NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1710644|sp|P50507|]
View 

RecName: Full=RNA polymerase sigma factor RpoH; AltName: Full=RNA polymerase sigma-32 factor

Protein Classification

RNA polymerase sigma factor RpoH( domain architecture ID 11482333)

RNA polymerase sigma factor RpoH is involved in regulating the expression of heat shock genes; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released

Gene Ontology:  GO:0016987|GO:0003677|GO:0006352
PubMed:  3315851|3052291

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 1-288 0e+00

RNA polymerase factor sigma-32; Reviewed


:

Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 503.55  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     1 MARNSLPTITAGEAGLNRYLDEIRKFPMLEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVS 80
Cdd:PRK06596   1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    81 EGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQAiddgdLKPEHVK 160
Cdd:PRK06596  81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGW-----LNPEEVE 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   161 EIATKLQVSEEEVISMNRRLHG-DASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNDRE 239
Cdd:PRK06596 156 MVAEELGVSEEEVREMESRLSGqDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERS 235

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 1710644   240 RRIFEARRLAEDPVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEA 288
Cdd:PRK06596 236 RDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEAAA 284
 
Name Accession Description Interval E-value
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 1-288 0e+00

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 503.55  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     1 MARNSLPTITAGEAGLNRYLDEIRKFPMLEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVS 80
Cdd:PRK06596   1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    81 EGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQAiddgdLKPEHVK 160
Cdd:PRK06596  81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGW-----LNPEEVE 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   161 EIATKLQVSEEEVISMNRRLHG-DASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNDRE 239
Cdd:PRK06596 156 MVAEELGVSEEEVREMESRLSGqDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERS 235

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 1710644   240 RRIFEARRLAEDPVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEA 288
Cdd:PRK06596 236 RDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEAAA 284
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 14-284 4.48e-141

alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 274107 [Multi-domain]  Cd Length: 270  Bit Score: 398.58  E-value: 4.48e-141
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     14 AGLNRYLDEIRKFPMLEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKF 93
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     94 DPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQaiddGDLKPEHVKEIATKLQVSEEEV 173
Cdd:TIGR02392  81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLQ----GWLNPEEVEAIAEELGVSEREV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    174 ISMNRRLHG-DASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNDRERRIFEARRLAEDP 252
Cdd:TIGR02392 157 REMESRLSGqDMSLNASIDDDEDDGGAPIAYLVDKRSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDDK 236

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1710644    253 VTLEELSSEFDISRERVRQIEVRAFEKVQEAV 284
Cdd:TIGR02392 237 LTLQELAAEYGVSAERIRQIEKNAMKKLKAAL 268
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 18-292 5.35e-110

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: 319.69  E-value: 5.35e-110
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   18 RYLDEIRKFPMLEPQEEYMLGKRYaEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPER 97
Cdd:COG0568   1 AYLREIGRVPLLTAEEEVELARRI-QAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPER 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   98 GFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKrlffnLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVISMN 177
Cdd:COG0568  80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAET-----LNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREML 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644  178 RRLHGDASLNAPIkaSEGESGQWQDWLVDDH-ESQEAVLIEQDeletRRRMLAKAMGVLNDRERRIFEARRLA--EDPVT 254
Cdd:COG0568 155 RLAREPVSLDAPV--GDDEDSELGDLLEDEEaPSPEEALEEEL----LREELREALDTLTEREREILRLRFGLddGEPHT 228

                       250       260       270
                ....*....|....*....|....*....|....*...
gi 1710644  255 LEELSSEFDISRERVRQIEVRAFEKVQEAVQKEALEAA 292
Cdd:COG0568 229 LEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRDY 266
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 53-121 4.87e-16

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: 71.08  E-value: 4.87e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1710644     53 LVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSW 121
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 225-281 1.59e-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: 50.18  E-value: 1.59e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 1710644  225 RRMLAKAMGVLNDRERRIFEARRLaeDPVTLEELSSEFDISRERVRQIEVRAFEKVQ 281
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRFG--EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 1-288 0e+00

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 503.55  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     1 MARNSLPTITAGEAGLNRYLDEIRKFPMLEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVS 80
Cdd:PRK06596   1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    81 EGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQAiddgdLKPEHVK 160
Cdd:PRK06596  81 EGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGW-----LNPEEVE 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   161 EIATKLQVSEEEVISMNRRLHG-DASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNDRE 239
Cdd:PRK06596 156 MVAEELGVSEEEVREMESRLSGqDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERS 235

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*....
gi 1710644   240 RRIFEARRLAEDPVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEA 288
Cdd:PRK06596 236 RDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEAAA 284
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 14-284 4.48e-141

alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 274107 [Multi-domain]  Cd Length: 270  Bit Score: 398.58  E-value: 4.48e-141
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     14 AGLNRYLDEIRKFPMLEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKF 93
Cdd:TIGR02392   1 GSLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     94 DPERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQaiddGDLKPEHVKEIATKLQVSEEEV 173
Cdd:TIGR02392  81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKRLQ----GWLNPEEVEAIAEELGVSEREV 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    174 ISMNRRLHG-DASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNDRERRIFEARRLAEDP 252
Cdd:TIGR02392 157 REMESRLSGqDMSLNASIDDDEDDGGAPIAYLVDKRSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDDK 236

