8 IFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQF-RGLKTWMARIATNHAIDYKRKKAREneeLSLCKETEENIKSSH- 85

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 766615769 110 DFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQKEQVEEIF 184
Cdd:PRK09642  86 NIEDLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEEFL 160
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
45-174 4.13e-05

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 42.41  E-value: 4.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  45 TDVDDVVQEIYIQLYESLRKYDSEKPFRPWLIGLA-IKQIHSYRRKRWMRLRI-IKKAEEqrkpvqIDFSNDVISKISNQ 122
Cdd:PRK12539  50 EEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIArYKLIDHLRRTRASLADVpIDDADE------LVAHDDHAAVESTL 123

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 766615769 123 KLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKL 174
Cdd:PRK12539 124 DLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAVKVSVHRGLKAL 175
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 48-181 6.93e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 41.87  E-value: 6.93e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  48 DDVVQEIYIQLYESLRKYDSEKPFRPWLIGLAIKQIHSYRRKRwmrlriikkAEEQRKPVQIdFSNDVISKISNQKLIEL 127
Cdd:PRK12516  38 DDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKR---------GREVQDTDGM-FTEQLAVHPSQYGTLDL 107

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769 128 ------IHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQKEQVE 181
Cdd:PRK12516 108 qdfraaLDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQIE 167
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 9-176 1.45e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 40.79  E-value: 1.45e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   9 DLIQLTLSGNKEAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDS-EKPFRPWLIGLAIKQihSYR 87
Cdd:PRK05602   9 ELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPgEARFDTWLHRVVLNL--CYD 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  88 RKRWMRLRIIKKAEEQ----RKPVqidfsNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTV 163
Cdd:PRK05602  87 RLRRRREVPVEDAPDVpdpaPGPD-----AGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDAL 161

                        170
                 ....*....|...
gi 766615769 164 KSRIHAALKKLRQ 176
Cdd:PRK05602 162 ESLLARGRRALRA 174
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
3-177 1.52e-04

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 41.05  E-value: 1.52e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   3 DETVYTDLIQLTLSGNKEAYSELYDKTIQEVYKTA--HFLIedKTDVDDVVQEIYIQLYESLRKYDSEK--PFR--PWL- 75
Cdd:PRK08295   7 DELEDEELVELARSGDKEALEYLIEKYKNFVRAKArsYFLI--GADREDIVQEGMIGLYKAIRDYDKDKlsSFKsfAELc 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  76 ----IGLAIKqihSYRRKRWMRL-------RIIKKAEEQRKPVQIDFSN-------DVISKISNQKLIELIHKLPYKLKK 137
Cdd:PRK08295  85 itrqIITAIK---TANRQKHIPLnsyvsldKPIYDEESDRTLLDVISEAkvtdpeeLIISKEELEDIEEKIEELLSELEK 161

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 766615769 138 VIILRYLHDYSQEEVAQILHIPigtVKSrIHAALKKLRQK 177
Cdd:PRK08295 162 EVLELYLDGKSYQEIAEELNRH---VKS-IDNALQRVKRK 197
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 20-175 2.69e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 40.04  E-value: 2.69e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  20 EAYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDS--EKPFRPWLIGLAI-KQIHSYRRKRWMRLRI 96
Cdd:PRK12542   9 EKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSlnTQELKRYILRVAKnKAIDSYRKNKRHETFL 88

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 766615769  97 IKKAEEQRKPVQIDFSNDVISKISNQKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLR 175
Cdd:PRK12542  89 EEYERESIEAVDENIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQ 167
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 2-89 2.92e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 39.68  E-value: 2.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   2 KDETVYTDLIQLTLSGNKEAYSELydktIQEVykTAHFLI----------EDKTDVDDVVQEIYIQLYESLRKYDSEKPF 71
Cdd:PRK12512   4 GREDEWTDLMRSANAGDAAAYRRL----LKAV--TPVLRAaarrglaragQPADQAEDIVQEILLAVHLKRHTWDPGAPF 77

