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Conserved domains on  [gi|1280939255|ref|WP_100263179|]
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RNA polymerase sigma-70 factor [Phocaeicola vulgatus]

Protein Classification

RNA polymerase sigma-70 factor( domain architecture ID 11496275)

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 26-176 8.70e-52

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: 163.12  E-value: 8.70e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQHIGDMRQKELalristL 105
Cdd:TIGR02985  17 FARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAEIEEREL------S 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1280939255 106 EACDPDKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQL 176
Cdd:TIGR02985  91 EADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
 
Name Accession Description Interval E-value
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 26-176 8.70e-52

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: 163.12  E-value: 8.70e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQHIGDMRQKELalristL 105
Cdd:TIGR02985  17 FARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAEIEEREL------S 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1280939255 106 EACDPDKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQL 176
Cdd:TIGR02985  91 EADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 10-180 1.10e-31

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: 112.78  E-value: 1.10e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  10 SELTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQh 89
Cdd:COG1595    17 AAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLD- 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  90 igdmrqkELALRISTLEACDPDKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSL 169
Cdd:COG1595    96 -------ELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRAR 168

                         170
                  ....*....|.
gi 1280939255 170 KQLRVQLKDYQ 180
Cdd:COG1595   169 KKLREALEEEG 179
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 14-180 8.43e-17

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 74.07  E-value: 8.43e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  14 EVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLqhleVRMRAEQHIGDM 93
Cdd:PRK09652   14 LLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYL----RKQGRRPPASDV 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  94 --------RQKELALRISTLEAcdpdKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHI 165
Cdd:PRK09652   90 daeeaedfDLADALRDISTPEN----ELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRI 165

                         170
                  ....*....|....*
gi 1280939255 166 TRSLKQLRVQLKDYQ 180
Cdd:PRK09652  166 FRAREALRAKLQPLL 180
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 122-172 2.29e-12

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 59.01  E-value: 2.29e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1280939255 122 VQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQL 172
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 119-173 1.75e-07

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: 45.94  E-value: 1.75e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1280939255 119 QTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLR 173
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 132-176 1.81e-07

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 45.98  E-value: 1.81e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1280939255  132 TSREVFILSR-MKNLPNKEIALRLDISVKTVEFHITRSLKQL----RVQL 176
Cdd:smart00421   5 TPREREVLRLlAEGLTNKEIAERLGISEKTVKTHLSNIMRKLgvrsRTQA 54
 
Name Accession Description Interval E-value
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 26-176 8.70e-52

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: 163.12  E-value: 8.70e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQHIGDMRQKELalristL 105
Cdd:TIGR02985  17 FARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAEIEEREL------S 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1280939255 106 EACDPDKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQL 176
Cdd:TIGR02985  91 EADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 10-180 1.10e-31

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: 112.78  E-value: 1.10e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  10 SELTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQh 89
Cdd:COG1595    17 AAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLD- 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  90 igdmrqkELALRISTLEACDPDKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSL 169
Cdd:COG1595    96 -------ELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRAR 168

                         170
                  ....*....|.
gi 1280939255 170 KQLRVQLKDYQ 180
Cdd:COG1595   169 KKLREALEEEG 179
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 10-176 4.47e-25

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: 95.11  E-value: 4.47e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  10 SELTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQhlevRMRAEQH 89
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLR----RKRRLRR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  90 IGDMRQKELALRISTLEAcdpdkLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSL 169
Cdd:TIGR02937  77 ELDLLEELLDSDPSPEEE-----LEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRAR 151


                  ....*..
gi 1280939255 170 KQLRVQL 176
Cdd:TIGR02937 152 KKLRELL 158
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 14-180 8.43e-17

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 74.07  E-value: 8.43e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  14 EVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLqhleVRMRAEQHIGDM 93
Cdd:PRK09652   14 LLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYL----RKQGRRPPASDV 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  94 --------RQKELALRISTLEAcdpdKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHI 165
Cdd:PRK09652   90 daeeaedfDLADALRDISTPEN----ELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRI 165

