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Conserved domains on  [gi|1547036127|gb|AZS28656|]
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RNA polymerase sigma-70 factor [Butyricimonas faecalis]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

RNA polymerase sigma factor plays a role in bacterial signal transduction and is regulated by anti-sigma factors. May belong to the ECF-type subfamily. Generally, sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released.

CATH:  1.10.1740.10
Gene Ontology:  GO:0016987|GO:0006352|GO:0003677
PubMed:  28575802
SCOP:  4003741

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-176 1.90e-44

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: 145.52  E-value: 1.90e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   1 MESDYILV-GLKHRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGC 79
Cdd:COG1595     1 MSSDEELLeRLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  80 LNYLKSLQIEDRNNRKYVEAYIESQNV--DMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTV 157
Cdd:COG1595    81 IDHLRKRRRRRELLDELAEELPDEAADpeEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTV 160

                         170
                  ....*....|....*....
gi 1547036127 158 KVQLHRGMERLRQAFSTYD 176
Cdd:COG1595   161 KSRLSRARKKLREALEEEG 179
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-176 1.90e-44

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: 145.52  E-value: 1.90e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   1 MESDYILV-GLKHRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGC 79
Cdd:COG1595     1 MSSDEELLeRLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  80 LNYLKSLQIEDRNNRKYVEAYIESQNV--DMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTV 157
Cdd:COG1595    81 IDHLRKRRRRRELLDELAEELPDEAADpeEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTV 160

                         170
                  ....*....|....*....
gi 1547036127 158 KVQLHRGMERLRQAFSTYD 176
Cdd:COG1595   161 KSRLSRARKKLREALEEEG 179
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 17-172 2.47e-43

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: 141.93  E-value: 2.47e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  17 ALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKSLQIEdrnnRKY 96
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVE----EKY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  97 VEAYIESQNVDM--------VEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:TIGR02985  78 QEELAEIEERELseadpeeeLEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFL 157


                  ....
gi 1547036127 169 RQAF 172
Cdd:TIGR02985 158 RKEL 161
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 12-172 3.99e-29

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 106.21  E-value: 3.99e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  12 HRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKslqieDR 91
Cdd:PRK11924    9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLR-----RR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  92 NNRKYVE---------AYIESQNVDMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLH 162
Cdd:PRK11924   84 RREKAVLsddalepefAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLR 163

                         170
                  ....*....|
gi 1547036127 163 RGMERLRQAF 172
Cdd:PRK11924  164 RARQLLRECL 173
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 115-168 4.24e-11

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 55.54  E-value: 4.24e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1547036127 115 LAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 115-169 3.53e-10

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: 53.26  E-value: 3.53e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1547036127 115 LAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLR 169
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 122-168 3.80e-05

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 39.82  E-value: 3.80e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1547036127  122 LDELPDRCREVCLLrFVEGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:smart00421   1 LASLTPREREVLRL-LAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-176 1.90e-44

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: 145.52  E-value: 1.90e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   1 MESDYILV-GLKHRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGC 79
Cdd:COG1595     1 MSSDEELLeRLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  80 LNYLKSLQIEDRNNRKYVEAYIESQNV--DMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTV 157
Cdd:COG1595    81 IDHLRKRRRRRELLDELAEELPDEAADpeEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTV 160

                         170
                  ....*....|....*....
gi 1547036127 158 KVQLHRGMERLRQAFSTYD 176
Cdd:COG1595   161 KSRLSRARKKLREALEEEG 179
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 17-172 2.47e-43

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: 141.93  E-value: 2.47e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  17 ALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKSLQIEdrnnRKY 96
Cdd:TIGR02985   2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVE----EKY 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  97 VEAYIESQNVDM--------VEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:TIGR02985  78 QEELAEIEERELseadpeeeLEAKELEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFL 157


                  ....
gi 1547036127 169 RQAF 172
Cdd:TIGR02985 158 RKEL 161
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 17-172 1.92e-32

RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the sigma-70 type sigma factors including the ECF subfamily. A number of sigma factors have names with a different number than 70 (i.e. sigma-38), but in fact, all except for the Sigma-54 family (TIGR02395) are included within this family. Several Pfam models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 113.98  E-value: 1.92e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  17 ALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKSLQIEDRNNRKY 96
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1547036127  97 VEAYIESQNVDM-VEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQAF 172
Cdd:TIGR02937  82 EELLDSDPSPEEeLEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 12-172 3.99e-29

