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Conserved domains on  [gi|492255764|ref|WP_005791946|]
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MULTISPECIES: RNA polymerase sigma-70 factor [Bacteroides]

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 ...
 18-174 2.92e-46

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: 149.25  E-value: 2.92e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   18 AFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKNLNEPFYQLSV 97
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEEL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   98 IEAVE---ESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRKNI 174
Cdd:TIGR02985  82 AEIEErelSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
 
Name Accession Description Interval E-value
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 18-174 2.92e-46

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: 149.25  E-value: 2.92e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   18 AFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKNLNEPFYQLSV 97
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEEL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   98 IEAVE---ESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRKNI 174
Cdd:TIGR02985  82 AEIEErelSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-175 1.30e-45

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: 148.22  E-value: 1.30e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   1 MNEKEAIIKLKTCNDKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLV 80
Cdd:COG1595    1 MSSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  81 FNRSRKNLNEPFYQLSVIEAV-EESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTV 159
Cdd:COG1595   81 IDHLRKRRRRRELLDELAEELpDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTV 160

                        170
                 ....*....|....*.
gi 492255764 160 EHHISDALKFLRKNIK 175
Cdd:COG1595  161 KSRLSRARKKLREALE 176
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 15-178 2.74e-25

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 96.03  E-value: 2.74e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKNLNEPfyQ 94
Cdd:PRK09652   8 DRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRP--P 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  95 LSVIEAVE-ESYDI----------EEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHI 163
Cdd:PRK09652  86 ASDVDAEEaEDFDLadalrdistpENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRI 165

                        170
                 ....*....|....*
gi 492255764 164 SDALKFLRKNIKLYL 178
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 ...
 120-170 1.50e-13

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 62.09  E-value: 1.50e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 492255764  120 ISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFL 170
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 117-171 3.72e-08

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: 47.87  E-value: 3.72e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 492255764 117 RTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLR 171
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 127-168 4.54e-08

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 47.52  E-value: 4.54e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 492255764   127 LPPRQQEVFRLSRdEELSYREIAERLQISERTVEHHISDALK 168
Cdd:smart00421   4 LTPREREVLRLLA-EGLTNKEIAERLGISEKTVKTHLSNIMR 44
 
Name Accession Description Interval E-value
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 18-174 2.92e-46

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: 149.25  E-value: 2.92e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   18 AFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKNLNEPFYQLSV 97
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEEL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   98 IEAVE---ESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRKNI 174
Cdd:TIGR02985  82 AEIEErelSEADPEEELEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-175 1.30e-45

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: 148.22  E-value: 1.30e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   1 MNEKEAIIKLKTCNDKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLV 80
Cdd:COG1595    1 MSSDEELLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  81 FNRSRKNLNEPFYQLSVIEAV-EESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTV 159
Cdd:COG1595   81 IDHLRKRRRRRELLDELAEELpDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTV 160

                        170
                 ....*....|....*.
gi 492255764 160 EHHISDALKFLRKNIK 175
Cdd:COG1595  161 KSRLSRARKKLREALE 176
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 17-174 6.26e-33

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: 115.14  E-value: 6.26e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   17 AAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKNLNEPFYQLS 96
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 492255764   97 VIEAVEESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRKNI 174
Cdd:TIGR02937  81 LEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 15-178 2.74e-25

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 96.03  E-value: 2.74e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKNLNEPfyQ 94
Cdd:PRK09652   8 DRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLRKQGRRP--P 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  95 LSVIEAVE-ESYDI----------EEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHI 163
Cdd:PRK09652  86 ASDVDAEEaEDFDLadalrdistpENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRI 165

                        170
                 ....*....|....*
gi 492255764 164 SDALKFLRKNIKLYL 178
Cdd:PRK09652 166 FRAREALRAKLQPLL 180
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 12-174 1.01e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 89.26  E-value: 1.01e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  12 TCNDKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKNLNEP 91
Cdd:PRK11924   8 ATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREK 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  92 FYQLSVIEAVEESY---DIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALK 168
Cdd:PRK11924  88 AVLSDDALEPEFAEtaeTPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQ 167


                 ....*.
gi 492255764 169 FLRKNI 174
Cdd:PRK11924 168 LLRECL 173
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 15-171 2.91e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 72.80  E-value: 2.91e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRK----NLNE 90
Cdd:PRK12513  24 DAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRRhgarQAPS 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  91 PFYQLSVIEAVEESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFL 170
Cdd:PRK12513 104 LDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKL 183