                         170
                  ....*....|....*
gi 1280939255 166 TRSLKQLRVQLKDYQ 180
Cdd:PRK09652  166 FRAREALRAKLQPLL 180
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 26-178 8.73e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 73.85  E-value: 8.73e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQhlEVRMRAEQHIGDMRQKELALRISTL 105
Cdd:PRK11924   29 YARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLR--RRRREKAVLSDDALEPEFAETAETP 106

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1280939255 106 EACDPDKLFCDEIqtlvQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKD 178
Cdd:PRK11924  107 EAALLAKDDLARI----DRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEA 175
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 122-172 2.29e-12

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 59.01  E-value: 2.29e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1280939255 122 VQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQL 172
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 25-178 1.85e-11

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 59.71  E-value: 1.85e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  25 QFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQHIGDMRQKELALRIST 104
Cdd:PRK09641   33 QLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRKPDYYLDAEVAGTEGLTMYSQLAA 112

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1280939255 105 LEACDPDKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKD 178
Cdd:PRK09641  113 DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLRH 186
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 27-179 1.00e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 58.15  E-value: 1.00e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  27 AYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQHIGDMRQKElALRISTLE 106
Cdd:PRK12519   46 ALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLTRSRAIDRLRSRRSRQRLLERWQQELLGE-ASEDTPLE 124

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1280939255 107 acdpdKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKDY 179
Cdd:PRK12519  125 -----QASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQDL 192
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 22-180 3.74e-10

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 55.94  E-value: 3.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  22 QFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAI-------KNRSLNHLQHLEVRMRAEQhigdmr 94
Cdd:PRK12527    7 ELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALnlvvdrhRRHRVRQAEPLEVLDEEER------ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  95 qkelalristLEACDPDK-LFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLR 173
Cdd:PRK12527   81 ----------LHSPSPQTrLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCR 150


                  ....*..
gi 1280939255 174 VQLKDYQ 180
Cdd:PRK12527  151 VRMRQWE 157
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 27-177 8.40e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 53.32  E-value: 8.40e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  27 AYSYVRNREEAEDIVMGAFTNVWEHRNELQED-TNISALLLTAIKNRSLnhlqhlevrmraeqhigDMRQKELALRISTL 105
Cdd:PRK12538   80 ALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGrAKFSTWLYRVVSNRCI-----------------DLRRKPRTENVDAV 142

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1280939255 106 -EACD--PDKLFC---DEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLK 177
Cdd:PRK12538  143 pEVADgkPDAVSVierNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 31-178 9.60e-09

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 52.35  E-value: 9.60e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  31 VRNREEAEDIVMGAFTNVWEHRNELQE-----DTNISALLLtaikNRSLNHLqhlevRMRAEQHIGDmrqkelalrisTL 105
Cdd:PRK05602   41 LGDPAEAEDVAQETFLRIWKQAPSWRPgearfDTWLHRVVL----NLCYDRL-----RRRREVPVED-----------AP 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1280939255 106 EACDP-----DKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKD 178
Cdd:PRK05602  101 DVPDPapgpdAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQLAD 178
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 14-177 2.74e-08

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 50.72  E-value: 2.74e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  14 EVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWehRNELQEDTNISALLLTAIKNRSLNHLqhlevrmRAEQHIgdm 93
Cdd:PRK09639    7 DLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLY--RSDFKGIENEKGWLIKSARNVAYNYL-------RSEKRR--- 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  94 RQKELAL----RISTLEACDPDKLFCDEIQtLVQEAISELPPTSREVFILsRMKNLPNKEIALRLDI---SVKTVefhIT 166
Cdd:PRK09639   75 RARILGEfqwqEVDNEPSPEEIWIRKEEIT-KVQEVLAKMTERDRTVLLL-RFSGYSYKEIAEALGIkesSVGTT---LA 149

                         170
                  ....*....|.
gi 1280939255 167 RSLKQLRVQLK 177
Cdd:PRK09639  150 RAKKKFRKIYE 160
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 104-178 5.39e-08