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 106.21  E-value: 3.99e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  12 HRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKslqieDR 91
Cdd:PRK11924    9 TGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLR-----RR 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  92 NNRKYVE---------AYIESQNVDMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLH 162
Cdd:PRK11924   84 RREKAVLsddalepefAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLR 163

                         170
                  ....*....|
gi 1547036127 163 RGMERLRQAF 172
Cdd:PRK11924  164 RARQLLRECL 173
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 21-170 1.65e-22

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 88.85  E-value: 1.65e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  21 LFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENaeRLELKSSIQHYLFTSVRNGCLNYLKSlqieDRNNRKYVEAY 100
Cdd:PRK09639    8 LFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRS--DFKGIENEKGWLIKSARNVAYNYLRS----EKRRRARILGE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1547036127 101 IESQNVDMVEDEDLLA-------KIRQVLDELPDRCREVCLLRFvEGYKYNEIAVALKMNENTVKVQLHRGMERLRQ 170
Cdd:PRK09639   82 FQWQEVDNEPSPEEIWirkeeitKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKKFRK 157
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 12-170 4.36e-19

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 80.24  E-value: 4.36e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  12 HRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYL----KSLQ 87
Cdd:PRK09652    6 RGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLrkqgRRPP 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  88 IEDRNNRKYVEAYIESQNVDMVEDEDLLAK------IRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQL 161
Cdd:PRK09652   86 ASDVDAEEAEDFDLADALRDISTPENELLSaeleqrVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRI 165


                  ....*....
gi 1547036127 162 HRGMERLRQ 170
Cdd:PRK09652  166 FRAREALRA 174
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 15-172 1.36e-17

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 76.32  E-value: 1.36e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  15 EVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKSLQIEDRNNR 94
Cdd:PRK09415   15 EDLIDEIMNEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSWHNKKVIVT 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  95 KYVEAYIESQN-------VDMVEDEDLLAKIRQvldeLPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMER 167
Cdd:PRK09415   95 EDIFTYMESQKesveeevIQNAEDERLASAVMS----LPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKEL 170


                  ....*
gi 1547036127 168 LRQAF 172
Cdd:PRK09415  171 LKKGL 175
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 2-171 1.04e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 75.00  E-value: 1.04e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   2 ESDYILVGL-KHRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCL 80
Cdd:PRK11922   15 ASDRELVARvLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEAL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  81 NYLKS---LQIEDRNNRKYVEAYIESQNVDMVED--EDLLAK--IRQVL----DELPDRCREVCLLRFVEGYKYNEIAVA 149
Cdd:PRK11922   95 GRLRRrrrLVNLAEMVMASTIAGGERTPLADPAEdpERAAARreIRALLeraiDALPDAFRAVFVLRVVEELSVEETAQA 174

                         170       180
                  ....*....|....*....|..
gi 1547036127 150 LKMNENTVKVQLHRGMERLRQA 171
Cdd:PRK11922  175 LGLPEETVKTRLHRARRLLRES 196
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 6-170 1.29e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 73.94  E-value: 1.29e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   6 ILVGLKHRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKS 85
Cdd:PRK12519   19 LFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSSYDPKRGSLSSYLLTLTRSRAIDRLRS 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  86 lqieDRNNRKYVEAYIESQNVDMVED--------EDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTV 157
Cdd:PRK12519   99 ----RRSRQRLLERWQQELLGEASEDtpleqaslAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTV 174

                         170
                  ....*....|...
gi 1547036127 158 KVQLHRGMERLRQ 170
Cdd:PRK12519  175 KARARQGLLKLRE 187
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 14-169 7.26e-14

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 66.20  E-value: 7.26e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  14 DEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKslqiedrnN 93
Cdd:PRK09638   16 DDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLR--------K 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  94 RKYVEAYIESQNVDMVEDEDLLAKIRQV--------LDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGM 165
Cdd:PRK09638   88 QKREKLRLQRAKEETLRKEKWEAAIKGAewsemldaLSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGI 167


                  ....
gi 1547036127 166 ERLR 169
Cdd:PRK09638  168 KQLR 171
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 10-172 9.81e-14

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 66.26  E-value: 9.81e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  10 LKHRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLK----- 84
Cdd:PRK09641   12 VKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLRkrkpd 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  85 -SLQIEDRNNRKY-VEAYIESQNV---DMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKV 159
Cdd:PRK09641   92 yYLDAEVAGTEGLtMYSQLAADDAlpeEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKT 171

