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Conserved domains on  [gi|492422421|ref|WP_005839094|]
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MULTISPECIES: RNA polymerase sigma-70 factor [Phocaeicola]

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 8.99e-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: 8.99e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421   26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQHIGDMRQKELalristL 105
Cdd:TIGR02985  17 FARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAEIEEREL------S 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492422421  106 EACDPDKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQL 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 8.99e-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: 8.99e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421   26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQHIGDMRQKELalristL 105
Cdd:TIGR02985  17 FARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAEIEEREL------S 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492422421  106 EACDPDKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQL 176
Cdd:TIGR02985  91 EADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 10-180 9.90e-32

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: 9.90e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  10 SELTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQh 89
Cdd:COG1595   17 AAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLD- 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  90 igdmrqkELALRISTLEACDPDKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSL 169
Cdd:COG1595   96 -------ELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRAR 168

                        170
                 ....*....|.
gi 492422421 170 KQLRVQLKDYQ 180
Cdd:COG1595  169 KKLREALEEEG 179
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 14-180 5.26e-17

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 74.46  E-value: 5.26e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  14 EVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLqhleVRMRAEQHIGDM 93
Cdd:PRK09652  14 LLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYL----RKQGRRPPASDV 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  94 --------RQKELALRISTLEAcdpdKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHI 165
Cdd:PRK09652  90 daeeaedfDLADALRDISTPEN----ELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRI 165

                        170
                 ....*....|....*
gi 492422421 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 2.71e-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: 58.62  E-value: 2.71e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 492422421  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 1.26e-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: 46.33  E-value: 1.26e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 492422421 119 QALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLR 173
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 132-176 1.86e-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: 1.86e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 492422421   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 8.99e-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: 8.99e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421   26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQHIGDMRQKELalristL 105
Cdd:TIGR02985  17 FARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAEIEEREL------S 90

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492422421  106 EACDPDKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQL 176
Cdd:TIGR02985  91 EADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 10-180 9.90e-32

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: 9.90e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  10 SELTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQh 89
Cdd:COG1595   17 AAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLD- 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  90 igdmrqkELALRISTLEACDPDKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSL 169
Cdd:COG1595   96 -------ELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRAR 168

                        170
                 ....*....|.
gi 492422421 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 3.93e-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: 3.93e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421   10 SELTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQhlevRMRAEQH 89
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLR----RKRRLRR 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421   90 IGDMRQKELALRISTLEAcdpdkLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSL 169
Cdd:TIGR02937  77 ELDLLEELLDSDPSPEEE-----LEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRAR 151


                  ....*..
gi 492422421  170 KQLRVQL 176
Cdd:TIGR02937 152 KKLRELL 158
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 14-180 5.26e-17

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 74.46  E-value: 5.26e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  14 EVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLqhleVRMRAEQHIGDM 93
Cdd:PRK09652  14 LLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYL----RKQGRRPPASDV 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  94 --------RQKELALRISTLEAcdpdKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHI 165
Cdd:PRK09652  90 daeeaedfDLADALRDISTPEN----ELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRI 165

                        170
                 ....*....|....*
gi 492422421 166 TRSLKQLRVQLKDYQ 180
Cdd:PRK09652 166 FRAREALRAKLQPLL 180
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 26-178 8.46e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 73.85  E-value: 8.46e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQhlEVRMRAEQHIGDMRQKELALRISTL 105
Cdd:PRK11924  29 YARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLR--RRRREKAVLSDDALEPEFAETAETP 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 492422421 106 EAcdpdKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKD 178
Cdd:PRK11924 107 EA----ALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEA 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 2.71e-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: 58.62  E-value: 2.71e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 492422421  122 VQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQL 172
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 25-178 1.99e-11

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 59.71  E-value: 1.99e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  25 QFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQHIGDMRQKELALRIST 104
Cdd:PRK09641  33 QLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRKRKPDYYLDAEVAGTEGLTMYSQLAA 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 492422421 105 LEACDPDKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKD 178
Cdd:PRK09641 113 DDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQLRH 186
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 27-179 3.58e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 59.30  E-value: 3.58e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  27 AYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQHIGDMRQKElALRISTLE 106
Cdd:PRK12519  46 ALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLTRSRAIDRLRSRRSRQRLLERWQQELLGE-ASEDTPLE 124