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: 50.98  E-value: 5.39e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1280939255 104 TLEACDPDKLFCD-EIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKD 178
Cdd:COG1191   161 LLESGDPEEELEHeELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLKE 236
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 119-173 1.75e-07

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: 45.94  E-value: 1.75e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1280939255 119 QTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLR 173
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 132-176 1.81e-07

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 45.98  E-value: 1.81e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1280939255  132 TSREVFILSR-MKNLPNKEIALRLDISVKTVEFHITRSLKQL----RVQL 176
Cdd:smart00421   5 TPREREVLRLlAEGLTNKEIAERLGISEKTVKTHLSNIMRKLgvrsRTQA 54
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 109-172 6.90e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 47.42  E-value: 6.90e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1280939255 109 DPDKLFC-DEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQL 172
Cdd:PRK12533  114 DPLALLLrAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRL 178
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 27-176 7.11e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 47.65  E-value: 7.11e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  27 AYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVR-----MRAEQHIGDMRQKELALR 101
Cdd:PRK11922   47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRLvnlaeMVMASTIAGGERTPLADP 126

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1280939255 102 IStleacDPDKLFCD-EIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVE--FHITRSLkqLRVQL 176
Cdd:PRK11922  127 AE-----DPERAAARrEIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKtrLHRARRL--LRESL 197
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 14-173 7.70e-07

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 46.99  E-value: 7.70e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  14 EVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNIsALLLTAIKNRSLNHL--QHLEVRMRAEQ--- 88
Cdd:PRK07037    2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPV-AYLFRIVRNLAIDHYrrQALENKYHGDEedg 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  89 ---HIGDMRQKELALRISTLEacdpdklfcdeiqtLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHI 165
Cdd:PRK07037   81 ldvPSPEASPEAALINRDTLR--------------HVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMI 146


                  ....*...
gi 1280939255 166 TRSLKQLR 173
Cdd:PRK07037  147 RDALVHCR 154
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 124-176 1.22e-06

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 45.65  E-value: 1.22e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1280939255 124 EAISELPpTSREVFILSRM-KNLPNKEIALRLDISVKTVEFHITRSLKQL----RVQL 176
Cdd:COG2197    64 EALRRLL-TPREREVLRLLaEGLSNKEIAERLGISERTVKTHVSNILRKLgvrnRTEL 120
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 26-173 2.12e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 45.93  E-value: 2.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQHIGDMRQ------KELA 99
Cdd:PRK12511   20 YARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEARRADELAVLADaslpaaQEHA 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1280939255 100 LRISTleacdpdklfcdeiqtlVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLR 173
Cdd:PRK12511  100 VRLAQ-----------------IRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALR 156
GerE pfam00196
Bacterial regulatory proteins, luxR family;
132-174 3.40e-06

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 42.57  E-value: 3.40e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1280939255 132 TSREVFILSRM-KNLPNKEIALRLDISVKTVEFHITRSLKQLRV 174
Cdd:pfam00196   4 SPREREVLRWLaAGKSNKEIADELGISEKTVKVHRSNIMRKLNV 47
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 26-178 3.60e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 45.22  E-value: 3.60e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNrslnhlQHLEVRMRAEQHIGDMrQKELALRISTL 105
Cdd:PRK12546   23 FAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRN------TFYSDRRKHKREVPDP-EGVHAASLAVK 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1280939255 106 EACDPDKLFCDeiqtlVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQL--RVQLKD 178
Cdd:PRK12546   96 PAHDGRLAMSD-----FRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLaeLLQLEE 165
PRK06930 PRK06930
positive control sigma-like factor; Validated
 122-181 3.75e-06

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 45.11  E-value: 3.75e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255 122 VQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKDYQF 181
Cdd:PRK06930  108 IEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINESLF 167
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 26-179 4.89e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 45.07  E-value: 4.89e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQhlevRMRAEQHIGDMRQKELALRIStl 105
Cdd:PRK12513   42 FLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWR----RHGARQAPSLDADEQLHALAD-- 115