                         170
                  ....*....|...
gi 1547036127 160 QLHRGMERLRQAF 172
Cdd:PRK09641  172 RIHRGREALRKQL 184
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 10-170 1.11e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 65.91  E-value: 1.11e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  10 LKHRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKSLQIE 89
Cdd:PRK12543    1 MLSGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKRWRR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  90 DRNNRKyVEAYIESQNVDMveDEDLLAK-----IRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRG 164
Cdd:PRK12543   81 FRIFEK-AEEQRKPVSIDF--SEDVLSKesnqeLIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAA 157


                  ....*.
gi 1547036127 165 MERLRQ 170
Cdd:PRK12543  158 LKKLRQ 163
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
14-175 1.14e-12

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 63.17  E-value: 1.14e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  14 DEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELK-SSIQHYLFTSVRNgclnylksLQIEDRN 92
Cdd:PRK09645    7 EAALMRALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTgRSARAWLFTVARN--------LVIDERR 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  93 NRKY--------VEAYIESQNVDMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRG 164
Cdd:PRK09645   79 SARArpveggddVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYA 158

                         170
                  ....*....|.
gi 1547036127 165 MERLRQAFSTY 175
Cdd:PRK09645  159 LRALRLALQER 169
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 29-170 1.23e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 63.06  E-value: 1.23e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  29 LYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNylkslQIEDRNNrkyveayiESQNVDM 108
Cdd:PRK12516   23 LRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNEFYS-----QMRKRGR--------EVQDTDG 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1547036127 109 VEDEDL-----------LAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQ 170
Cdd:PRK12516   90 MFTEQLavhpsqygtldLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQE 162
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 10-174 1.38e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 63.41  E-value: 1.38e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  10 LKHRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLE-LKSSIQHYLFTSVRNGCLNYLKslqi 88
Cdd:PRK12531   21 VKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDgQKSALSTWIYTIIRNLCFDLLR---- 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  89 edrnNRKYVEAYIESQNV--------DMVE----DEDLLA-KIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNEN 155
Cdd:PRK12531   97 ----KQKGKDLHIHADDIwpsdyyppDLVDhyspEQDMLKeQVMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLG 172

                         170
                  ....*....|....*....
gi 1547036127 156 TVKVQLHRGMERLRQAFST 174
Cdd:PRK12531  173 TVKSRLRLAVEKLRHSMDA 191
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 14-170 4.69e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 61.72  E-value: 4.69e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  14 DEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLE-LKSSIQHYLFTSVRNGCLNYLKSLQIEDRN 92
Cdd:PRK12537   21 DRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDpARGSARGWIYSVTRHLALNVLRDTRREVVL 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  93 NRKYVEAYieSQNVDMVEDEDL---LAKIRQVLDELpDRCREVCLLR-FVEGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:PRK12537  101 DDDAEETA--QTLHEIIDDFDLwanSGKIHRCLEQL-EPARRNCILHaYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKAL 177


                  ..
gi 1547036127 169 RQ 170
Cdd:PRK12537  178 RE 179
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 32-168 1.89e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 59.85  E-value: 1.89e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  32 FAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNgclnylkSLQIEDRNNRKYVE----AYIESQNVD 107
Cdd:PRK12546   23 FAISLTRNVAVADDLVQDTIVKAWTNFDKFQEGTNLRAWLFTILRN-------TFYSDRRKHKREVPdpegVHAASLAVK 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1547036127 108 MVEDEDL-LAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:PRK12546   96 PAHDGRLaMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARL 157
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 115-168 4.24e-11

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 55.54  E-value: 4.24e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1547036127 115 LAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 2-161 1.66e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 57.43  E-value: 1.66e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   2 ESDYILVG-LKHRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCL 80
Cdd:PRK12515    7 TTDEMLLArIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLLSIARFKAL 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  81 NYLKSLQIEDrnnrkyveayIESQNVDMVED-----------EDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVA 149
Cdd:PRK12515   87 SALRRRKHEE----------IDDEAAAAIEDgadtpevalqkSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEI 156

                         170
                  ....*....|..
gi 1547036127 150 LKMNENTVKVQL 161
Cdd:PRK12515  157 VGIPESTVKTRM 168
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 115-169 3.53e-10

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: 53.26  E-value: 3.53e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1547036127 115 LAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLR 169
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 39-175 5.95e-10

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 55.36  E-value: 5.95e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  39 DSDRAHDIVQDVFLKIWEN-AERLE----------LKSSIQ-HYLFTSVRNGCLNYLKSLQI-EDRNNRKYVEAYIESQN 105
Cdd:PRK09047    3 DDDAALDIVQDAMIKLAEKyGDRPAaewpplfqriLQNRIHdWFRRQKVRNTWVSLFSSFSDdDDDDDFDPLETLDSADE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1547036127 106 -----VDMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQAFSTY 175
Cdd:PRK09047   83 gaespADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEAK 157
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 14-172 6.94e-10