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 492422421 107 acdpdKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKDY 179
Cdd:PRK12519 125 -----QASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRELLQDL 192
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 22-180 9.83e-11

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 57.48  E-value: 9.83e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  22 QFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAI-------KNRSLNHLQHLEVRMRAEQhigdmr 94
Cdd:PRK12527   7 ELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALnlvvdrhRRHRVRQAEPLEVLDEEER------ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  95 qkelalristLEACDPDK-LFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLR 173
Cdd:PRK12527  81 ----------LHSPSPQTrLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCR 150


                 ....*..
gi 492422421 174 VQLKDYQ 180
Cdd:PRK12527 151 VRMRQWE 157
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 31-178 4.89e-09

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 53.12  E-value: 4.89e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  31 VRNREEAEDIVMGAFTNVWEHRNELQE-----DTNISALLLtaikNRSLNHLqhlevRMRAEQHIGDmrqkelalrisTL 105
Cdd:PRK05602  41 LGDPAEAEDVAQETFLRIWKQAPSWRPgearfDTWLHRVVL----NLCYDRL-----RRRREVPVED-----------AP 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 492422421 106 EACDP-----DKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKD 178
Cdd:PRK05602 101 DVPDPapgpdAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQLAD 178
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 27-177 9.36e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 52.94  E-value: 9.36e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  27 AYSYVRNREEAEDIVMGAFTNVWEHRNELQED-TNISALLLTAIKNRSLnhlqhlevrmraeqhigDMRQKELALRISTL 105
Cdd:PRK12538  80 ALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGrAKFSTWLYRVVSNRCI-----------------DLRRKPRTENVDAV 142

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 492422421 106 -EACD--PDKLFC---DEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLK 177
Cdd:PRK12538 143 pEVADgkPDAVSVierNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 14-177 2.97e-08

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 50.72  E-value: 2.97e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  14 EVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWehRNELQEDTNISALLLTAIKNRSLNHLqhlevrmRAEQHIgdm 93
Cdd:PRK09639   7 DLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLY--RSDFKGIENEKGWLIKSARNVAYNYL-------RSEKRR--- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  94 RQKELAL----RISTLEACDPDKLFCDEIQaLVQEAISELPPTSREVFILsRMKNLPNKEIALRLDI---SVKTVefhIT 166
Cdd:PRK09639  75 RARILGEfqwqEVDNEPSPEEIWIRKEEIT-KVQEVLAKMTERDRTVLLL-RFSGYSYKEIAEALGIkesSVGTT---LA 149

                        170
                 ....*....|.
gi 492422421 167 RSLKQLRVQLK 177
Cdd:PRK09639 150 RAKKKFRKIYE 160
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 104-178 3.06e-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: 51.75  E-value: 3.06e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492422421 104 TLEACDPDKLFCD-EIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKD 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 1.26e-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: 46.33  E-value: 1.26e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 492422421 119 QALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLR 173
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 132-176 1.86e-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: 1.86e-07
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 492422421   132 TSREVFILSR-MKNLPNKEIALRLDISVKTVEFHITRSLKQL----RVQL 176
Cdd:smart00421   5 TPREREVLRLlAEGLTNKEIAERLGISEKTVKTHLSNIMRKLgvrsRTQA 54
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 27-176 2.67e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 48.81  E-value: 2.67e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  27 AYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVR-----MRAEQHIGDMRQKELALR 101
Cdd:PRK11922  47 ARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRLvnlaeMVMASTIAGGERTPLADP 126

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 492422421 102 IStleacDPDK-LFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVE--FHITRSLkqLRVQL 176
Cdd:PRK11922 127 AE-----DPERaAARREIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKtrLHRARRL--LRESL 197
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 109-172 7.39e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 47.42  E-value: 7.39e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492422421 109 DPDKLFC-DEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQL 172
Cdd:PRK12533 114 DPLALLLrAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARARRRL 178
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 14-173 9.03e-07

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 46.60  E-value: 9.03e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  14 EVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNIsALLLTAIKNRSLNHL--QHLEVRMRAEQ--- 88
Cdd:PRK07037   2 DVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPV-AYLFRIVRNLAIDHYrrQALENKYHGDEedg 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  89 ---HIGDMRQKELALRISTLEacdpdklfcdeiqaLVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHI 165
Cdd:PRK07037  81 ldvPSPEASPEAALINRDTLR--------------HVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMI 146