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1280939255 106 EACDPDKLFCD-EIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKDY 179
Cdd:PRK12513  116 DGAAPEQQLSLfRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAEE 190
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 122-164 6.56e-06

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 44.71  E-value: 6.56e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1280939255 122 VQEAISELPPTSREVFILSrMKNLPNKEIALRLDISVKTVEFH 164
Cdd:COG4566   131 LRARLASLTPREREVLDLV-VAGLSNKQIARELGISPRTVEVH 172
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
31-179 8.23e-06

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 43.91  E-value: 8.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  31 VRNREEAEDIVMGAFTNVWEHRNEL-QEDTNISALLLTAIKNRSLNhlQHLEVRMRAEQhIGDmrqkelalriSTLEACD 109
Cdd:PRK09645   30 TGDRARAEDVVQETLLRAWQHPEVLaDTGRSARAWLFTVARNLVID--ERRSARARPVE-GGD----------DVLGVPE 96

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1280939255 110 PDKLfcDEIQT-----LVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKDY 179
Cdd:PRK09645   97 QSAP--DEVDRaldrlLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQER 169
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 36-178 9.65e-06

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 44.13  E-value: 9.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  36 EAEDIVMGAFTNVWEHRNELQ-EDTNISALLLTAIKNRSLNHLQHLEVRMRAEQhiGDMRQKElalristleACDPDKLF 114
Cdd:PRK13919   49 AAEDVVQEVFIRVWKKAKEFDpRRGSARAWLLALAHHAAVDHVRRRAARPQPLE--PDEREPE---------AFDLPGPG 117

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1280939255 115 CDEIQTL----VQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKD 178
Cdd:PRK13919  118 LDEEGHLdrtrLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLRE 185
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 12-177 9.66e-06

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 43.97  E-value: 9.66e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  12 LTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVR------MR 85
Cdd:PRK09415   18 IDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSWHNKkvivteDI 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  86 AEQHIGDMRQKELALRIStleacdpdklfcDEIQTLVqEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEfhi 165
Cdd:PRK09415   98 FTYMESQKESVEEEVIQN------------AEDERLA-SAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVK--- 161

                         170
                  ....*....|..
gi 1280939255 166 TRsLKQLRVQLK 177
Cdd:PRK09415  162 TR-LKKAKELLK 172
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 26-177 3.02e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 42.64  E-value: 3.02e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHlevRMRAEQHIGDMRQKELALRISTL 105
Cdd:PRK12516   26 FAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRK---RGREVQDTDGMFTEQLAVHPSQY 102

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1280939255 106 EACDpdklfcdeIQTLvQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLK 177
Cdd:PRK12516  103 GTLD--------LQDF-RAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 132-175 3.14e-05

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 40.21  E-value: 3.14e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1280939255 132 TSREVFILSRMKN-LPNKEIALRLDISVKTVEFHITRSLKQLRVQ 175
Cdd:cd06170     2 TPREREVLRLLAEgKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 18-171 3.69e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 42.40  E-value: 3.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  18 KRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMraeqhigdMRQKE 97
Cdd:PRK12518   18 RRYQQKVRSTLYQLCGRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQFAQRP--------SRIQD 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1280939255  98 LALRISTLEACDPDKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVE---FHITRSLKQ 171
Cdd:PRK12518   90 DSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKsrlFYARRQLRK 166
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 132-176 4.27e-05

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 40.33  E-value: 4.27e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1280939255 132 TSREVFILSR-MKNLPNKEIALRLDISVKTVEFHITRSLKQL----RVQL 176
Cdd:COG5905    14 TKREREVLELlAEGLTNKEIARQLFISEKTVKNHVSNILRKLgvrnRVQA 63
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 10-176 5.01e-05

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: 41.54  E-value: 5.01e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  10 SELTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQ-----HLEVRM 84
Cdd:TIGR02989   1 KAFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRklgrdRLVFDD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  85 RAEQHIGDM----RQKELALRISTLEACdpdklfcdeiqtlvqeaISELPPTSREVFILSRMKNLPNKEIALRLDISVKT 160
Cdd:TIGR02989  81 DLLEALAAEaeptEAERLSDDRQALEGC-----------------LEKLPERQRELLDLRYQRGQKATALAEQTGRTVNA 143