                         250       260       270
                  ....*....|....*....|....*....|..
gi 1710644    253 VTLEELSSEFDISRERVRQIEVRAFEKVQEAV 284
Cdd:TIGR02392 237 LTLQELAAEYGVSAERIRQIEKNAMKKLKAAL 268
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 18-292 5.35e-110

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: 319.69  E-value: 5.35e-110
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   18 RYLDEIRKFPMLEPQEEYMLGKRYaEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPER 97
Cdd:COG0568   1 AYLREIGRVPLLTAEEEVELARRI-QAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPER 79

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   98 GFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKrlffnLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVISMN 177
Cdd:COG0568  80 GFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAET-----LNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREML 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644  178 RRLHGDASLNAPIkaSEGESGQWQDWLVDDH-ESQEAVLIEQDeletRRRMLAKAMGVLNDRERRIFEARRLA--EDPVT 254
Cdd:COG0568 155 RLAREPVSLDAPV--GDDEDSELGDLLEDEEaPSPEEALEEEL----LREELREALDTLTEREREILRLRFGLddGEPHT 228

                       250       260       270
                ....*....|....*....|....*....|....*...
gi 1710644  255 LEELSSEFDISRERVRQIEVRAFEKVQEAVQKEALEAA 292
Cdd:COG0568 229 LEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRKLRDY 266
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 27-295 5.29e-96

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 285.01  E-value: 5.29e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    27 PMLEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAM 106
Cdd:PRK07500  19 PYLEREEEHALAYRWKDHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYAT 98

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   107 WWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVISMNRRLHG-DAS 185
Cdd:PRK07500  99 WWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGpDAS 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   186 LNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNDRERRIFEARRLAEDPVTLEELSSEFDIS 265
Cdd:PRK07500 179 LNAPQSEEDEGRSERMDFLVDDSPLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLREDGATLEALGEELGIS 258

                        250       260       270
                 ....*....|....*....|....*....|
gi 1710644   266 RERVRQIEVRAFEKVQEAVQKEALEAARAL 295
Cdd:PRK07500 259 KERVRQIEARALEKLRRALLSQSPEVAYFA 288
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 19-289 8.95e-49

RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393). [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 131447 [Multi-domain]  Cd Length: 285  Bit Score: 163.74  E-value: 8.95e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     19 YLDEIRKFPMLEPQEEYMLGKRyAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERG 98
Cdd:TIGR02394  18 YLREIGFKPLLTAEEEIAYARR-ALAGDFEARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERG 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     99 FRLATYAMWWIKASIQEYILRSWSLVKMGTTAnQKRLFFNLRRLKGRIQAIDdgdlKPEHVKEIATKLQVSEEEVISMNR 178
Cdd:TIGR02394  97 FRFSTYATWWIRQTIERAIMNQARTIRLPVHV-IKELNVYLRAARQLEKKLG----REPSVEEIAELLDKPVEDVSRVLA 171

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    179 RLHGDASLNAPIKASEGESgqWQDWLVDDHESQEAVLIEQDELETR-RRMLAKamgvLNDRERRIFEAR--RLAEDPVTL 255
Cdd:TIGR02394 172 LNERITSLDAPLDDDSSKS--LLDTIADEQSIDPESLVQNDDLKQLiEAWLAE----LNERQREVLARRfgLLGYEPATL 245

                         250       260       270
                  ....*....|....*....|....*....|....
gi 1710644    256 EELSSEFDISRERVRQIEVRAFEKVQEAVQKEAL 289
Cdd:TIGR02394 246 EEVAAEVGLTRERVRQIQVEALKKLRRILERDGV 279
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 19-289 1.56e-43

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 151.26  E-value: 1.56e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    19 YLDEIRKFPMLEPQEEYMLGKRyAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERG 98
Cdd:PRK05657  58 YLNEIGYSPLLTAEEEVYFARR-ALRGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERG 136

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    99 FRLATYAMWWIKASIQEYILrswslvkmgttaNQKRlffNLR-------------RLKGRIQAIDDGDLKPEhvkEIATK 165
Cdd:PRK05657 137 FRFSTYATWWIRQTIERAIM------------NQTR---TIRlpvhvvkelnvylRAARELEHKLDHEPSAE---EIAEL 198

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   166 LQVSEEEV---ISMNRRLhgdASLNAPIKASEGESgqWQDWLVDDHESQEAVLIEQDELETRRRmlaKAMGVLNDRERRI 242
Cdd:PRK05657 199 LDKPVDDVsrmLALNERI---TSLDTPLGGDPEKS--LLDILADEQENGPEDTTQDDDMKQSIV---KWLFELNDKQREV 270

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|
gi 1710644   243 FEaRR---LAEDPVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEAL 289
Cdd:PRK05657 271 LA-RRfglLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQGL 319
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 19-279 1.54e-35

RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).