                 ....*...
gi 492422421 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 1.33e-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: 1.33e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 492422421 124 EAISELPpTSREVFILSRM-KNLPNKEIALRLDISVKTVEFHITRSLKQL----RVQL 176
Cdd:COG2197   64 EALRRLL-TPREREVLRLLaEGLSNKEIAERLGISERTVKTHVSNILRKLgvrnRTEL 120
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 26-173 1.47e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 46.32  E-value: 1.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNrslnhlqhlevrmraeQHIGDMRQKE-LALRIST 104
Cdd:PRK12511  20 YARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHN----------------AFIDELRRRRvEARRADE 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 492422421 105 LEACDPDKLFCDEIQAL----VQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLR 173
Cdd:PRK12511  84 LAVLADASLPAAQEHAVrlaqIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALR 156
PRK06930 PRK06930
positive control sigma-like factor; Validated
 109-181 2.68e-06

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 45.49  E-value: 2.68e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 492422421 109 DPDKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKDYQF 181
Cdd:PRK06930  95 EPESVISEWDKIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQINESLF 167
GerE pfam00196
Bacterial regulatory proteins, luxR family;
132-174 3.43e-06

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 42.57  E-value: 3.43e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 492422421  132 TSREVFILSRM-KNLPNKEIALRLDISVKTVEFHITRSLKQLRV 174
Cdd:pfam00196   4 SPREREVLRWLaAGKSNKEIADELGISEKTVKVHRSNIMRKLNV 47
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 119-164 3.45e-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: 45.48  E-value: 3.45e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 492422421 119 QALVQEAISELPPTSREVFILSrMKNLPNKEIALRLDISVKTVEFH 164
Cdd:COG4566  128 RAELRARLASLTPREREVLDLV-VAGLSNKQIARELGISPRTVEVH 172
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 26-179 3.51e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 45.45  E-value: 3.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQhlevRMRAEQHIGDMRQKELALRIStl 105
Cdd:PRK12513  42 FLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWR----RHGARQAPSLDADEQLHALAD-- 115

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492422421 106 EACDPDKLFCD-EIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKDY 179
Cdd:PRK12513 116 DGAAPEQQLSLfRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAEE 190
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 26-178 3.98e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 45.22  E-value: 3.98e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNrslnhlQHLEVRMRAEQHIGDMrQKELALRISTL 105
Cdd:PRK12546  23 FAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRN------TFYSDRRKHKREVPDP-EGVHAASLAVK 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492422421 106 EACDPDKLFCDeiqalVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQL--RVQLKD 178
Cdd:PRK12546  96 PAHDGRLAMSD-----FRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARLaeLLQLEE 165
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
31-179 9.26e-06

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 43.91  E-value: 9.26e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  31 VRNREEAEDIVMGAFTNVWEHRNEL-QEDTNISALLLTAIKNRSLNhlQHLEVRMRAEQhIGDmrqkelalriSTLEACD 109
Cdd:PRK09645  30 TGDRARAEDVVQETLLRAWQHPEVLaDTGRSARAWLFTVARNLVID--ERRSARARPVE-GGD----------DVLGVPE 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492422421 110 PDKLfcDEIQA-----LVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKDY 179
Cdd:PRK09645  97 QSAP--DEVDRaldrlLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQER 169
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 492422421  12 LTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVR------MR 85
Cdd:PRK09415  18 IDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSWHNKkvivteDI 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  86 AEQHIGDMRQKELALRIStleacdpdklfcDEIQALVqEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEfhi 165
Cdd:PRK09415  98 FTYMESQKESVEEEVIQN------------AEDERLA-SAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVK--- 161

                        170
                 ....*....|..
gi 492422421 166 TRsLKQLRVQLK 177
Cdd:PRK09415 162 TR-LKKAKELLK 172
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 36-178 1.33e-05

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 43.75  E-value: 1.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  36 EAEDIVMGAFTNVWEHRNELQ-EDTNISALLLTAIKNRSLNHLQHLEVRMRAEQhiGDMRQKElalristleACDPDKLF 114
Cdd:PRK13919  49 AAEDVVQEVFIRVWKKAKEFDpRRGSARAWLLALAHHAAVDHVRRRAARPQPLE--PDEREPE---------AFDLPGPG 117