                 .
gi 492255764 171 R 171
Cdd:PRK12513 184 R 184
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 15-174 3.40e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 67.07  E-value: 3.40e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLF-ITMRNLvfNRSRKNLNEPFY 93
Cdd:PRK12543   5 DQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIgLVIKQI--HSWRRKRWRRFR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  94 QLSVIEAVEE--SYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLR 171
Cdd:PRK12543  83 IFEKAEEQRKpvSIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLR 162


                 ...
gi 492255764 172 KNI 174
Cdd:PRK12543 163 QKE 165
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 120-170 1.50e-13

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 62.09  E-value: 1.50e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 492255764  120 ISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFL 170
Cdd:pfam08281   4 LLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 15-178 2.82e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 64.70  E-value: 2.82e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKNLNepfyQ 94
Cdd:PRK12519  27 QSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLTRSRAIDRLRSRRS----R 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  95 LSVIEAVEESYDIE-------EELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDAL 167
Cdd:PRK12519 103 QRLLERWQQELLGEasedtplEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGL 182

                        170
                 ....*....|.
gi 492255764 168 KFLRKNIKLYL 178
Cdd:PRK12519 183 LKLRELLQDLL 193
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 7-172 2.54e-11

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 59.32  E-value: 2.54e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   7 IIKLKTCNDKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRK 86
Cdd:PRK09641   8 LIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRK 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  87 NlnEPFYQL-------------SVIEAVEESydIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQ 153
Cdd:PRK09641  88 R--KPDYYLdaevagtegltmySQLAADDAL--PEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILD 163

                        170
                 ....*....|....*....
gi 492255764 154 ISERTVEHHISDALKFLRK 172
Cdd:PRK09641 164 LPVGTVKTRIHRGREALRK 182
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
45-171 8.93e-11

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 57.78  E-value: 8.93e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  45 EEIVQEVFIKIWENREALDEEQNFA-GYLFITMRNLVFN--RSRKNLNEpfyqlSVIEAVEESYDI--EEELDAANLRTH 119
Cdd:PRK09645  37 EDVVQETLLRAWQHPEVLADTGRSArAWLFTVARNLVIDerRSARARPV-----EGGDDVLGVPEQsaPDEVDRALDRLL 111

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 492255764 120 ISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLR 171
Cdd:PRK09645 112 VADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALR 163
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 15-171 1.56e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 57.63  E-value: 1.56e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQN-FAGYLFITMRNLVFNRSRKNLN---- 89
Cdd:PRK12531  25 DKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKSaLSTWIYTIIRNLCFDLLRKQKGkdlh 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  90 --------EPFYQLSVIeaveESYDIEEELdaanLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEH 161
Cdd:PRK12531 105 ihaddiwpSDYYPPDLV----DHYSPEQDM----LKEQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKS 176

                        170
                 ....*....|
gi 492255764 162 HISDALKFLR 171
Cdd:PRK12531 177 RLRLAVEKLR 186
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 18-172 1.88e-10

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: 56.56  E-value: 1.88e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   18 AFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFN------RSRKNLNEp 91
Cdd:TIGR02989   2 AFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNyrrklgRDRLVFDD- 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   92 fyqlSVIEAVEESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTvehhISDALKFLR 171
Cdd:TIGR02989  81 ----DLLEALAAEAEPTEAERLSDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNA----VYKALQRIR 152


                  .
gi 492255764  172 K 172
Cdd:TIGR02989 153 V 153
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 40-170 2.59e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 56.63  E-value: 2.59e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  40 SAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKNLNEPFYQlsvIEAVEESYDIEEELDAANlRTH 119
Cdd:PRK12512  49 PADQAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKLIDALRRRGRRVFVD---IDDFAETLPAEPATETLP-AGD 124

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 492255764 120 ISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFL 170
Cdd:PRK12512 125 VGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAAL 175
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 2-171 4.60e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 55.98  E-value: 4.60e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   2 NEKEAIIKLKTCNDKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWE--NREALDEEQNFAGYLFITmRNL 79
Cdd:PRK12514   4 DDIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTkaDRFAVSGLSPMTWLITIA-RNH 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  80 VFN--RSRKNLNEPFYQlsVIEAVEESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISER 157
Cdd:PRK12514  83 AIDrlRARKAVAVDIDE--AHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLN 160