Pssm-ID: 274382 [Multi-domain]  Cd Length: 298  Bit Score: 129.67  E-value: 1.54e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     19 YLDEIRKFPMLEPQEEYMLGKRYAE----------------------------------------HGDRdAAHKLVTSHL 58
Cdd:TIGR02997   6 YLQEIGRVPLLTPEEEIELARQVQQmmvleelreeleeqlgrepskeewaaaaglseaelrqrlrQGQR-AKEKMIKANL 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     59 RLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYIlrswslvkmgttANQKR---- 134
Cdd:TIGR02997  85 RLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAI------------ANQSRtirl 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    135 ---LFFNLRRLK----------GRIQAIDdgdlkpehvkEIATKLQVSEEEVISMNRRLHGDASLNAPIkASEGESgQWQ 201
Cdd:TIGR02997 153 pihITEKLNKIKkvqrelsqklGRTPSEA----------EIAEALELEPEQVRELLQRARQPVSLDAPV-GDEEDT-ELG 220

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    202 DWLVDDHESQEAVlIEQDELetrRRMLAKAMGVLNDRERRIFEAR--RLAEDPVTLEELSSEFDISRERVRQIEVRAFEK 279
Cdd:TIGR02997 221 DLLEDDGESPEEQ-VERESL---RQDLESLLAELTPRERQVLRLRfgLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRK 296
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 19-279 2.53e-32

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 122.79  E-value: 2.53e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    19 YLDEIRKFPMLEPQEEYMLGKRyAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERG 98
Cdd:PRK09210 101 YLKEIGRVPLLTAEEEIELAKR-IEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKG 179

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    99 FRLATYAMWWIKASIQEYI---LRSWSL-VKMGTTAN-----QKRLFFNLRRLKGRIQAIDDGDLKPEHVKEIatkLQVS 169
Cdd:PRK09210 180 FKFSTYATWWIRQAITRAIadqARTIRIpVHMVETINklirvQRQLLQELGREPTPEEIAEEMDMPPEKVREI---LKIA 256

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   170 EEEVismnrrlhgdaSLNAPIkaSEGESGQWQDWlVDDHESQEAVliEQDELETRRRMLAKAMGVLNDRERRIFEARRLA 249
Cdd:PRK09210 257 QEPV-----------SLETPI--GEEDDSHLGDF-IEDQDATSPA--DHAAYELLKEQLEDVLDTLTDREENVLRLRFGL 320

                        250       260       270
                 ....*....|....*....|....*....|..
gi 1710644   250 ED--PVTLEELSSEFDISRERVRQIEVRAFEK 279
Cdd:PRK09210 321 DDgrTRTLEEVGKVFGVTRERIRQIEAKALRK 352
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 19-291 8.23e-24

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 98.65  E-value: 8.23e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    19 YLDEIRKFPMLEPQEEYMLGKR-----YAEH----------------------GDRDAAHkLVTSHLRLVAKIAMGYRGY 71
Cdd:PRK07921  31 YLNGIGKTALLTAADEVELAKRieaglYAEHlletrkrlsearkrdlaavvrdGEAARRH-LLEANLRLVVSLAKRYTGR 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    72 GLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYIL---RSWSL-VKMGTTANQkrlffnLRRLK---- 143
Cdd:PRK07921 110 GMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMAdqsRTIRLpVHLVEQVNK------LARIKrelh 183

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   144 ---GRiQAIDDgdlkpehvkEIATKLQVSEEEVISMNRRLHGDASLNAPIkASEGESgQWQDWLVD-DHESQEAVLIEQD 219
Cdd:PRK07921 184 qqlGR-EATDE---------ELAEESGIPEEKIADLLEHSRDPVSLDMPV-GSDEEA-PLGDFIEDsEATSAENAVIAGL 251

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1710644   220 ELETRRRMLAkamgVLNDRERRIFEARRLAED--PVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEALEA 291
Cdd:PRK07921 252 LHTDIRSVLA----TLDEREQQVIRLRFGLDDgqPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRS 321
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 45-286 1.10e-22

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: 93.73  E-value: 1.10e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   45 GDRDAAHKLVTSHLRLVAKIAMGYRG-YGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYiLRSWSL 123
Cdd:COG1191  12 GDEEAREELIEEYLPLVKKIASRLAGrLPAELDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDY-LRDEDW 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644  124 VKmgttanqkrlffnlRRLKGRIQAIDDGDLKPEH-------VKEIATKLQVSEEEVISMNRRLHGD--ASLNAPIKASE 194
Cdd:COG1191  91 VP--------------RSVRELARKIEEAIEELEQelgreptDEEIAEELGISLEEVQEALEAANAYqlLSLDEPLEDGD 156

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644  195 GESGQWqdwlvdDHESQEAVLIEQDeletRRRMLAKAMGVLNDRERRIFEARRLAEdpVTLEELSSEFDISRERVRQIEV 274
Cdd:COG1191 157 DLLDLL------ESGDPEEELEHEE----LREALAEAIEQLPERERLVLSLYYFEE--LTLKEIAEVLGVSESRVSRLHK 224

                       250
                ....*....|..
gi 1710644  275 RAFEKVQEAVQK 286
Cdd:COG1191 225 KALARLREYLKE 236
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 19-273 3.54e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 96.22  E-value: 3.54e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    19 YLDEIRKFPMLEPQEEYMLGKR-----YAEH----------------------GDRdAAHKLVTSHLRLVAKIAMGYRGY 71
Cdd:PRK05901 216 YLKQIGKVKLLNAEEEVELAKRieaglYAEEllaegekldpelrrdlqwigrdGKR-AKNHLLEANLRLVVSLAKRYTNR 294