                         90
                 ....*....|....*....
gi 766615769  72 RPWLIGLA-IKQIHSYRRK 89
Cdd:PRK12512  78 APWLFAIArNKLIDALRRR 96
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 48-174 3.55e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 39.56  E-value: 3.55e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  48 DDVVQEiyiQLYESLRKYDSEKP---FRPWLIGLAIKQIHS-YRRKRwmrlRIIKKAEEqrkpvqiDFSNDVISKISNQK 123
Cdd:PRK12540  33 DDLVQE---TLLRALANIDSFQPgsnLPAWLFTILRNLFRSdYRKRR----REVEDADG-------SYAKTLKSQPGQNA 98

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 766615769 124 LIEL------IHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKL 174
Cdd:PRK12540  99 HLEFeefraaLDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKL 155
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 15-176 3.63e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 37.14  E-value: 3.63e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  15 LSGNKE-AYSELYDKTIQEVYKTAHFLIEDKTDVDDVVQEIYIQLYESLRKYDSEKP-FRPWLiglaikqihsYR--RKR 90
Cdd:PRK12538  57 LATDDEaAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRAkFSTWL----------YRvvSNR 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  91 WMRLRIIKKAEE-QRKPVQIDFSNDVISKISNQKLIEL----IHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKS 165
Cdd:PRK12538 127 CIDLRRKPRTENvDAVPEVADGKPDAVSVIERNELSDLleaaMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVES 206

                        170
                 ....*....|.
gi 766615769 166 RIHAALKKLRQ 176
Cdd:PRK12538 207 LLKRGRQQLRD 217
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
140-174 3.76e-03

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 36.66  E-value: 3.76e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 766615769 140 ILRYL-HDYSQEEVAQILHIPIGTVKSRIHAALKKL 174
Cdd:COG2771  135 VLRLLaEGLTLKEIARILGISERTVRTHLKRIYRKL 170
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 46-177 4.70e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 36.18  E-value: 4.70e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769  46 DVDDVVQEIYIQLYESLRKYDSEKPFRPWliglaIKQIHSYRRKRWMRLRiiKKAEEQRKPVQIDF----SNDVISKISN 121
Cdd:PRK12536  48 EVEDLVQEILLAVHNARHTYRADQPLTAW-----VHAIARYKLMDFLRSR--ARREALHDPLDDESelfaTSDDEAAEAR 120

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 766615769 122 QKLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVKSRIHAALKKLRQK 177
Cdd:PRK12536 121 RDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
112-177 4.93e-03

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 36.49  E-value: 4.93e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 766615769 112 SNDVISKISnqkLIELIHKLPYKLKKVIILRYLHDYSQEEVAQILHIPIGTVkSRIHA-ALKKLRQK 177
Cdd:PRK05572 187 EEDWFDKIA---LKEAIRELDERERLIVYLRYFKDKTQSEVAKRLGISQVQV-SRLEKkILKQMKEK 249
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 8-180 5.69e-03

ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.


Pssm-ID: 254323 [Multi-domain]  Cd Length: 185  Bit Score: 36.24  E-value: 5.69e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769    8 TDLIQLTLSGNKEAYSELYDKTIQEVYKTA-HFLIEDKTDVDD----VVQEIYIQL--YESLRKYDSEKPFrpWLIGL-A 79
Cdd:pfam07638   5 TQLLQQVKDGDAAATEQLLPLVYDELRRLAgSKLQNERRGHTLqptaLVHEAFVRLvdTEDFPDWSGRGHF--FAAAAeA 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 766615769   80 IKQI---HSYRRKRWMRLRIIKKAEEQRKPVQIDFSNDVISKISNQKLIELIhKLPYKLKKVIILRYLHDYSQEEVAQIL 156
Cdd:pfam07638  83 MRRIlidHARRRQRQKRGGDVQRRELDEVVDNGDSPNPDLLLDLDEALEQLF-SLSPRQARLVELRFFAGLSNDEIAERL 161

                         170       180
                  ....*....|....*....|....
gi 766615769  157 HIPIGTVKSRIHAALKKLRQKEQV 180
Cdd:pfam07638 162 GVSERTVERNWALARAWLHRELRD 185
 
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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