                        170
                 ....*....|....
gi 492255764 158 TVEHHISDALKFLR 171
Cdd:PRK12514 161 TMRTWLRRSLLKLR 174
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 43-175 1.07e-09

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: 55.60  E-value: 1.07e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  43 DVEEIVQEVFIKiwENREALDEEQnfAGYL------FITMRNLVFNRSRKNLNEPFYQLSVIEAVEESYDIEEELDAANL 116
Cdd:COG1191  101 KIEEAIEELEQE--LGREPTDEEI--AEELgisleeVQEALEAANAYQLLSLDEPLEDGDDLLDLLESGDPEEELEHEEL 176

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 492255764 117 RTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRKNIK 175
Cdd:COG1191  177 REALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVSRLHKKALARLREYLK 235
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 14-172 1.35e-09

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 54.66  E-value: 1.35e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  14 NDKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDE-EQNFAGYLFITMRNLVFNRSRKNLNEPF 92
Cdd:PRK05602  17 GDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPgEARFDTWLHRVVLNLCYDRLRRRREVPV 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  93 YQLSviEAVEESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRK 172
Cdd:PRK05602  97 EDAP--DVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRA 174
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 26-155 1.40e-09

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 54.61  E-value: 1.40e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  26 YWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKnlNEPFYQLSVIEAVEESy 105
Cdd:PRK09637  10 YKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRK--KNRSEELPDDLLFEDE- 86

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 492255764 106 DIEEELDaANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQIS 155
Cdd:PRK09637  87 EREENAK-KELAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLS 135
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 5-171 2.24e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 54.42  E-value: 2.24e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   5 EAIIKLKTCNDKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAG-YLFITMRNLVFNR 83
Cdd:PRK12526  26 QWLILVAISRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGAATtWVYTVMRNAAFDM 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  84 SRK-------NLNEPFYQLSviEAVEESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISE 156
Cdd:PRK12526 106 LRKikakkeqNLGDDIWPIE--QALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPL 183

                        170
                 ....*....|....*
gi 492255764 157 RTVEHHISDALKFLR 171
Cdd:PRK12526 184 GTVKSRLRLALAKLK 198
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 19-172 3.53e-09

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 53.03  E-value: 3.53e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  19 FAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEeqNFAGYLFITMRNLVFNRSRKNLNEPFYQLSVI 98
Cdd:PRK09639   5 FEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFKGIE--NEKGWLIKSARNVAYNYLRSEKRRRARILGEF 82

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492255764  99 EAVEESYDI--EEELDAANLRTHISALISMLPPRQQEVFRLsRDEELSYREIAERLQISERTVEHHISDALKFLRK 172
Cdd:PRK09639  83 QWQEVDNEPspEEIWIRKEEITKVQEVLAKMTERDRTVLLL-RFSGYSYKEIAEALGIKESSVGTTLARAKKKFRK 157
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 22-87 3.65e-09

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: 51.05  E-value: 3.65e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 492255764   22 LYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQ--NFAGYLFITMRNLVFNRSRKN 87
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERgvSFSTWLYTIIRNAIIDYLRKQ 68
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 123-172 3.81e-09

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 50.12  E-value: 3.81e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 492255764  123 LISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRK 172
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 45-172 4.33e-09

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 52.77  E-value: 4.33e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  45 EEIVQEVFIKIWENREALDEEQNFAgYLFITMRNLVFNRSRKnlnepfyqlsviEAVEESYDIEEE--LD---------A 113
Cdd:PRK07037  26 EDVVQDAFVKLVEAPNQDAVKQPVA-YLFRIVRNLAIDHYRR------------QALENKYHGDEEdgLDvpspeaspeA 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 492255764 114 ANLR----THISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRK 172
Cdd:PRK07037  93 ALINrdtlRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCRK 155
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 1-172 5.01e-09