                         170
                  ....*....|....*.
gi 1280939255 161 vefhITRSLKQLRVQL 176
Cdd:TIGR02989 144 ----VYKALQRIRVSL 155
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 83-175 5.53e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 41.64  E-value: 5.53e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  83 RMRAEQHIGDMRQKELALristleacDPDKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVE 162
Cdd:PRK12543   80 RFRIFEKAEEQRKPVSID--------FSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVK 151

                          90
                  ....*....|...
gi 1280939255 163 FHITRSLKQLRVQ 175
Cdd:PRK12543  152 SRIHAALKKLRQK 164
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 31-177 5.63e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 41.96  E-value: 5.63e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  31 VRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAI-KNRSLNHLqhlevRMRAEQhigdmRQKELALRISTLEACD 109
Cdd:PRK12534   46 IPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLAMIaRNKAIDHL-----RANAPQ-----RRNVALDDAGELRAAD 115

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1280939255 110 PDKLFCDEIQTL---VQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLK 177
Cdd:PRK12534  116 ASPLERTERASTrrrIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAKLKACLE 186
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
132-174 7.52e-05

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 41.67  E-value: 7.52e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1280939255 132 TSREVFILSRM-KNLPNKEIALRLDISVKTVEFHITRSLKQLRV 174
Cdd:COG2771   129 TPREREVLRLLaEGLTLKEIARILGISERTVRTHLKRIYRKLGV 172
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 125-173 1.01e-04

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 38.56  E-value: 1.01e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1280939255 125 AISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLR 173
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 27-178 1.48e-04

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 40.92  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  27 AYSYVRNREEAEDIVMGAFTNV--------------WEHRNElqedTNisaLLLTAIKNRSlnhlqhlEVRMRA-----E 87
Cdd:PRK09647   45 AYRLSGNQHDAEDLTQETFIRVfrslqnyqpgtfegWLHRIT----TN---LFLDMVRRRA-------RIRMEAlpedyD 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  88 QHIGDMRQKELALRISTLeacDPDklfcdeiqtlVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITR 167
Cdd:PRK09647  111 RVPGDEPNPEQIYHDARL---DPD----------LQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHR 177

                         170
                  ....*....|.
gi 1280939255 168 SLKQLRVQLKD 178
Cdd:PRK09647  178 GRQQLRAALAA 188
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 15-173 1.58e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 40.68  E-value: 1.58e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  15 VFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWeHRNEL--QEDTNISALLLTAIKNRSLNHLQHLEVRmraEQHIgd 92
Cdd:PRK12531   32 VFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVW-QKAHLfdGQKSALSTWIYTIIRNLCFDLLRKQKGK---DLHI-- 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  93 mrqkeLALRISTLEACDPDKL--FCDEiQTLVQEAISE----LPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHIT 166
Cdd:PRK12531  106 -----HADDIWPSDYYPPDLVdhYSPE-QDMLKEQVMKfldrLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLR 179


                  ....*..
gi 1280939255 167 RSLKQLR 173
Cdd:PRK12531  180 LAVEKLR 186
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 125-172 1.95e-04

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 40.40  E-value: 1.95e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1280939255 125 AISELppTSREVFILSRM-KNLPNKEIALRLDISVKTVEFHITRSLKQL 172
Cdd:PRK10651  152 DVNQL--TPRERDILKLIaQGLPNKMIARRLDITESTVKVHVKHMLKKM 198
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 14-178 2.59e-04

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 40.00  E-value: 2.59e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  14 EVFSKRQQQFVQFAYSYV----RNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQH 89
Cdd:PRK09638   18 AALTTLFQQHYSFLYKYLlkltLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKREKLRLQR 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  90 IGD--MRQKELALRISTLEACDpdklfcdeiqtlVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITR 167
Cdd:PRK09638   98 AKEetLRKEKWEAAIKGAEWSE------------MLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHH 165