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


Pssm-ID: 213752 [Multi-domain]  Cd Length: 169  Bit Score: 55.49  E-value: 6.94e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  14 DEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKSLQ--IEDR 91
Cdd:TIGR02954  14 NKPAFESLIKKHKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPKYFNTWLTRILINECIDLLKKKKkvIPFD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  92 NNRKYVEayiESQNVDMVEDEDLLAkirqVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQA 171
Cdd:TIGR02954  94 PNTSIEK---GECETHADSRLDLYK----AIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166


                  .
gi 1547036127 172 F 172
Cdd:TIGR02954 167 L 167
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 8-173 7.48e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 55.60  E-value: 7.48e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   8 VGLKHRDevALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELK-SSIQHYLFTSVRNGCLNYLKSl 86
Cdd:PRK12514   13 VSLGDRD--AFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSgLSPMTWLITIARNHAIDRLRA- 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  87 qiedrnnRKYVEAYIESQNvDMVEDE----------DLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENT 156
Cdd:PRK12514   90 -------RKAVAVDIDEAH-DLADPSpgpeaeviagDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNT 161

                         170
                  ....*....|....*..
gi 1547036127 157 VKVQLHRGMERLRQAFS 173
Cdd:PRK12514  162 MRTWLRRSLLKLRECLS 178
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 18-172 1.00e-09

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 54.99  E-value: 1.00e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  18 LSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNY----LKSLQIEDrnn 93
Cdd:PRK09637    3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFyrkkNRSEELPD--- 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1547036127  94 rkyVEAYIESQNVDMVEDEdLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQAF 172
Cdd:PRK09637   80 ---DLLFEDEEREENAKKE-LAPCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 14-168 1.09e-09

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 55.10  E-value: 1.09e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  14 DEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLnylkslqieDRNN 93
Cdd:PRK09643   25 DRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGDAAVSSWLHRIVVNACL---------DRLR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  94 RKYV-------EAYIESQNV-DMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGM 165
Cdd:PRK09643   96 RAKArptvpldDVYPVAQLErDPTARVETALAVQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARGR 175


                  ...
gi 1547036127 166 ERL 168
Cdd:PRK09643  176 ARL 178
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 39-169 1.28e-09

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


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 54.70  E-value: 1.28e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  39 DSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKSLQIEDRNNRKYVEAYIEsqnvDMVEDEDLLAKI 118
Cdd:TIGR02983  29 DPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLELPTRELPDAAAP----DPAPDVALRAAL 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1547036127 119 RQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLR 169
Cdd:TIGR02983 105 ARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLR 155
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 3-170 2.04e-09

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 54.53  E-value: 2.04e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   3 SDYILVGLKHR-DEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLE-LKSSIQHYLFTSVRNGCL 80
Cdd:PRK13919    9 SDEALLALVARgEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDpRRGSARAWLLALAHHAAV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  81 NYLKSLQIEDRN---NRKYVEAY-IESQNVDMVEDEDLLaKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENT 156
Cdd:PRK13919   89 DHVRRRAARPQPlepDEREPEAFdLPGPGLDEEGHLDRT-RLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGT 167

                         170
                  ....*....|....
gi 1547036127 157 VKVQLHRGMERLRQ 170
Cdd:PRK13919  168 LKTRARRALSRLKE 181
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 41-168 2.15e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 54.32  E-value: 2.15e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  41 DRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLK------SLQIEDrnnrkYVEAYIESQNVDMVEDEDl 114
Cdd:PRK12512   51 DQAEDIVQEILLAVHLKRHTWDPGAPFAPWLFAIARNKLIDALRrrgrrvFVDIDD-----FAETLPAEPATETLPAGD- 124

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1547036127 115 lakIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:PRK12512  125 ---VGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVALHRGLAAL 175
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
1-170 2.65e-09

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 54.29  E-value: 2.65e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   1 MESDYILVGLKHRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLE-LKSSIQHYLFTSVRNGC 79
Cdd:PRK09646   15 PDLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDpARGSALAWLLTLAHRRA 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  80 LNYLKSLQIEDRNNRKYVEAYIE---SQNVDMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENT 156
Cdd:PRK09646   95 VDRVRSEQAASQREVRYGARNVDpafDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGT 174

                         170
                  ....*....|....
gi 1547036127 157 VKVQLHRGMERLRQ 170
Cdd:PRK09646  175 VKTRMRDGLIRLRD 188
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 3-173 3.20e-09