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 53.10  E-value: 5.01e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   1 MNEKEAIIKLKTcNDKAAFAFLYRSYWAKVYNFTrLYITSAVDV-EEIVQEVFIKIWENREALDEEQNFAGYLFITMRNL 79
Cdd:PRK09638   3 MDEKELIQKAKK-GDDAALTTLFQQHYSFLYKYL-LKLTLDPDLaEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  80 VFNRSRKNLNEpfyqlsviEAVEESYDiEEELDAANLRTHISA--------LISMLPPRQQEVFRLSRDEELSYREIAER 151
Cdd:PRK09638  81 YKDHLRKQKRE--------KLRLQRAK-EETLRKEKWEAAIKGaewsemldALSKLDPEFRAPVILKHYYGYTYEEIAKM 151

                        170       180
                 ....*....|....*....|.
gi 492255764 152 LQISERTVEHHISDALKFLRK 172
Cdd:PRK09638 152 LNIPEGTVKSRVHHGIKQLRK 172
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 120-168 5.26e-09

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: 52.20  E-value: 5.26e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 492255764 120 ISALISMLPPRQQEVFRLSRdEELSYREIAERLQISERTVEHHISDALK 168
Cdd:COG2197   63 LEALRRLLTPREREVLRLLA-EGLSNKEIAERLGISERTVKTHVSNILR 110
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 43-177 1.18e-08

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 51.70  E-value: 1.18e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  43 DVEEIVQEVFIKIWENREALDEEQNFAgYLFITMRNLVFNRSRKNLNEPFYQLSVIEAVE--ESYDIEEELDAANLRTHI 120
Cdd:PRK12527  21 AAEDVAHDAYLRVLERSSSAQIEHPRA-FLYRTALNLVVDRHRRHRVRQAEPLEVLDEEErlHSPSPQTRLDLGQRLALL 99

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 492255764 121 SALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRKNIKLY 177
Cdd:PRK12527 100 QRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW 156
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 15-171 1.82e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 51.59  E-value: 1.82e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDeEQNFAGYLFITM--RNLVFNRSRKnlNEPF 92
Cdd:PRK12534  23 DRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFD-PSRARGLTWLAMiaRNKAIDHLRA--NAPQ 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  93 YQLSVI----EAVEESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALK 168
Cdd:PRK12534 100 RRNVALddagELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLA 179


                 ...
gi 492255764 169 FLR 171
Cdd:PRK12534 180 KLK 182
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 117-171 3.72e-08

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: 47.87  E-value: 3.72e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 492255764 117 RTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLR 171
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 127-168 4.54e-08

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 47.52  E-value: 4.54e-08
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|..
gi 492255764   127 LPPRQQEVFRLSRdEELSYREIAERLQISERTVEHHISDALK 168
Cdd:smart00421   4 LTPREREVLRLLA-EGLTNKEIAERLGISEKTVKTHLSNIMR 44
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 116-168 1.23e-07

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: 46.88  E-value: 1.23e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 492255764 116 LRTHISALISMLPPRQQEVFRLSRdEELSYREIAERLQISERTVEHHISDALK 168
Cdd:COG5905    2 MPSSSTSHPSLLTKREREVLELLA-EGLTNKEIARQLFISEKTVKNHVSNILR 53
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 5-172 1.66e-07

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 49.14  E-value: 1.66e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   5 EAIIKLKTCNDKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFA-GYLFITMRNLVFNR 83
Cdd:PRK13919  11 EALLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSArAWLLALAHHAAVDH 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  84 SRKNLNEPfYQLSVIEAVEESYDI-------EEELDaanlRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISE 156
Cdd:PRK13919  91 VRRRAARP-QPLEPDEREPEAFDLpgpgldeEGHLD----RTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPL 165

                        170
                 ....*....|....*.
gi 492255764 157 RTVEHHISDALKFLRK 172
Cdd:PRK13919 166 GTLKTRARRALSRLKE 181
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
15-172 1.79e-07

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 48.90  E-value: 1.79e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITM--RNLVfNRSR------- 85
Cdd:PRK09646  28 DQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARGSALAWLLTLahRRAV-DRVRseqaasq 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  86 -------KNLNEPFYQlsVIEAVEESydIEEELDAANLRThisalismLPPRQQEVFRLSRDEELSYREIAERLQISERT 158
Cdd:PRK09646 107 revrygaRNVDPAFDQ--VAEEVEAR--LERERVRDCLDA--------LTDTQRESVTLAYYGGLTYREVAERLAVPLGT 174

                        170
                 ....*....|....
gi 492255764 159 VEHHISDALKFLRK 172
Cdd:PRK09646 175 VKTRMRDGLIRLRD 188
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 98-162 3.68e-07