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    72 GLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASI------QEYILRswSLVKMGTTANqkRLffnlrrlkGR 145
Cdd:PRK05901 295 GLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAItramadQARTIR--IPVHMVETIN--KL--------GR 362

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   146 IQAIDDGDL----KPEhvkEIATKLQVSEEEVI---SMNRrlhgDA-SLNAPIkASEGESgQWQDwLVDDHESQEAV--- 214
Cdd:PRK05901 363 IERELLQELgrepTPE---ELAKEMGFTPEKVReiqKYNR----EPiSLDKTI-GKEGDS-QFGD-FIEDSEAVSPVdav 432

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1710644   215 ----LIEQ--DELETrrrmlakamgvLNDRERRIFEARRLAED--PVTLEELSSEFDISRERVRQIE 273
Cdd:PRK05901 433 sftlLQDQlqEVLET-----------LSEREAGVIRMRFGLTDgqPKTLDEIGQVYGVTRERIRQIE 488
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 47-279 6.79e-22

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 94.08  E-value: 6.79e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    47 RDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYIlrswslvkm 126
Cdd:PRK07406 135 RRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAI--------- 205

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   127 gttANQKR-------LFFNLRRLK----------GRiqaiddgdlKPEHvKEIATKLQVSEEEVISMNRRLHGDASLNAP 189
Cdd:PRK07406 206 ---ADQSRtirlpvhLYETISRIKkttkvlsqefGR---------KPTE-EEIAESMEMTIEKLRFIAKSAQLPISLETP 272

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   190 IkaSEGESGQWQDWLVDDHESQE----AVLIEQDeletrrrmLAKAMGVLNDRERRIFEARRLAED--PVTLEELSSEFD 263
Cdd:PRK07406 273 I--GKEEDSRLGDFIEADGETPEddvaKNLLRED--------LEGVLATLSPRERDVLRLRYGLDDgrMKTLEEIGQIFN 342

                        250
                 ....*....|....*.
gi 1710644   264 ISRERVRQIEVRAFEK 279
Cdd:PRK07406 343 VTRERIRQIEAKALRK 358
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 22-282 1.43e-21

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 93.78  E-value: 1.43e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    22 EIRKFPMLEPQEEYMLGKRYAEHgdrdaahkLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRL 101
Cdd:PRK07598 157 EIAKLTVEELEQIQKQGLRAKEH--------MIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRF 228

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   102 ATYAMWWIKASIQEYILRSWSLVKMGTTANQKrlffnLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVISMNRRLH 181
Cdd:PRK07598 229 STYAYWWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVP 303

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   182 GDASLNapIKASEGESGQWQDWLVDDHESQEAVLIEqdelETRRRMLAKAMGVLNDRERRIFEARRLAED--PVTLEELS 259
Cdd:PRK07598 304 RSVSLE--TKVGKDKDTELGDLLETDDISPEEMLMR----ESLQRDLQHLLADLTSRERDVIRMRFGLADghTYSLAEIG 377

                        250       260
                 ....*....|....*....|...
gi 1710644   260 SEFDISRERVRQIEVRAFEKVQE 282
Cdd:PRK07598 378 RALDLSRERVRQIESKALQKLRQ 400
SigBFG TIGR02980
RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors ...
 46-285 5.23e-19

RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.


Pssm-ID: 274373 [Multi-domain]  Cd Length: 227  Bit Score: 83.81  E-value: 5.23e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     46 DRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYiLR--SWSL 123
Cdd:TIGR02980   1 DKEAREKLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMGEIKRF-FRddTWAV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    124 vkmgttanqkRLFFNLRRLKGRI-QAIDDgdLKPEH-----VKEIATKLQVSEEEV---ISMNRRLHGDaSLNAPIKASE 194
Cdd:TIGR02980  80 ----------RVPRRLKELGVKInKATEE--LTQRLgrsptIAEIAERLGVSEEEVveaLEAGNAYQAL-SLDASIEDDD 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    195 GESGQWQDWLVDDHESQEAVLieqdeletRRRMLAKAMGVLNDRERRIFEARRLAEdpVTLEELSSEFDISRERVRQIEV 274
Cdd:TIGR02980 147 GDPIALLDTLGDEDDALETVE--------DRLALKPLLAALPERERRILLLRFFED--KTQSEIAERLGISQMHVSRLLR 216

                         250
                  ....*....|.
gi 1710644    275 RAFEKVQEAVQ 285
Cdd:TIGR02980 217 RALKKLREQLL 227
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
26-279 2.05e-18

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 82.30  E-value: 2.05e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    26 FPM-LEPQEEYMLGKRYAEhGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATY 104
Cdd:PRK05803  27 FPQpLSEEEERKYLELMKE-GDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATY 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   105 AmwwiKASIQEYILrswslvkmgttanqkrlfFNLRRLKgriqaiddgdlkpehvkeiATKLQVSEEEVISMNRrlhgda 184
Cdd:PRK05803 106 A----ARCIENEIL------------------MHLRNLK-------------------KTKKEVSLQDPIGVDK------ 138