                         170
                  ....*....|.
gi 1280939255 168 SLKQLRVQLKD 178
Cdd:PRK09638  166 GIKQLRKEWGQ 176
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 16-77 3.46e-04

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: 37.57  E-value: 3.46e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1280939255  16 FSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNIS--ALLLTAIKNRSLNHL 77
Cdd:pfam04542   2 VERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSfsTWLYTIIRNAIIDYL 65
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 11-178 6.64e-04

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 38.71  E-value: 6.64e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  11 ELTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRnELQEDTNISALLLTAIKNRSLNHLQhlevRMRAEQHI 90
Cdd:PRK09644    2 EIEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYL-EDYDNQKVKPWLFKVAYHTFIDFVR----KEKKVSFV 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  91 GDMRqkelalrISTLEACDPDKLFCD-EIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSL 169
Cdd:PRK09644   77 GTDE-------IEAIQAESTEEYVVAkNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGR 149


                  ....*....
gi 1280939255 170 KQLRVQLKD 178
Cdd:PRK09644  150 KRLKALLKE 158
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 18-168 7.14e-04

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 38.63  E-value: 7.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  18 KRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVR--------MRAEQH 89
Cdd:PRK11923   28 KYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLVSRGRRppdsdvssEDAEFY 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1280939255  90 IGDMRQKElalrISTLEAcdpdKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRS 168
Cdd:PRK11923  108 DGDHALKD----IESPER----ALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRA 178
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 12-178 7.80e-04

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 38.43  E-value: 7.80e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  12 LTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLqhlevRMRAeqhig 91
Cdd:PRK09637    3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFY-----RKKN----- 72

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  92 dmrQKELALRISTLEACDPDKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQ 171
Cdd:PRK09637   73 ---RSEELPDDLLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVK 149


                  ....*..
gi 1280939255 172 LRVQLKD 178
Cdd:PRK09637  150 LKELLEG 156
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 89-178 1.79e-03

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 37.74  E-value: 1.79e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  89 HIGDmRQKELALrISTLE---ACDPDKLFCD-EIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTV-EF 163
Cdd:PRK06288  171 FGGD-EGDEVSL-MDTLEspaALNPDEIAEReEIKRVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRIsQL 248

                          90
                  ....*....|....*
gi 1280939255 164 HiTRSLKQLRVQLKD 178
Cdd:PRK06288  249 H-TKAVLQLRAKLAE 262
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 12-151 2.02e-03

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 38.02  E-value: 2.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  12 LTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWehRNELQEDTNISALLLTAIKNRSLNHLQhlEVRMRAEQhIG 91
Cdd:PRK09635    7 VSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLL--RAPVGDIDDERGWLIVVTSRLCLDHIK--SASTRRER-PQ 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1280939255  92 DMRQKELALriSTLEACDP-DKL-FCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIA 151
Cdd:PRK09635   82 DIAAWHDGD--ASVSSVDPaDRVtLDDEVRLALLIMLERLGPAERVVFVLHEIFGLPYQQIA 141
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 55-162 2.29e-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: 37.01  E-value: 2.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  55 LQEDTNISALLLTAIKNRSLNHLQhlevRMRAEQHIGDMRQKELALRISTLEACDPDKLFcdEIQTLVqEAISELPPTSR 134
Cdd:pfam07638  69 WSGRGHFFAAAAEAMRRILIDHAR----RRQRQKRGGDVQRRELDEVVDNGDSPNPDLLL--DLDEAL-EQLFSLSPRQA 141

                          90       100
                  ....*....|....*....|....*...
gi 1280939255 135 EVFILSRMKNLPNKEIALRLDISVKTVE 162
Cdd:pfam07638 142 RLVELRFFAGLSNDEIAERLGVSERTVE 169
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 33-176 3.00e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 36.79  E-value: 3.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  33 NREEAEDIVMGAFTNVWEHRNELQE-DTNISALLLTAIKNRSLNHLqhlevRMRAEQHIGDMRQKELALRISTLEACDPD 111
Cdd:PRK12524   49 DRAEAEDVTQEAMLRLWRIAPDWRQgEARVSTWLYRVVCNLCTDRL-----RRRRRASVDLDDAPEPADAAPGAEEALIE 123