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: 48.17  E-value: 3.68e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492255764  98 IEAVEESYDIEEELDAANLRTH-ISALISMLPPRQQEVFRLSRDEELSyREIAERLQISERTVEHH 162
Cdd:COG4566  108 LDAVRRALARDRARRAERARRAeLRARLASLTPREREVLDLVVAGLSN-KQIARELGISPRTVEVH 172
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 40-166 1.92e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 45.61  E-value: 1.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  40 SAVDveeIVQEVFIKIWENREA--LDEEQNFagyLFITMRNLVFNRSRKNLNEPFYQLSVIEAVEESYDIEEElDAANLR 117
Cdd:PRK12528  30 SAAD---LAQDTFVKVLVARETaqIIEPRAF---LTTIAKRVLCNHYRRQDLERAYLEALAQLPERVAPSEEE-RAIILE 102

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 492255764 118 T--HISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDA 166
Cdd:PRK12528 103 TlvELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKA 153
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 5-160 3.47e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 45.27  E-value: 3.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   5 EAIIKLKTCNDKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWenREALDEEQNFA---GYLFITMRNLVF 81
Cdd:PRK12524  14 EALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLW--RIAPDWRQGEArvsTWLYRVVCNLCT 91

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492255764  82 NRSRKNLNEPFYQLSVIEAVEESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVE 160
Cdd:PRK12524  92 DRLRRRRRASVDLDDAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVE 170
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 12-168 4.24e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 45.04  E-value: 4.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  12 TCNDKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDE--EQNFAGYLFITMRNLVFNRSRKN-L 88
Cdd:PRK12542   4 TNNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSlnTQELKRYILRVAKNKAIDSYRKNkR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  89 NEPF---YQLSVIEAVEEsyDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISD 165
Cdd:PRK12542  84 HETFleeYERESIEAVDE--NIEEWEKRKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFER 161


                 ...
gi 492255764 166 ALK 168
Cdd:PRK12542 162 ARK 164
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 15-175 4.40e-06

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 44.93  E-value: 4.40e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKN-----LN 89
Cdd:PRK09640  24 VTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKErrkrrLM 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  90 EPFYQLSVIEAVEESYDIEEEldaanlRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKF 169
Cdd:PRK09640 104 DALSLDPLEEASEEKAPKPEE------RGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDK 177


                 ....*.
gi 492255764 170 LRKNIK 175
Cdd:PRK09640 178 LREKFA 183
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 102-175 4.48e-06

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 45.22  E-value: 4.48e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 492255764 102 EESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRKNIK 175
Cdd:PRK06986 160 HQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARLG 233
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 5-159 5.99e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 44.72  E-value: 5.99e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   5 EAIIKLKTCNDKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRS 84
Cdd:PRK12515  10 EMLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKALSAL 89

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492255764  85 RKNLNEPFYQLSVIEAVEESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTV 159
Cdd:PRK12515  90 RRRKHEEIDDEAAAAIEDGADTPEVALQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTV 164
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 102-179 6.57e-06

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 45.04  E-value: 6.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764 102 EESYDIEEELDAANLRTHISALISMLPPRQQEVFR----LSRDEELSYREIAERLQIS-ERT--VEhhiSDALKFLRKNI 174
Cdd:COG0568  182 EEAPSPEEALEEELLREELREALDTLTEREREILRlrfgLDDGEPHTLEEIGKEFGVSrERVrqIE---AKALRKLRHPL 258


                 ....*
gi 492255764 175 KLYLL 179
Cdd:COG0568  259 RSRKL 263
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 1-176 9.44e-06

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 44.16  E-value: 9.44e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764   1 MNEKEAIIKLKTCNDKAaFAFLYRSYWAKVYNFTR---LYITSAVDVEEIVQEVFIKIWENREALDEEQ-NFAGYLFITM 76
Cdd:PRK06811   3 INEDNFIKELKKKNEKA-LEFIVDTYGNLVKKIVHkvlGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKgSFKKWIAAIS 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  77 RNLVFNRSRKNLNEPFYQLSVIEAVEESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISE 156
Cdd:PRK06811  82 KYKAIDYKRKLTKNNEIDSIDEFILISEESIENEIILKENKEEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTR 161