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   185 slnapikasEGESGQWQDWLVDDHESqeavLIEQDELETRRRMLAKAMGVLNDRERRIFEARR--LAEDPVTLEELSSEF 262
Cdd:PRK05803 139 ---------EGNEISLIDILGSEEDD----VIEQVELKMEVEKLYKKIDILDEREKEVIEMRYglGNGKEKTQREIAKAL 205

                        250
                 ....*....|....*..
gi 1710644   263 DISRERVRQIEVRAFEK 279
Cdd:PRK05803 206 GISRSYVSRIEKRALKK 222
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 39-276 1.97e-17

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 81.04  E-value: 1.97e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    39 KRYAEHGDRdAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYIL 118
Cdd:PRK05949  83 KQTLKQGKR-AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIA 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   119 RSWSLVKMGTTANQKrlffnLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEE---EVISMNRRlhgDASLNapIKASEG 195
Cdd:PRK05949 162 QQARTIRLPIHITEK-----LNKIKKTQRELSQKLGRSATPAEIAKELELEPSqirEYLSMARQ---PISLD--VRVGDN 231

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   196 ESGQWQDWLVDDHESQEAVLIEqdelETRRRMLAKAMGVLNDRERRIFEARRLAED--PVTLEELSSEFDISRERVRQIE 273
Cdd:PRK05949 232 QDTELSELLEDEGPSPDQYITQ----ELLRQDLNNLLAELTPQQREVLTLRFGLEDgkELSLAKVGERLNLSRERVRQLE 307


                 ...
gi 1710644   274 VRA 276
Cdd:PRK05949 308 HQA 310
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 49-283 3.64e-16

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 77.49  E-value: 3.64e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    49 AAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSWSLVKMGT 128
Cdd:PRK07405  82 AKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPI 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   129 TANQKrlffnLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVISMNRRLHGDASLNapIKASEGESGQWQDWLVDDH 208
Cdd:PRK07405 162 HITEK-----LNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLD--LRVGDNQDTELGELLEDTG 234

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1710644   209 ESQEAVLIEQdeleTRRRMLAKAMGVLNDRERRIFEARRLAED--PVTLEELSSEFDISRERVRQIEVRAFEKVQEA 283
Cdd:PRK07405 235 ASPEDFATQS----SLQLDLERLMEDLTPQQKEVIALRFGLEDgqPLTLAKIGERLNISRERVRQIEREALSKLRKR 307
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 53-121 4.87e-16

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: 71.08  E-value: 4.87e-16
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1710644     53 LVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRSW 121
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQR 69
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 53-282 1.44e-15

RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.


Pssm-ID: 274153 [Multi-domain]  Cd Length: 224  Bit Score: 74.23  E-value: 1.44e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     53 LVTSHLRLVAKIAMGYRGyGLP----IGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYiLRSWSLVKMGT 128
Cdd:TIGR02479   1 LIRRYLPLVKRIAGRLSV-GLPssveLDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMLDE-LRRLDWVPRSL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    129 TANQKRLFFNLRRLKGRIqaiddgdLKPEHVKEIATKLQVSEEEVISMNRRLHGDA--SLNAPIkASEGESGQWQDWLVD 206
Cdd:TIGR02479  79 RQKARKLERAIRELEARL-------GREPTEEEIAEELGMDLKEYRQALNEINALSlvSLDELL-ESGDDGGSLIDRIED 150

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1710644    207 DHESQEAVLIEQDELetrRRMLAKAMGVLNDRERRIFEARRlaEDPVTLEELSSEFDISRERVRQIEVRAFEKVQE 282
Cdd:TIGR02479 151 DKSEDPEEELEREEL---REALAEAIESLSEREQLVLSLYY--YEELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 29-288 5.96e-15

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 73.19  E-value: 5.96e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    29 LEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRLVAKIAMGYrGYGLPIGE-VVSEGNVGLMQAVKKFDPERGFRLATYAMW 107
Cdd:PRK08583  10 LTKEEVNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKY-SKGQSHHEdLVQVGMVGLLGAIRRYDPSFGRSFEAFAVP 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   108 WIKASIQEYIL-RSWSL-VKmgttanqkrlffnlRRLK---GRIQ-AIDDgdLKPE-----HVKEIATKLQVSEEEVI-S 175
Cdd:PRK08583  89 TIIGEIKRYLRdKTWSVhVP--------------RRIKelgPKIKkAVDE--LTTElqrspKISEIADRLGVSEEEVLeA 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   176 MN-----RRLHGDASLNApikASEGESGQwqdwLVDDHESQEavliEQDELETRRRMLAKAMGVLNDRERRIFEArrLAE 250
Cdd:PRK08583 153 MEmgksyQALSVDHSIEA---DSDGSTVT----LLDIVGQQE----DGYELTEQRMILEKILPVLSDREKSIIQC--TFI 219

                        250       260       270
                 ....*....|....*....|....*....|....*...
gi 1710644   251 DPVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEA 288
Cdd:PRK08583 220 ENLSQKETGERLGISQMHVSRLQRQAIKKLREAAFLDT 257
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 38-279 3.36e-14

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 72.52  E-value: 3.36e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    38 GKRYAehgdRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYI 117
Cdd:PRK05658 374 GEAKA----RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 449