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1280939255 112 KlfcDEIQTLvQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQL 176
Cdd:PRK12524  124 G---DRMRAL-DAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAALL 184
PRK09642 PRK09642
RNA polymerase sigma factor;
111-182 3.03e-03

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 36.62  E-value: 3.03e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1280939255 111 DKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKDYQFL 182
Cdd:PRK09642   89 DLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEEFL 160
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
143-174 3.44e-03

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 36.61  E-value: 3.44e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1280939255 143 KNLPNKEIALRLDISVKTVEFHITRSLKQLRV 174
Cdd:COG2909   136 EGLSNKEIAERLFISVNTVKTHLRNIYRKLGV 167
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 26-71 3.52e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 36.39  E-value: 3.52e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1280939255  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKN 71
Cdd:PRK12547   22 FAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRN 67
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 34-176 4.28e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 36.37  E-value: 4.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  34 REEAEDIVMGAFTNVWeHRNELQEDTNISALLLTAIKNRSLNHLQhlevRMRAEQhigdMRQKELALrisTLEACDPDKl 113
Cdd:PRK12523   34 RQRAEDLSQDTFVRLL-GRPELPTPREPRAFLAAVAKGLMFDHFR----RAALEQ----AYLAELAL---VPEAEQPSP- 100

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255 114 fcdEIQTLVQEAISE-------LPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQL 176
Cdd:PRK12523  101 ---EEQHLILEDLKAidrllgkLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167
Sig70_famx1 TIGR02943
RNA polymerase sigma-70 factor, TIGR02943 family; This group of sigma factors are members of ...
 22-173 6.62e-03

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: 35.90  E-value: 6.62e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  22 QFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLqhlevrmRAEQhigdmRQKELALR 101
Cdd:TIGR02943  14 DLLRFARLQLRDRDLAEDAVQETLLAALSHRDSFAGRSALKTWLFAILKNKIIDAL-------RAKG-----REVKVSDL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255 102 ISTLEACDPDKLFCD-----------------------EIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISV 158
Cdd:TIGR02943  82 DDELDDEAFNALFTQnghwaqhgqpqhwntpekqlenkEFWEVFEACLYHLPEQTARVFMMREVLGFESDEICQELEIST 161

                         170
                  ....*....|....*
gi 1280939255 159 KTVEFHITRSLKQLR 173
Cdd:TIGR02943 162 SNCHVLLYRARLSLR 176
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 14-161 6.97e-03

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 35.84  E-value: 6.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  14 EVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEqhIGDm 93
Cdd:PRK09643   31 ELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLRRAKARPTVP--LDD- 107

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1280939255  94 rqkelALRISTLEacdPDKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTV 161
Cdd:PRK09643  108 -----VYPVAQLE---RDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTV 167
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 11-177 8.29e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 35.62  E-value: 8.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  11 ELTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNrslNHLQHLEVRMRAEQHI 90
Cdd:PRK12522    4 KVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVR---TFYDFYRKKKRWKDRI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  91 GDMRQKELALRISTLEACD-PDKLFCDEIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSL 169
Cdd:PRK12522   81 LDLFHKEDGGEIEFADDVNiSEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAK 160


                  ....*...
gi 1280939255 170 KQLRVQLK 177
Cdd:PRK12522  161 KQMREHLE 168
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 26-178 9.29e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 35.43  E-value: 9.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1280939255  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTaIKNRslnhlqhlEVRMRAEQHIGDMRQKELALRISTL 105
Cdd:PRK12517   39 YAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLIT-ILRR--------ENARRFERKQFDLVDIEDDSIEDDA 109

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1280939255 106 EACDPDKLfcdeIQTLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVefhITRsLKQLRVQLKD 178
Cdd:PRK12517  110 SHSSEEEM----EQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTV---MTR-LFRARNQLKE 174
 
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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