                        170       180
                 ....*....|....*....|
gi 492255764 157 RTVEHHISDALKFLRKNIKL 176
Cdd:PRK06811 162 SAIDNRLSRGRKKLQKNKLN 181
PRK06930 PRK06930
positive control sigma-like factor; Validated
 117-175 1.17e-05

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 43.56  E-value: 1.17e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 492255764 117 RTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRKNIK 175
Cdd:PRK06930 105 KIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 15-174 1.19e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 44.18  E-value: 1.19e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKNLNEPfYQ 94
Cdd:PRK11922  28 DEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRLV-NL 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  95 LSVIEAVEESYDIEEELDAAN-----------LRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHI 163
Cdd:PRK11922 107 AEMVMASTIAGGERTPLADPAedperaaarreIRALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRL 186

                        170
                 ....*....|.
gi 492255764 164 SDALKFLRKNI 174
Cdd:PRK11922 187 HRARRLLRESL 197
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 19-180 2.60e-05

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 42.49  E-value: 2.60e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  19 FAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWeNREALDEEQNFAGYLFITMRNLVFNRSRKNLNEPFYqLSVI 98
Cdd:PRK09651  12 FESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVM-VSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAY-LEML 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  99 EAVEESYDIEEELDAANLRT--HISALISMLPPRQQEVFRLSRDEELSYREIAERLQISertvehhISDALKFLRKNIKL 176
Cdd:PRK09651  90 ALMPEGGAPSPEERESQLETlqLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVS-------VSSVKKYVAKATEH 162


                 ....
gi 492255764 177 YLLF 180
Cdd:PRK09651 163 CLLF 166
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 15-171 2.63e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 42.84  E-value: 2.63e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFA-GYLFITMRNLVFNRSRKNLNEPFY 93
Cdd:PRK12537  21 DRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSArGWIYSVTRHLALNVLRDTRREVVL 100

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 492255764  94 QLSVIEAVEESYDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLR 171
Cdd:PRK12537 101 DDDAEETAQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 22-175 2.65e-05

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 42.56  E-value: 2.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  22 LYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEeQNFAGYLFITMRNLVFNRSRKNLNEPFYQLSVIEAV 101
Cdd:PRK09644   6 IYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDN-QKVKPWLFKVAYHTFIDFVRKEKKVSFVGTDEIEAI 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 492255764 102 EESyDIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRKNIK 175
Cdd:PRK09644  85 QAE-STEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 14-160 3.03e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 42.92  E-value: 3.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  14 NDKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDE-EQNFAGYLFITMRNLVFNRSRKNLNEPf 92
Cdd:PRK12538  60 DDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHgRAKFSTWLYRVVSNRCIDLRRKPRTEN- 138

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 492255764  93 yqlsvIEAVEESYDIEEELDAANLRTHISAL----ISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVE 160
Cdd:PRK12538 139 -----VDAVPEVADGKPDAVSVIERNELSDLleaaMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVE 205
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 15-172 3.24e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 42.40  E-value: 3.24e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSYWAKVYNfTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLF-ITM-------RNLVFNRSRK 86
Cdd:PRK12518   9 DRQSFRQLYRRYQQKVRS-TLYQLCGRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYrITWnvatdarRQFAQRPSRI 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  87 NLNEPFYQLSVIEaveesydieeelDAANL-RTHISALIS----MLPPRQQEVFRLSRDEELSYREIAERLQISERTVEH 161
Cdd:PRK12518  88 QDDSLNDQPSRPS------------DTPDLmQLHYQDLVQqglqTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKS 155

                        170
                 ....*....|.
gi 492255764 162 HISDALKFLRK 172
Cdd:PRK12518 156 RLFYARRQLRK 166
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 15-175 3.63e-05

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 42.48  E-value: 3.63e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFI----TMRNLVFNRSRKnlnE 90
Cdd:PRK11923  18 DKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRiainTAKNHLVSRGRR---P 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  91 PFYQLSVIEAveESYDIEEEL------DAANLRTHISAL----ISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVE 160
Cdd:PRK11923  95 PDSDVSSEDA--EFYDGDHALkdiespERALLRDEIEGTvhrtIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVR 172