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   118 lrswslvkmgttANQKRLFfnlrrlkgRIqaiddgdlkPEH------------------------VKEIATKLQVSEEEV 173
Cdd:PRK05658 450 ------------ADQARTI--------RI---------PVHmietinklnrisrqmlqeigreptPEELAERLGMPEDKV 500

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   174 ----------ISMnrrlhgdaslNAPIkaSEGESGQWQDWLvddhESQEAVL----IEQDEL-ETRRRMLAKamgvLNDR 238
Cdd:PRK05658 501 rkvlkiakepISL----------ETPI--GDDEDSHLGDFI----EDKNAELpidaAIQESLrEATTDVLAS----LTPR 560

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|...
gi 1710644   239 ERRIFEARRLAED--PVTLEELSSEFDISRERVRQIEVRAFEK 279
Cdd:PRK05658 561 EAKVLRMRFGIDMntDHTLEEVGKQFDVTRERIRQIEAKALRK 603
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 52-254 2.13e-11

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 62.63  E-value: 2.13e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    52 KLVTSHLRLVAKIAMGY-RGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEY---------ILRSW 121
Cdd:PRK07408  29 QLVELNLGLVRKEAHRWsNQCSEPYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYlrdksptvrIPRRW 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   122 -SLVKMGTTANQKrlffnLRRLKGRiQAIDDgdlkpehvkEIATKLQVSEEE-----VISMNRRLhgdASLNAPIKASEG 195
Cdd:PRK07408 109 qELQRQAKKVRQE-----LRQELGR-QPTDQ---------EIAQALDISLEEwqeikLALQNRTP---LSLDAPVNQDED 170

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1710644   196 ESGQWQDwLVDDHESQEAVLIEQDELEtrrrmLAKAMGVLNDRERRIFE------------ARRLAEDPVT 254
Cdd:PRK07408 171 GSTSLGD-LLPDPRYRSFQLAQEDRIR-----LQQALAQLEERTREVLEfvflhdltqkeaAERLGISPVT 235
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
25-285 7.16e-11

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 61.12  E-value: 7.16e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    25 KFPMLEPQEEYMLGKRYaEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATY 104
Cdd:PRK08215  15 KLPVLKNEEMRELFERM-QNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTY 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   105 AMWWIKASIQEYiLR-------SWSLVKMGTTAnqkrlffnlrrLKGRIQAIDDGDLKPEhVKEIATKLQVSEEEVISMN 177
Cdd:PRK08215  94 AVPMIIGEIRRY-LRdnnpirvSRSLRDIAYKA-----------LQVREKLINENSKEPT-VEEIAKELEVPREEVVFAL 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   178 RRLHGDASLNAPIKASEGESGQWQDWlVDDHESQEAVLIEQDELEtrrrmlaKAMGVLNDRER-----RIFEARrlaedp 252
Cdd:PRK08215 161 DAIQDPVSLFEPIYHDGGDPIYVMDQ-ISDEKNKDENWLEEIALK-------EAMKKLNDREKlilnlRFFQGK------ 226

                        250       260       270
                 ....*....|....*....|....*....|...
gi 1710644   253 vTLEELSSEFDISRERVRQIEVRAFEKVQEAVQ 285
Cdd:PRK08215 227 -TQMEVAEEIGISQAQVSRLEKAALKHMRKYIQ 258
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
33-286 2.25e-10

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 59.67  E-value: 2.25e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    33 EEYMLGKRYAEHGDRDAAHKLVTSHLRLVA----KIAMGyrgygLPIG----EVVSEGNVGLMQAVKKFDPERGFRLATY 104
Cdd:PRK07670   7 EEQKLWDRWKEERDPDAADELIRRYMPLVHyhvqRISVG-----LPKSvskdDLKSLGMLGLYDALEKFDPSRDLKFDTY 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   105 AMWWIKASIQEYiLRS--WslvkMGTTANQKrlffnLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEV--------- 173
Cdd:PRK07670  82 ASFRIRGAIIDG-LRKedW----LPRSMREK-----TKKVEAAIEKLEQRYMRNVTPKEVAAELGMTEEEVeatmnegff 151

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   174 ---ISMNRRLHGDaslnapikaSEGESGQWQdwLVDDH-ESQEAVLIEQDELETrrrmLAKAMGVLNDRERRIFEARRLA 249
Cdd:PRK07670 152 anlLSIDEKTHDQ---------DDGENVSVT--IRDDKtPTPEEKLLKEELIEE----LAEKIKQLSEKEQLVISLFYKE 216

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 1710644   250 EdpVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQK 286
Cdd:PRK07670 217 E--LTLTEIGQVLNLSTSRISQIHSKALFKLKKLLEK 251
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 231-282 3.28e-10

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: 54.74  E-value: 3.28e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1710644    231 AMGVLNDRERRIFEARRlaEDPVTLEELSSEFDISRERVRQIEVRAFEKVQE 282
Cdd:pfam04545   1 ALASLPPRERQVLVLRY--GEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 48-284 4.42e-10

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: 57.36  E-value: 4.42e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     48 DAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRlaTYAMWWIKASIQEYilrswslvkmg 127
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFK--AWLFRIARNLILDY----------- 67

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    128 ttanqkrlffnLRRLKGRIQAIDDgdlkpehvkeiatklqvseeevismnrrlhgdaslnapikasegesgqWQDWLVDD 207
Cdd:TIGR02937  68 -----------LRRKRRLRRELDL------------------------------------------------LEELLDSD 88