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 492422421 115 CDEIQAL----VQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKD 178
Cdd:PRK13919 118 LDEEGHLdrtrLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLRE 185
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 10-178 2.81e-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: 42.31  E-value: 2.81e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421   10 SELTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQ-----HLEVRM 84
Cdd:TIGR02989   1 KAFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRklgrdRLVFDD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421   85 RAEQHIGDMRQKELALRIStleacdpdklfcDEIQALvQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTvefh 164
Cdd:TIGR02989  81 DLLEALAAEAEPTEAERLS------------DDRQAL-EGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNA---- 143

                         170
                  ....*....|....
gi 492422421  165 ITRSLKQLRVQLKD 178
Cdd:TIGR02989 144 VYKALQRIRVSLRE 157
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 132-175 3.04e-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: 3.04e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 492422421 132 TSREVFILSRMKN-LPNKEIALRLDISVKTVEFHITRSLKQLRVQ 175
Cdd:cd06170    2 TPREREVLRLLAEgKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 26-177 4.15e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 42.26  E-value: 4.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHlevRMRAEQHIGDMRQKELALRISTL 105
Cdd:PRK12516  26 FAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRK---RGREVQDTDGMFTEQLAVHPSQY 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 492422421 106 EACDpdklfcdeIQALvQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLK 177
Cdd:PRK12516 103 GTLD--------LQDF-RAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165
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 492422421 132 TSREVFILSR-MKNLPNKEIALRLDISVKTVEFHITRSLKQL----RVQL 176
Cdd:COG5905   14 TKREREVLELlAEGLTNKEIARQLFISEKTVKNHVSNILRKLgvrnRVQA 63
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 18-171 4.44e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 42.01  E-value: 4.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  18 KRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMraeqhigdMRQKE 97
Cdd:PRK12518  18 RRYQQKVRSTLYQLCGRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQFAQRP--------SRIQD 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 492422421  98 LALRISTLEACDPDKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVE---FHITRSLKQ 171
Cdd:PRK12518  90 DSLNDQPSRPSDTPDLMQLHYQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKsrlFYARRQLRK 166
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 31-177 6.09e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 41.96  E-value: 6.09e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  31 VRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAI-KNRSLNHLqhlevRMRAEQhigdmRQKELALRISTLEACD 109
Cdd:PRK12534  46 IPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLAMIaRNKAIDHL-----RANAPQ-----RRNVALDDAGELRAAD 115

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492422421 110 PDKLFCDEIQAL---VQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLK 177
Cdd:PRK12534 116 ASPLERTERASTrrrIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAKLKACLE 186
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
25-174 9.94e-05

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 41.28  E-value: 9.94e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  25 QFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQHIGDMRQKELALRIST 104
Cdd:COG2771   14 LLLLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLAL 93

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492422421 105 LEACDPDKLFCDEIQALVQEAISELPPTSREVFILSR---------MKNLPNKEIALRLDISVKTVEFHITRSLKQLRV 174
Cdd:COG2771   94 LAALLARLAALLLALALAALLLAALARLLARAPGLTPrerevlrllAEGLTLKEIARILGISERTVRTHLKRIYRKLGV 172
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 27-178 1.08e-04

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 41.31  E-value: 1.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  27 AYSYVRNREEAEDIVMGAFTNV--------------WEHRNElqedTNisaLLLTAIKNRSlnhlqhlEVRMRAeqhigd 92
Cdd:PRK09647  45 AYRLSGNQHDAEDLTQETFIRVfrslqnyqpgtfegWLHRIT----TN---LFLDMVRRRA-------RIRMEA------ 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  93 mrQKELALRISTLEAcDPDKLFCD-EIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQ 171
Cdd:PRK09647 105 --LPEDYDRVPGDEP-NPEQIYHDaRLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQ 181


                 ....*..
gi 492422421 172 LRVQLKD 178
Cdd:PRK09647 182 LRAALAA 188
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 125-173 1.09e-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: 38.18  E-value: 1.09e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 492422421  125 AISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLR 173
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 83-175 1.36e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 40.87  E-value: 1.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  83 RMRAEQHIGDMRQKELALristleacDPDKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVE 162
Cdd:PRK12543  80 RFRIFEKAEEQRKPVSID--------FSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVK 151

                         90
                 ....*....|...
gi 492422421 163 FHITRSLKQLRVQ 175
Cdd:PRK12543 152 SRIHAALKKLRQK 164
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 15-173 2.03e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 40.30  E-value: 2.03e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  15 VFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWeHRNEL--QEDTNISALLLTAIKNRSLNHLQHLEVRmraEQHIgd 92
Cdd:PRK12531  32 VFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVW-QKAHLfdGQKSALSTWIYTIIRNLCFDLLRKQKGK---DLHI-- 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  93 mrqkeLALRISTLEACDPDKL--FCDEiQALVQEAISE----LPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHIT 166
Cdd:PRK12531 106 -----HADDIWPSDYYPPDLVdhYSPE-QDMLKEQVMKfldrLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLR 179


                 ....*..
gi 492422421 167 RSLKQLR 173
Cdd:PRK12531 180 LAVEKLR 186
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 125-172 2.09e-04

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 40.40  E-value: 2.09e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 492422421 125 AISELppTSREVFILSRM-KNLPNKEIALRLDISVKTVEFHITRSLKQL 172
Cdd:PRK10651 152 DVNQL--TPRERDILKLIaQGLPNKMIARRLDITESTVKVHVKHMLKKM 198
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 14-178 2.56e-04

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 40.00  E-value: 2.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  14 EVFSKRQQQFVQFAYSYV----RNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEQH 89
Cdd:PRK09638  18 AALTTLFQQHYSFLYKYLlkltLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRKQKREKLRLQR 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  90 IGD--MRQKELALRISTLEACDpdklfcdeiqalVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITR 167
Cdd:PRK09638  98 AKEetLRKEKWEAAIKGAEWSE------------MLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHH 165

                        170
                 ....*....|.
gi 492422421 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 3.71e-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: 3.71e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 492422421   16 FSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNIS--ALLLTAIKNRSLNHL 77
Cdd:pfam04542   2 VERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSfsTWLYTIIRNAIIDYL 65
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 12-178 4.06e-04

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 39.20  E-value: 4.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  12 LTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLqhlevRMRAeqhig 91
Cdd:PRK09637   3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFY-----RKKN----- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  92 dmrQKELALRISTLEACDPDKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQ 171
Cdd:PRK09637  73 ---RSEELPDDLLFEDEEREENAKKELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVK 149


                 ....*..
gi 492422421 172 LRVQLKD 178
Cdd:PRK09637 150 LKELLEG 156
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 18-168 4.06e-04

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 39.40  E-value: 4.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  18 KRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVR--------MRAEQH 89
Cdd:PRK11923  28 KYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLVSRGRRppdsdvssEDAEFY 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492422421  90 IGDMRQKElalrISTLEAcdpdKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRS 168
Cdd:PRK11923 108 DGDHALKD----IESPER----ALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRA 178
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 11-178 6.39e-04

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 38.71  E-value: 6.39e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  11 ELTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRnELQEDTNISALLLTAIKNRSLNHLQhlevRMRAEQHI 90
Cdd:PRK09644   2 EIEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYL-EDYDNQKVKPWLFKVAYHTFIDFVR----KEKKVSFV 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  91 GDMRqkelalrISTLEACDPDKLFCD-EIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSL 169
Cdd:PRK09644  77 GTDE-------IEAIQAESTEEYVVAkNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGR 149


                 ....*....
gi 492422421 170 KQLRVQLKD 178
Cdd:PRK09644 150 KRLKALLKE 158
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 33-176 6.46e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 38.72  E-value: 6.46e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  33 NREEAEDIVMGAFTNVWEHRNELQE-DTNISALLLTAIKNRSLNHLqhlevRMRAEQHIGDMRQKELALRISTLEACDPD 111
Cdd:PRK12524  49 DRAEAEDVTQEAMLRLWRIAPDWRQgEARVSTWLYRVVCNLCTDRL-----RRRRRASVDLDDAPEPADAAPGAEEALIE 123

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492422421 112 KlfcDEIQALvQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQL 176
Cdd:PRK12524 124 G---DRMRAL-DAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAALL 184
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 55-162 1.21e-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: 38.17  E-value: 1.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421   55 LQEDTNISALLLTAIKNRSLNHLQhlevRMRAEQHIGDMRQKELALRISTLEACDPDKLFcDEIQALvqEAISELPPTSR 134
Cdd:pfam07638  69 WSGRGHFFAAAAEAMRRILIDHAR----RRQRQKRGGDVQRRELDEVVDNGDSPNPDLLL-DLDEAL--EQLFSLSPRQA 141

                          90       100
                  ....*....|....*....|....*...
gi 492422421  135 EVFILSRMKNLPNKEIALRLDISVKTVE 162
Cdd:pfam07638 142 RLVELRFFAGLSNDEIAERLGVSERTVE 169
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 89-178 2.16e-03

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 37.74  E-value: 2.16e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  89 HIGDmRQKELALrISTLE---ACDPDKLFCD-EIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTV-EF 163
Cdd:PRK06288 171 FGGD-EGDEVSL-MDTLEspaALNPDEIAEReEIKRVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRIsQL 248

                         90
                 ....*....|....*
gi 492422421 164 HiTRSLKQLRVQLKD 178
Cdd:PRK06288 249 H-TKAVLQLRAKLAE 262
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 34-176 2.86e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 36.75  E-value: 2.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  34 REEAEDIVMGAFTNVWeHRNELQEDTNISALLLTAIKNRSLNHLQhlevRMRAEQhigdMRQKELALrisTLEACDPDKl 113
Cdd:PRK12523  34 RQRAEDLSQDTFVRLL-GRPELPTPREPRAFLAAVAKGLMFDHFR----RAALEQ----AYLAELAL---VPEAEQPSP- 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421 114 fcdEIQALVQEAISE-------LPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQL 176
Cdd:PRK12523 101 ---EEQHLILEDLKAidrllgkLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167
PRK09642 PRK09642
RNA polymerase sigma factor;
111-182 3.24e-03

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 36.62  E-value: 3.24e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 492422421 111 DKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLKDYQFL 182
Cdd:PRK09642  89 DLLLTKEQKLLIAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEEFL 160
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 26-71 3.84e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 36.39  E-value: 3.84e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 492422421  26 FAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKN 71
Cdd:PRK12547  22 FAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRN 67
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
143-174 4.04e-03

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 36.61  E-value: 4.04e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 492422421 143 KNLPNKEIALRLDISVKTVEFHITRSLKQLRV 174
Cdd:COG2909  136 EGLSNKEIAERLFISVNTVKTHLRNIYRKLGV 167
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 25-177 5.28e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 36.25  E-value: 5.28e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  25 QFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLqhlevRMRAEQHIGDmrqkELALRIST 104
Cdd:PRK12515  37 RFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSAL-----RRRKHEEIDD----EAAAAIED 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 492422421 105 lEACDPD-KLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSLKQLRVQLK 177
Cdd:PRK12515 108 -GADTPEvALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 11-177 7.98e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 35.62  E-value: 7.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  11 ELTEVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNrslNHLQHLEVRMRAEQHI 90
Cdd:PRK12522   4 KVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVR---TFYDFYRKKKRWKDRI 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  91 GDMRQKELALRISTLEACD-PDKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTVEFHITRSL 169
Cdd:PRK12522  81 LDLFHKEDGGEIEFADDVNiSEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAK 160


                 ....*...
gi 492422421 170 KQLRVQLK 177
Cdd:PRK12522 161 KQMREHLE 168
fixJ PRK09390
response regulator FixJ; Provisional
 116-164 8.41e-03

response regulator FixJ; Provisional


Pssm-ID: 181815 [Multi-domain]  Cd Length: 202  Bit Score: 35.75  E-value: 8.41e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 492422421 116 DEIQALVQEAISELPPTSREVfILSRMKNLPNKEIALRLDISVKTVEFH 164
Cdd:PRK09390 129 EAVAADIRARIASLSERERQV-MDGLVAGLSNKVIARDLDISPRTVEVY 176
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 14-161 9.79e-03

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 35.46  E-value: 9.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492422421  14 EVFSKRQQQFVQFAYSYVRNREEAEDIVMGAFTNVWEHRNELQEDTNISALLLTAIKNRSLNHLQHLEVRMRAEqhIGDm 93
Cdd:PRK09643  31 ELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACLDRLRRAKARPTVP--LDD- 107

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 492422421  94 rqkelALRISTLEacdPDKLFCDEIQALVQEAISELPPTSREVFILSRMKNLPNKEIALRLDISVKTV 161
Cdd:PRK09643 108 -----VYPVAQLE---RDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTV 167
 
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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