                        170
                 ....*....|....*
gi 492255764 161 HHISDALKFLRKNIK 175
Cdd:PRK11923 173 SRIFRAREAIDKALQ 187
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 127-168 7.07e-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: 39.05  E-value: 7.07e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 492255764 127 LPPRQQEVFRLSRdEELSYREIAERLQISERTVEHHISDALK 168
Cdd:cd06170    1 LTPREREVLRLLA-EGKTNKEIADILGISEKTVKTHLRNIMR 41
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 45-168 7.65e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 41.08  E-value: 7.65e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  45 EEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKNLNEPFYQL--SVIEAVEESYDIEEELDAANLRthISA 122
Cdd:PRK12525  37 EDIASETFLQVLALPDPASIREPRALLTTIARRLMYEGWRRQDLERAYLQSlaEAPEAVQPSPEEQWMVIETLLA--IDR 114

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 492255764 123 LISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALK 168
Cdd:PRK12525 115 LLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFK 160
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 43-175 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 492255764  43 DVEEIVQEVFIKIWEnreALDEEQ--NFAGYLFITMRNLVFNRSRKNlnepfyQLSVIEAVEESYD--------IEEELD 112
Cdd:PRK09647  54 DAEDLTQETFIRVFR---SLQNYQpgTFEGWLHRITTNLFLDMVRRR------ARIRMEALPEDYDrvpgdepnPEQIYH 124

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 492255764 113 AANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRKNIK 175
Cdd:PRK09647 125 DARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
127-168 1.13e-04

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 40.89  E-value: 1.13e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 492255764 127 LPPRQQEVFRLSRdEELSYREIAERLQISERTVEHHISDALK 168
Cdd:COG2771  128 LTPREREVLRLLA-EGLTLKEIARILGISERTVRTHLKRIYR 168
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 22-168 1.48e-04

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 40.60  E-value: 1.48e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  22 LYRSYWAKVYNFTRLYITSAVDVEEIVQEVFIKIWeNREALDEEQNFAGYLFITMRNLVFNRSRKNLNEPFY--QLSVIE 99
Cdd:PRK12523  15 LYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLL-GRPELPTPREPRAFLAAVAKGLMFDHFRRAALEQAYlaELALVP 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492255764 100 AVEESYDIEEELDAANLRThISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALK 168
Cdd:PRK12523  94 EAEQPSPEEQHLILEDLKA-IDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLR 161
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 26-178 1.77e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 40.24  E-value: 1.77e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  26 YWAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRK-----NLNEPFYQLSVIEA 100
Cdd:PRK12522  12 YKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYRKkkrwkDRILDLFHKEDGGE 91

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764 101 VEESYD--IEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRKNIKLYL 178
Cdd:PRK12522  92 IEFADDvnISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEGFV 171
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 108-172 2.60e-04

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 39.57  E-value: 2.60e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492255764 108 EEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRK 172
Cdd:PRK09047  88 ADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAK 152
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 116-178 4.27e-04

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 39.83  E-value: 4.27e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764 116 LRTHISALISMLPPRQQEV----FRLSRDEELSYREIAERLQISE---RTVEHHISDALKFLRKNIKLYL 178
Cdd:PRK05949 256 LRQDLNNLLAELTPQQREVltlrFGLEDGKELSLAKVGERLNLSRervRQLEHQALAHLRRRRANVKEYL 325
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 45-176 5.12e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 39.18  E-value: 5.12e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  45 EEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKN---LNEPFYQLSVIEAVEES-YDieeELDAANLRthi 120
Cdd:PRK12516  38 DDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYSQMRKRgreVQDTDGMFTEQLAVHPSqYG---TLDLQDFR--- 111

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 492255764 121 sALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRKNIKL 176
Cdd:PRK12516 112 -AALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 43-175 6.22e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 38.88  E-value: 6.22e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  43 DVEEIVQEVFIKIWENREALDEEQNFAGYLFITMR----NLVFNRSRKN-LNEPFyqlsvieavEESYDI--EEELDAAN 115
Cdd:PRK12536  48 EVEDLVQEILLAVHNARHTYRADQPLTAWVHAIARyklmDFLRSRARREaLHDPL---------DDESELfaTSDDEAAE 118

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 492255764 116 LRTHISALISMLPPRQqevfRLS----RDEELSYREIAERLQISERTVEHHISDALKFLRKNIK 175
Cdd:PRK12536 119 ARRDLGKLLEQLPDRQ----RLPivhvKLEGLSVAETAQLTGLSESAVKVGIHRGLKALAAKIR 178
GerE pfam00196
Bacterial regulatory proteins, luxR family;
127-168 7.03e-04