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1710644    208 HESQEAVLIEQdeletRRRMLAKAMGVLNDRERRIFEARRLAEdpVTLEELSSEFDISRERVRQIEVRAFEKVQEAV 284
Cdd:TIGR02937  89 PSPEEELEQEE-----EREALREALEKLPEREREVLVLRYLEG--LSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 21-276 6.86e-10

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 58.55  E-value: 6.86e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    21 DEIRKFPMLEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRLVAKIAmGYRGYGLP----IGEVVSEGNVGLMQAVKKFDPE 96
Cdd:PRK06288   4 KMSGKIPKYAQQDETELWREYKKTGDPKIREYLILKYSPLVKYVA-GRIAVGMPqnveFDDLVSYGVFGLIDAIEKFDPE 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    97 RGFRLATYAMWWIKASIQEYiLRSWSLVKMGTTANQKRLFFNLRRLKGRI-QAIDDGDLKPE---HVKEI-ATKLQVSEE 171
Cdd:PRK06288  83 REIKFKTYAVTRIRGAIFDE-LRSIDWIPRSVRQKARQIERAIAMLEARLgRTPSDEEIADElgiSLEEYnSLLSKLSGT 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   172 EVISMNRRLHGDaslnapikaSEGESGQWQDWLVDDHESQEAVLIEQDELetrRRMLAKAMGVLNDRERRI-----FEAr 246
Cdd:PRK06288 162 SVVSLNDLWFGG---------DEGDEVSLMDTLESPAALNPDEIAEREEI---KRVIVEAIKTLPEREKKVlilyyYED- 228

                        250       260       270
                 ....*....|....*....|....*....|
gi 1710644   247 rlaedpVTLEELSSEFDISRERVRQIEVRA 276
Cdd:PRK06288 229 ------LTLKEIGKVLGVTESRISQLHTKA 252
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 42-282 9.22e-10

RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131931 [Multi-domain]  Cd Length: 231  Bit Score: 57.80  E-value: 9.22e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644     42 AEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYiLRSW 121
Cdd:TIGR02885   5 AQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRF-LRDD 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    122 SLVKMGTTAnqKRLFFNLRRLKGRIQAiddgDLKPE-HVKEIATKLQVSEEEVISMNRRLHGDASLNAPIKASEGESGQW 200
Cdd:TIGR02885  84 GIIKVSRSL--KELARKIRYMKEELSK----ELGREpTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYL 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    201 QDWLVDDHESqeavliEQDELEtrRRMLAKAMGVLNDRERRIFEARRLAEDpvTLEELSSEFDISRERVRQIEVRAFEKV 280
Cdd:TIGR02885 158 LDQIADKGSE------DSDWLE--KIALKEAISKLDERERQIIMLRYFKDK--TQTEVANMLGISQVQVSRLEKKVLKKM 227


                  ..
gi 1710644    281 QE 282
Cdd:TIGR02885 228 KE 229
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
27-246 1.50e-09

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 57.17  E-value: 1.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    27 PMLEPQEEYMLGKRYaEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAM 106
Cdd:PRK08301  32 PPLSKEEEEYLLNKL-PKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYAS 110

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   107 WWIKASIQEYILRswslvkmgttaNQKrlffnlrrlkgriqaiddgdlkpehvkeiaTKLQVSEEEvismnrrlhgdaSL 186
Cdd:PRK08301 111 RCIENEILMYLRR-----------NNK------------------------------VKAEVSFDE------------PL 137

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1710644   187 NApikasegesgqwqDW-----LVDDHESQEAVLIEQD-ELETRRRMLAKAMGVLNDRERRIFEAR 246
Cdd:PRK08301 138 NI-------------DWdgnelLLSDVLGTDNDIIYKDiEDEVDRKLLKKALKKLSDREKQIMELR 190
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 225-281 1.59e-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: 50.18  E-value: 1.59e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 1710644  225 RRMLAKAMGVLNDRERRIFEARRLaeDPVTLEELSSEFDISRERVRQIEVRAFEKVQ 281
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRFG--EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
40-282 1.90e-07

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 51.13  E-value: 1.90e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    40 RYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYiLR 119
Cdd:PRK05572  24 KKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRF-LR 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   120 SWSLVKMG----TTANQkrlffnLRRLKGRIQAIDDGDlkpEHVKEIATKLQVSEEEVISMNRRLHGDASLNAPIKASEG 195
Cdd:PRK05572 103 DDGTVKVSrslkETANK------IRKDKDELSKELGRE---PTIEELAEYLGVTPEEVVLAQEASRSPQSIHETVHENDG 173

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   196 ESGQWQDWLVDDHesqeavliEQDELEtrRRMLAKAMGVLNDRERRIFEARRLAEDpvTLEELSSEFDISRERVRQIEVR 275
Cdd:PRK05572 174 DPITLLDQIADQS--------EEDWFD--KIALKEAIRELDERERLIVYLRYFKDK--TQSEVAKRLGISQVQVSRLEKK 241


                 ....*..
gi 1710644   276 AFEKVQE 282
Cdd:PRK05572 242 ILKQMKE 248
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 53-284 2.25e-06