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 53.79  E-value: 3.20e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   3 SDYILVGLKH----RDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNG 78
Cdd:PRK09640    9 NDEELVARVHvelfHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNE 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  79 CLNylkslQIEDRNNRKYVEAYIESQNVDMVEDE-----DLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMN 153
Cdd:PRK09640   89 CIT-----QYRKERRKRRLMDALSLDPLEEASEEkapkpEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMG 163

                         170       180
                  ....*....|....*....|
gi 1547036127 154 ENTVKVQLHRGMERLRQAFS 173
Cdd:PRK09640  164 LSATKMRYKRALDKLREKFA 183
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 29-175 1.97e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 51.61  E-value: 1.97e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  29 LYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKSlqiEDRNNRKYVEaYIESQNVDM 108
Cdd:PRK12513   39 LYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPRARFRTWLYQIARNLLIDHWRR---HGARQAPSLD-ADEQLHALA 114

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1547036127 109 VEDED---------LLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQAFSTY 175
Cdd:PRK12513  115 DDGAApeqqlslfrDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAEE 190
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 29-170 2.15e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 51.42  E-value: 2.15e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  29 LYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYL--KSLQIEDRNNrkyveAYIESQNV 106
Cdd:PRK12547   19 LRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEFYSQMrkRGREVQDSDG-----VFTARVAV 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1547036127 107 DMVEDEDL-LAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQ 170
Cdd:PRK12547   94 HPAQYGSLdLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 38-170 2.37e-08

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: 51.17  E-value: 2.37e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  38 YDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKSLQIEDRNNRKYVEAYIESQnVDMVEDEDLLAK 117
Cdd:TIGR02989  23 ADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRDRLVFDDDLLEALAAE-AEPTEAERLSDD 101

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1547036127 118 ---IRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQ 170
Cdd:TIGR02989 102 rqaLEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLRE 157
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 13-171 6.64e-08

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 50.04  E-value: 6.64e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  13 RDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERL-ELKSSIQHYLFTSVRNGCLNYLkslqiedr 91
Cdd:PRK05602   17 GDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWrPGEARFDTWLHRVVLNLCYDRL-------- 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  92 nnRKYVEAYIESQN---------VDMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLH 162
Cdd:PRK05602   89 --RRRREVPVEDAPdvpdpapgpDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLA 166


                  ....*....
gi 1547036127 163 RGMERLRQA 171
Cdd:PRK05602  167 RGRRALRAQ 175
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 29-168 1.04e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 49.58  E-value: 1.04e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  29 LYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNgclnylkSLQIEDRNNRKYVE----AYIESQ 104
Cdd:PRK12540   18 LRAFAISLSGNGDRADDLVQETLLRALANIDSFQPGSNLPAWLFTILRN-------LFRSDYRKRRREVEdadgSYAKTL 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1547036127 105 NVDMVEDEDL-LAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:PRK12540   91 KSQPGQNAHLeFEEFRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKL 155
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 2-170 1.96e-07

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 48.78  E-value: 1.96e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   2 ESDYIlVGLKHRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDI---VQDVFLKIWENAERL-ELKSSIQHYLFTSVRN 77
Cdd:PRK06811    5 EDNFI-KELKKKNEKALEFIVDTYGNLVKKIVHKVLGTVNYSQLIeecVNDIFLSIWNNIDKFdEEKGSFKKWIAAISKY 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  78 GCLNYLKSL----QIEDRNNrkYVEAYIESQNVDMVEDEDLlAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMN 153
Cdd:PRK06811   84 KAIDYKRKLtknnEIDSIDE--FILISEESIENEIILKENK-EEILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLT 160

                         170
                  ....*....|....*..
gi 1547036127 154 ENTVKVQLHRGMERLRQ 170
Cdd:PRK06811  161 RSAIDNRLSRGRKKLQK 177
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 25-171 2.58e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 48.53  E-value: 2.58e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  25 YYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRngclnylkslqiedRNNRKYVEAY---- 100
Cdd:PRK12517   32 LHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEKAAKAWLITILR--------------RENARRFERKqfdl 97

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1547036127 101 --IES---QNVDMVEDEDLLAK--IRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQA 171
Cdd:PRK12517   98 vdIEDdsiEDDASHSSEEEMEQewLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEA 175
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 32-170 2.61e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 48.63  E-value: 2.61e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  32 FAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKSLQIEDRnnRKYVEAYIESQNVDMVED 111
Cdd:PRK12511   20 YARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSILHNAFIDELRRRRVEAR--RADELAVLADASLPAAQE 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127 112 EDL-LAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQ 170
Cdd:PRK12511   98 HAVrLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 18-170 2.72e-07

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 48.34  E-value: 2.72e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  18 LSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLElKSSIQHYLFTSVRNGCLNYLKSLQIEDRNNRKYV 97
Cdd:PRK09644    3 IEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYD-NQKVKPWLFKVAYHTFIDFVRKEKKVSFVGTDEI 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1547036127  98 EAYIESQNVDMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQ 170
Cdd:PRK09644   82 EAIQAESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 121-170 3.64e-07

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: 45.11  E-value: 3.64e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1547036127 121 VLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQ 170
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 6-170 6.14e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 47.87  E-value: 6.14e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   6 ILVGLKhRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERL-ELKSSIQHYLFTSVRNGCLNYLK 84
Cdd:PRK12526   29 ILVAIS-RDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYnGDKGAATTWVYTVMRNAAFDMLR 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  85 SLQIEDRNNRK-----YVEAYIESQNVDMVEDEDLLAK-IRQVLDELPDRCREVcllrfVEGYKYNE-----IAVALKMN 153
Cdd:PRK12526  108 KIKAKKEQNLGddiwpIEQALAESQSESEEFSDHLMDKqILSYIEKLPEAQQTV-----VKGVYFQElsqeqLAQQLNVP 182

                         170
                  ....*....|....*..
gi 1547036127 154 ENTVKVQLHRGMERLRQ 170
Cdd:PRK12526  183 LGTVKSRLRLALAKLKV 199
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 21-87 9.05e-07

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


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 44.50  E-value: 9.05e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1547036127  21 LFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERL--ELKSSIQHYLFTSVRNGCLNYLKSLQ 87
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFdpERGVSFSTWLYTIIRNAIIDYLRKQR 69
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 15-170 9.41e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 46.79  E-value: 9.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  15 EVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSvrngCLNYLKSLQIEDRNNR 94
Cdd:PRK12522    2 EEKVEELIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTI----CVRTFYDFYRKKKRWK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  95 KYVEAYIESQNVDMVE-------DEDLLAK-----IRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLH 162
Cdd:PRK12522   78 DRILDLFHKEDGGEIEfaddvniSEEFIQKveaemIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLN 157


                  ....*...
gi 1547036127 163 RGMERLRQ 170
Cdd:PRK12522  158 YAKKQMRE 165
PRK09648 PRK09648
RNA polymerase sigma factor ShbA;
116-171 1.94e-06

RNA polymerase sigma factor ShbA;


Pssm-ID: 236607 [Multi-domain]  Cd Length: 189  Bit Score: 46.12  E-value: 1.94e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1547036127 116 AKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQA 171
Cdd:PRK09648  131 NRMRELLDTLPEKQREILILRVVVGLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 43-150 7.51e-06

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 44.91  E-value: 7.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  43 AHDIVQDVFLKiWENAERLELKsSIQHYLFTSVRNGCLNYLKSLqiedRNNRkyvEAYI------------ESQNVDMVE 110
Cdd:PRK09636   31 AEDIVQEAWLR-WNNADRAQIR-DPRAWLTRVVTRLCLDRLRSA----RHRR---ETYVgpwlpepvveelDDPLEAVVA 101

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1547036127 111 DEDL-LAKIRqVLDELPDRCREVCLLRFVEGYKYNEIAVAL 150
Cdd:PRK09636  102 AEDLsLALML-ALERLSPLERAAFLLHDVFGVPFDEIASTL 141
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 25-170 7.91e-06

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 44.00  E-value: 7.91e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  25 YYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAErlelKSSIQH---YLFTSV--------RNGCLNYLKSLQIEDRNN 93
Cdd:PRK12527    4 YYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSS----SAQIEHpraFLYRTAlnlvvdrhRRHRVRQAEPLEVLDEEE 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  94 RKYVEayieSQNVDMVEDEDLlAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGME----RLR 169
Cdd:PRK12527   80 RLHSP----SPQTRLDLGQRL-ALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKhcrvRMR 154


                  .
gi 1547036127 170 Q 170
Cdd:PRK12527  155 Q 155
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 2-170 9.08e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 44.46  E-value: 9.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   2 ESDYILVGLKHRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLEL-KSSIQHYLFTSVRNGCL 80
Cdd:PRK12538   49 EDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHgRAKFSTWLYRVVSNRCI 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  81 NYLKSLQIEDrnnrkyVEAYIESQN-----VDMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNEN 155
Cdd:PRK12538  129 DLRRKPRTEN------VDAVPEVADgkpdaVSVIERNELSDLLEAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVA 202

                         170
                  ....*....|....*
gi 1547036127 156 TVKVQLHRGMERLRQ 170
Cdd:PRK12538  203 AVESLLKRGRQQLRD 217
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 2-173 1.06e-05

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 44.02  E-value: 1.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   2 ESDYILVGLKHR-DEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCL 80
Cdd:PRK11923    5 EEDQQLVERVQRgDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAK 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  81 NYLKS---------LQIEDrnnrkyVEAY--------IESQNVDMVEDEdLLAKIRQVLDELPDRCREVCLLRFVEGYKY 143
Cdd:PRK11923   85 NHLVSrgrrppdsdVSSED------AEFYdgdhalkdIESPERALLRDE-IEGTVHRTIQQLPEDLRTALTLREFDGLSY 157

                         170       180       190
                  ....*....|....*....|....*....|
gi 1547036127 144 NEIAVALKMNENTVKVQLHRGMERLRQAFS 173
Cdd:PRK11923  158 EDIASVMQCPVGTVRSRIFRAREAIDKALQ 187
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 110-171 1.50e-05

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 43.62  E-value: 1.50e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1547036127 110 EDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQA 171
Cdd:PRK09647  124 HDARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAA 185
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 2-169 3.09e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 42.73  E-value: 3.09e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127   2 ESDYILVGLKHRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLE-LKSSIQHYLFTSVRNGCL 80
Cdd:PRK12534   11 ETGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDpSRARGLTWLAMIARNKAI 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  81 NYLKSLQIEDRNNRKYVEAYIESQNVDMVEDEDLLAKIRQV---LDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTV 157
Cdd:PRK12534   91 DHLRANAPQRRNVALDDAGELRAADASPLERTERASTRRRIdhcLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTV 170

                         170
                  ....*....|..
gi 1547036127 158 KVQLHRGMERLR 169
Cdd:PRK12534  171 KSWIRRGLAKLK 182
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 122-168 3.80e-05

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 39.82  E-value: 3.80e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1547036127  122 LDELPDRCREVCLLrFVEGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:smart00421   1 LASLTPREREVLRL-LAEGLTNKEIAERLGISEKTVKTHLSNIMRKL 46
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
41-168 5.34e-05

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 42.02  E-value: 5.34e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  41 DRAHDIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLkslqiedRNNRKYVeAYIESQNVD-MVEDEDLLA--- 116
Cdd:PRK12539   50 EEAEDLVQEALMAIHTRRHTYDPEQPLTPWVYAIARYKLIDHL-------RRTRASL-ADVPIDDADeLVAHDDHAAves 121

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1547036127 117 --KIRQVLDELPDRCRevCLLRFV--EGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:PRK12539  122 tlDLGRLLARLPEKMR--LAIQAVklEGLSVAEAATRSGMSESAVKVSVHRGLKAL 175
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 12-169 8.55e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 41.58  E-value: 8.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  12 HRDEVALSTLFDMYYEKLYLFAEKYIYDSDRAHDIVQDVFLKIWENAERLELKSS--IQHYLFTSVRNGCLNYLKSLQIE 89
Cdd:PRK12542    5 NNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTqeLKRYILRVAKNKAIDSYRKNKRH 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  90 DRNNRKYVEAYIESQNVDMVEDEDLL---AKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGME 166
Cdd:PRK12542   85 ETFLEEYERESIEAVDENIEEWEKRKmseVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARK 164


                  ...
gi 1547036127 167 RLR 169
Cdd:PRK12542  165 RVQ 167
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 45-172 8.98e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 41.24  E-value: 8.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  45 DIVQDVFLKIWENAERLELKSSIQHYLFTSVRNGCLNYLKSLQiedrNNRKYVEAYIESQNVDMVEDEDLLAK------I 118
Cdd:PRK12518   39 DLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQFA----QRPSRIQDDSLNDQPSRPSDTPDLMQlhyqdlV 114

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1547036127 119 RQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQAF 172
Cdd:PRK12518  115 QQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 39-170 9.44e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 41.08  E-value: 9.44e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  39 DSDRAHDIVQDVFLKIWENAERLElKSSIQHYLFTSVRNGCLNYLkslqiedRNNRKYVEAYIES---QNVDMVEDEDLL 115
Cdd:PRK12541   28 DSHFAEDLMQETFYRMLVHIDYYK-GEEIRPWLFTIAYNAFIDWY-------RKEKKYKTTTIEEfhlPNVPSTEHEYFI 99

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1547036127 116 -AKIRQVLDE---LPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQ 170
Cdd:PRK12541  100 kHEIASWLDSlssLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 42-162 2.31e-04

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 40.05  E-value: 2.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  42 RAHDIVQDVFLKIWENAERLELKSSIQhYLFTSVRNGCLNYLKSLQIEdrnnRKYVEAYIESQNVDMVED--------ED 113
Cdd:PRK07037   24 RAEDVVQDAFVKLVEAPNQDAVKQPVA-YLFRIVRNLAIDHYRRQALE----NKYHGDEEDGLDVPSPEAspeaalinRD 98

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1547036127 114 LLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLH 162
Cdd:PRK07037   99 TLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIR 147
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 107-173 2.94e-04

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: 40.19  E-value: 2.94e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1547036127 107 DMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKvQLH-RGMERLRQAFS 173
Cdd:COG1191   169 EELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESRVS-RLHkKALARLREYLK 235
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 33-173 3.00e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 39.87  E-value: 3.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  33 AEKYIYDSDRAHDIVQDVFLKIWENAERLEL-KSSIQHYLFTSVRNGCLNYLKslqiedRNNRKYV-------------- 97
Cdd:PRK12524   43 ATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQgEARVSTWLYRVVCNLCTDRLR------RRRRASVdlddapepadaapg 116

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1547036127  98 --EAYIESQNVDMVEDedllakirqVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQAFS 173
Cdd:PRK12524  117 aeEALIEGDRMRALDA---------ALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTARGKRALAALLA 185
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 130-168 5.60e-04

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: 36.74  E-value: 5.60e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1547036127 130 REVCLLRFV-EGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:cd06170     4 REREVLRLLaEGKTNKEIADILGISEKTVKTHLRNIMRKL 43
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 102-168 5.82e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 38.88  E-value: 5.82e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1547036127 102 ESQNVDMVEDEDLLAK-----------IRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:PRK12536   96 EALHDPLDDESELFATsddeaaearrdLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRGLKAL 173
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 97-173 6.89e-04

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: 38.94  E-value: 6.89e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1547036127  97 VEAYIESQNVDMVED-EDLLAKirqvLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQAFS 173
Cdd:pfam07638 111 VVDNGDSPNPDLLLDlDEALEQ----LFSLSPRQARLVELRFFAGLSNDEIAERLGVSERTVERNWALARAWLHRELR 184
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 41-167 2.20e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 37.13  E-value: 2.20e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  41 DRAHDIVQDVFLKIWENAERLELKSSiQHYLFTSVRNGCLNYLKSLQIEdrnnRKYVEAYIE-SQNVDMVEDE-----DL 114
Cdd:PRK12528   29 QSAADLAQDTFVKVLVARETAQIIEP-RAFLTTIAKRVLCNHYRRQDLE----RAYLEALAQlPERVAPSEEEraiilET 103

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1547036127 115 LAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMER 167
Cdd:PRK12528  104 LVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNKAAMR 156
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 99-168 3.20e-03

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: 36.02  E-value: 3.20e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1547036127  99 AYIESQNVDMV------EDEDLLAKIRQVLDElpdRCREVcLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERL 168
Cdd:COG2197    41 ELLEELRPDVVlldirmPGMDGLEALRRLLTP---REREV-LRLLAEGLSNKEIAERLGISERTVKTHVSNILRKL 112
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 106-169 4.29e-03

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 36.97  E-value: 4.29e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1547036127 106 VDMVEDEDLLAKIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKvQLH-RGMERLR 169
Cdd:PRK06288  194 DEIAEREEIKRVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRIS-QLHtKAVLQLR 257
PRK09642 PRK09642
RNA polymerase sigma factor;
43-178 4.34e-03

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 36.23  E-value: 4.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1547036127  43 AHDIVQDVFLKIWENAERLELKSsIQHYLFTSVRNGCLNYL--KSLQIEDRNNRKYVEAYIES-QNVD---MVEDEDLLa 116
Cdd:PRK09642   22 AKDVTQEVFVKIHASLPNYQFRG-LKTWMARIATNHAIDYKrkKARENEELSLCKETEENIKSsHNIEdllLTKEQKLL- 99

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1547036127 117 kIRQVLDELPDRCREVCLLRFVEGYKYNEIAVALKMNENTVKVQLHRGMERLRQAFSTYDYI 178
Cdd:PRK09642  100 -IAQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKHWKEEEFL 160
 
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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