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 36.41  E-value: 7.03e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 492255764  127 LPPRQQEVFRLSRdEELSYREIAERLQISERTVEHHISDALK 168
Cdd:pfam00196   3 LSPREREVLRWLA-AGKSNKEIADELGISEKTVKVHRSNIMR 43
PRK15369 PRK15369
two component system response regulator;
124-172 8.80e-04

two component system response regulator;


Pssm-ID: 185267 [Multi-domain]  Cd Length: 211  Bit Score: 38.52  E-value: 8.80e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 492255764 124 ISMLPPRQQEVFRLSrDEELSYREIAERLQISERTVEHHisdALKFLRK 172
Cdd:PRK15369 147 PPLLTPRERQILKLI-TEGYTNRDIAEQLSISIKTVETH---RLNMMRK 191
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 45-175 1.07e-03

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 38.19  E-value: 1.07e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  45 EEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLV--FNRSRKNLNEPFYQLSVIEAVEESYDIEEELDAANLRTHISA 122
Cdd:PRK09415  44 EDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCkdYLKSWHNKKVIVTEDIFTYMESQKESVEEEVIQNAEDERLAS 123

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 492255764 123 LISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLRKNIK 175
Cdd:PRK09415 124 AVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLE 176
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
143-163 1.97e-03

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 37.38  E-value: 1.97e-03
                         10        20
                 ....*....|....*....|.
gi 492255764 143 LSYREIAERLQISERTVEHHI 163
Cdd:COG2909  138 LSNKEIAERLFISVNTVKTHL 158
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 45-150 2.06e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 37.51  E-value: 2.06e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  45 EEIVQEVFIKIWENREALDEEQNFAGYLFITMRNLVFNRSRKNLNEpfyqLSVIEAVE-ESYDIEEELDAANLRTHISAL 123
Cdd:PRK12546  35 DDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRNTFYSDRRKHKRE----VPDPEGVHaASLAVKPAHDGRLAMSDFRAA 110

                         90       100
                 ....*....|....*....|....*..
gi 492255764 124 ISMLPPRQQEVFRLSRDEELSYREIAE 150
Cdd:PRK12546 111 FAQLPDEQREALILVGASGFSYEEAAE 137
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 15-166 2.83e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 36.84  E-value: 2.83e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  15 DKAAFAFLYRSY--WAKVYNFTRLYITSAVDVEEIVQEVFIKIWENREALDE---EQNFAGYLFITMRNLVFNRSRKNLN 89
Cdd:PRK12529  11 DRDKVATLYRENhaWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQReaiRQPRAYLARIANCVLVSWRRRQSLE 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 492255764  90 EPFyqLSVIEAVEESYDIEEELDAANLRT--HISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDA 166
Cdd:PRK12529  91 LAW--LEALATLPEPLHPSPEQQSVILETlhEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQA 167
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 106-171 3.49e-03

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 37.06  E-value: 3.49e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492255764 106 DIEEELDAANLRTHISALISMLPPRQQEVFRLSRDEELSYREIAERLQISERTVEHHISDALKFLR 171
Cdd:PRK07122 195 DVDAGLDQIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTLARLR 260
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 127-160 5.50e-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: 35.86  E-value: 5.50e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 492255764  127 LPPRQQEVFRLSRDEELSYREIAERLQISERTVE 160
Cdd:pfam07638 136 LSPRQARLVELRFFAGLSNDEIAERLGVSERTVE 169
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 40-156 7.37e-03

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 36.05  E-value: 7.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492255764  40 SAVDVEEIVQEVFIKiWENREAlDEEQNFAGYLFITMRNLVFN-----RSRKN------LNEPfyqlsVIEavEESYDIE 108
Cdd:PRK09636  27 SVADAEDIVQEAWLR-WNNADR-AQIRDPRAWLTRVVTRLCLDrlrsaRHRREtyvgpwLPEP-----VVE--ELDDPLE 97

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 492255764 109 EELDAANLRThiSALISM--LPPRQQEVFRLSRDEELSYREIAERLQISE 156
Cdd:PRK09636  98 AVVAAEDLSL--ALMLALerLSPLERAAFLLHDVFGVPFDEIASTLGRSP 145
 
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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