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 48.08  E-value: 2.25e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    53 LVTSHLRLVAKIAMGYRGyGLP----IGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASI------QEYILRSws 122
Cdd:PRK05911  28 LIEFYLPLVKNVAHRLIS-GMPshvkTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAIiddlrkQDWVPRS-- 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   123 lvkmgttANQKRlffnlRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVIS--MNRRLHGDASLNAPIKA-SEGESGQ 199
Cdd:PRK05911 105 -------VHQKA-----NKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGwfSSARPALILSLNEEFPCqSDDEAGL 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   200 WQDWLVDDHESQEAV-LIEQDELETrrrMLAKAMGVLNDRERRIFeARRLAEDPVtLEELSSEFDISRERVRQIEVRAFE 278
Cdd:PRK05911 173 ALEERIADERAETGYdVVDKKEFSS---ILAEAILALEEKERKVM-ALYYYEELV-LKEIGKILGVSESRVSQIHSKALL 247


                 ....*.
gi 1710644   279 KVQEAV 284
Cdd:PRK05911 248 KLRATL 253
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 52-246 5.04e-04

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 40.91  E-value: 5.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    52 KLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYIL-RSWSlvkMGTTA 130
Cdd:PRK07122  44 RIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRdNSWS---VKVPR 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   131 NQKRLFFNLRR----LKGRIQaiddgdlKPEHVKEIATKLQVSEEEVISMnrRLHGDA----SLNAPIKASEGESGQWQD 202
Cdd:PRK07122 121 RLKELHLRLGRataeLSQRLG-------RAPTASELAAELGMDREEVVEG--LVAGSAyntlSIDSGGGSGDDDARAIAD 191

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 1710644   203 WLVDDHESQEAVlieqDELETRRRMLAKamgvLNDRERRIFEAR 246
Cdd:PRK07122 192 TLGDVDAGLDQI----ENREALRPLLAA----LPERERTVLVLR 227
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 202-290 2.50e-03

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: 38.05  E-value: 2.50e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644  202 DWLVDDHESQEAVLIEQDeletRRRMLAKAMGVLNDRERRIFEARRLAEdpVTLEELSSEFDISRERVRQIEVRAFEKVQ 281
Cdd:COG1595  99 EELPDEAADPEEALEAEE----LLEALLAALERLPPRQREVLVLRYLEG--LSYAEIAEILGISEGTVKSRLSRARKKLR 172


                ....*....
gi 1710644  282 EAVQKEALE 290
Cdd:COG1595 173 EALEEEGAL 181
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 41-285 2.51e-03

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 38.68  E-value: 2.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644    41 YAEHGdRDAAHKLVTSHLRLVAKIAMGYRGYgLP----IGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEY 116
Cdd:PRK06986   2 YTAEG-KMDQDELVEQYAPLVKRIALRLKAR-LPasvdLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDE 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   117 iLRSWSLVKMGTTANQKRLFFNLRRLKGRIQ--AIDdgdlkpehvKEIATKLQVSEEEVISMnrRLHGDASLNAPIKASE 194
Cdd:PRK06986  80 -LRSLDWVPRSVRRNAREVAQAIRQLEQELGrePTD---------TEVAEKLGLSLEEYREM--LLDTNISQLFSIDELR 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   195 GESGQWQDWLVDDHESQEAVLIEQDELetrRRMLAKAMGVLNDRERRI-----FEArrlaedpVTLEELSSEFDISRERV 269
Cdd:PRK06986 148 GEHGDSILVTEDHQDEDPLQQLEDEEL---REALVEAIESLPEREQLVlslyyQEE-------LNLKEIGAVLGVSESRV 217

                        250
                 ....*....|....*.
gi 1710644   270 RQIEVRAFEKVQEAVQ 285
Cdd:PRK06986 218 SQIHSQAIKRLRARLG 233
BglG COG3711
Transcriptional antiterminator [Transcription];
159-266 3.99e-03

Transcriptional antiterminator [Transcription];


Pssm-ID: 442925 [Multi-domain]  Cd Length: 618  Bit Score: 38.69  E-value: 3.99e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644  159 VKEIATKLQVSEE----EVISMNRRLhgdASLNAPIKASEGeSGQWQDwlvddhesqeavlIEQDELETRRRMLAKAMGV 234
Cdd:COG3711  14 AKELAKKLNVSERtiryDIKKINEWL---KKNGLEIISKKG-IGFRLD-------------IDDEQKEKLLQLLEKSEDP 76

                        90       100       110
                ....*....|....*....|....*....|....
gi 1710644  235 LNDRERRIFEARRL--AEDPVTLEELSSEFDISR 266
Cdd:COG3711  77 LSPKERVAYILLRLllAGDPISLDDLAEELFVSR 110
PRK06930 PRK06930
positive control sigma-like factor; Validated
 206-286 6.04e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 37.02  E-value: 6.04e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1710644   206 DDHEsQEAVLIEQDeletrRRMLAKAMGVLNDRERRIFEARRlaEDPVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQ 285
Cdd:PRK06930  92 DIEE-PESVISEWD-----KIRIEDALSVLTEREKEVYLMHR--GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163


                 .
gi 1710644   286 K 286
Cdd:PRK06930 164 E 164
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH