NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2760432372|ref|WP_358096411|]
View 

ECF RNA polymerase sigma factor SigK [Nocardia asteroides]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK09646 super family cl32399
ECF RNA polymerase sigma factor SigK;
24-209 7.89e-81

ECF RNA polymerase sigma factor SigK;


The actual alignment was detected with superfamily member PRK09646:

Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 239.57  E-value: 7.89e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  24 ATAGPDRAVQARLVTLLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIG 103
Cdd:PRK09646    5 VPMTGPPAESPDLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARGSALA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 104 WLMMLTHRRAVDRVRAEQSATSRDLVFGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEV 183
Cdd:PRK09646   85 WLLTLAHRRAVDRVRSEQAASQREVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREV 164

                         170       180
                  ....*....|....*....|....*.
gi 2760432372 184 SETLAVPLPTVKSRIRDGLKRLENCL 209
Cdd:PRK09646  165 AERLAVPLGTVKTRMRDGLIRLRDCL 190
 
Name Accession Description Interval E-value
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
24-209 7.89e-81

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 239.57  E-value: 7.89e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  24 ATAGPDRAVQARLVTLLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIG 103
Cdd:PRK09646    5 VPMTGPPAESPDLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARGSALA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 104 WLMMLTHRRAVDRVRAEQSATSRDLVFGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEV 183
Cdd:PRK09646   85 WLLTLAHRRAVDRVRSEQAASQREVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREV 164

                         170       180
                  ....*....|....*....|....*.
gi 2760432372 184 SETLAVPLPTVKSRIRDGLKRLENCL 209
Cdd:PRK09646  165 AERLAVPLGTVKTRMRDGLIRLRDCL 190
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 39-211 2.92e-39

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: 133.20  E-value: 2.92e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  39 LLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDpDKASPIGWLMMLTHRRAVDRVR 118
Cdd:COG1595     7 LLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFR-GRGSFRAWLYRIARNLAIDHLR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 119 AEQSATsRDLVFGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRI 198
Cdd:COG1595    86 KRRRRR-ELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRL 164

                         170
                  ....*....|...
gi 2760432372 199 RDGLKRLENCLTG 211
Cdd:COG1595   165 SRARKKLREALEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 50-209 5.59e-33

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


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 116.29  E-value: 5.59e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  50 AFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKaSPIGWLMMLTHRRAVDRVRAEQSatSRDLV 129
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG-SFKAWLFRIARNLILDYLRRKRR--LRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 130 FGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRLENCL 209
Cdd:TIGR02937  79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 54-121 1.08e-12

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: 61.06  E-value: 1.08e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2760432372  54 FYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKA-SPIGWLMMLTHRRAVDRVRAEQ 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 ...
 153-205 1.07e-09

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: 52.49  E-value: 1.07e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2760432372 153 QSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRL 205
Cdd:cd06171     2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
 
Name Accession Description Interval E-value
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
24-209 7.89e-81

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 239.57  E-value: 7.89e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  24 ATAGPDRAVQARLVTLLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIG 103
Cdd:PRK09646    5 VPMTGPPAESPDLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARGSALA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 104 WLMMLTHRRAVDRVRAEQSATSRDLVFGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEV 183
Cdd:PRK09646   85 WLLTLAHRRAVDRVRSEQAASQREVRYGARNVDPAFDQVAEEVEARLERERVRDCLDALTDTQRESVTLAYYGGLTYREV 164

                         170       180
                  ....*....|....*....|....*.
gi 2760432372 184 SETLAVPLPTVKSRIRDGLKRLENCL 209
Cdd:PRK09646  165 AERLAVPLGTVKTRMRDGLIRLRDCL 190
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 39-211 2.92e-39

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: 133.20  E-value: 2.92e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  39 LLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDpDKASPIGWLMMLTHRRAVDRVR 118
Cdd:COG1595     7 LLERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFR-GRGSFRAWLYRIARNLAIDHLR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 119 AEQSATsRDLVFGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRI 198
Cdd:COG1595    86 KRRRRR-ELLDELAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRL 164

                         170
                  ....*....|...
gi 2760432372 199 RDGLKRLENCLTG 211
Cdd:COG1595   165 SRARKKLREALEE 177
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 39-209 5.28e-34

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 119.77  E-value: 5.28e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  39 LLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIGWLMMLTHRRAVDRVR 118
Cdd:PRK12534   15 LLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLAMIARNKAIDHLR 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 119 AEQSATSRDLVFGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRI 198
Cdd:PRK12534   95 ANAPQRRNVALDDAGELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWI 174

                         170
                  ....*....|.
gi 2760432372 199 RDGLKRLENCL 209
Cdd:PRK12534  175 RRGLAKLKACL 185
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 39-211 7.71e-34

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 119.78  E-value: 7.71e-34
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  39 LLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGdYDPDKASPIGWLMMLTHRRAVDRVR 118
Cdd:PRK12519   19 LFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSS-YDPKRGSLSSYLLTLTRSRAIDRLR 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 119 AEQSATSRDLVFGHTHLGRD-HDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSR 197
Cdd:PRK12519   98 SRRSRQRLLERWQQELLGEAsEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKAR 177

                         170
                  ....*....|....
gi 2760432372 198 IRDGLKRLENCLTG 211
Cdd:PRK12519  178 ARQGLLKLRELLQD 191
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 50-209 5.59e-33

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


Pssm-ID: 274357 [Multi-domain]  Cd Length: 158  Bit Score: 116.29  E-value: 5.59e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  50 AFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKaSPIGWLMMLTHRRAVDRVRAEQSatSRDLV 129
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG-SFKAWLFRIARNLILDYLRRKRR--LRREL 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 130 FGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRLENCL 209
Cdd:TIGR02937  79 DLLEELLDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 38-209 6.72e-31

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 111.45  E-value: 6.72e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  38 TLLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIGWLMMLTHRRAVDRV 117
Cdd:PRK12514    8 KLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIARNHAIDRL 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 118 RAEQSATSrDLVFGHtHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSR 197
Cdd:PRK12514   88 RARKAVAV-DIDEAH-DLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTW 165

                         170
                  ....*....|..
gi 2760432372 198 IRDGLKRLENCL 209
Cdd:PRK12514  166 LRRSLLKLRECL 177
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 44-215 6.15e-29

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 106.59  E-value: 6.15e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  44 ASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDpDKASPIGWLMMLTHRRAVD---RVRAE 120
Cdd:PRK11924    8 ATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN-GKGSARTWLLTIARNVCYDllrRRRRE 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 121 QSATSRDLvfGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRD 200
Cdd:PRK11924   87 KAVLSDDA--LEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRR 164

                         170
                  ....*....|....*
gi 2760432372 201 GLKRLENCLTGGNSR 215
Cdd:PRK11924  165 ARQLLRECLEAQWEA 179
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 42-207 1.44e-25

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 97.96  E-value: 1.44e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  42 EVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDkASPIGWLMMLTHRRAVDRVRAEQ 121
Cdd:PRK09652    3 RVQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGG-AAFYTWLYRIARNTAINYLRKQG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 122 S-------ATSRDLVFGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTV 194
Cdd:PRK09652   82 RrppasdvDAEEAEDFDLADALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTV 161

                         170
                  ....*....|...
gi 2760432372 195 KSRIRDGLKRLEN 207
Cdd:PRK09652  162 RSRIFRAREALRA 174
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 44-210 4.41e-24

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 94.07  E-value: 4.41e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  44 ASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIGWLMMLTHRRAVDRVRaeqsA 123
Cdd:PRK12537   18 ARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSARGWIYSVTRHLALNVLR----D 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 124 TSRDLVFGHTHLgrDHDSVAEEVTQRLDEQS----VQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIR 199
Cdd:PRK12537   94 TRREVVLDDDAE--ETAQTLHEIIDDFDLWAnsgkIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIK 171

                         170
                  ....*....|.
gi 2760432372 200 DGLKRLENCLT 210
Cdd:PRK12537  172 RSLKALRECMG 182
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 39-209 1.98e-22

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 89.97  E-value: 1.98e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  39 LLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIGWLMMLTHRRAVDRVR 118
Cdd:PRK13919   13 LLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLLALAHHAAVDHVR 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 119 -------AEQSATSRDLVFGHTHLGRDHDSvaeevtqRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPL 191
Cdd:PRK13919   93 rraarpqPLEPDEREPEAFDLPGPGLDEEG-------HLDRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPL 165

                         170
                  ....*....|....*...
gi 2760432372 192 PTVKSRIRDGLKRLENCL 209
Cdd:PRK13919  166 GTLKTRARRALSRLKEVL 183
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 39-207 1.33e-20

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 85.13  E-value: 1.33e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  39 LLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPD-KASPigWLMMLTHRRAVDRV 117
Cdd:PRK09641    8 LIKQVKKGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINrKFST--WLYRIATNLTIDRL 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 118 R---------AEQSATsrDLVFGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLA 188
Cdd:PRK09641   86 RkrkpdyyldAEVAGT--EGLTMYSQLAADDALPEEQVVSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILD 163

                         170       180
                  ....*....|....*....|...
gi 2760432372 189 VPLPTVKSRI---RDGL-KRLEN 207
Cdd:PRK09641  164 LPVGTVKTRIhrgREALrKQLRH 186
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
52-205 8.16e-20

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 82.43  E-value: 8.16e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  52 AEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIGWLMMLTHRRAVDRVRAEQsatSRDLVFG 131
Cdd:PRK09645   12 RALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERRSAR---ARPVEGG 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2760432372 132 HTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRL 205
Cdd:PRK09645   89 DDVLGVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRAL 162
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 38-211 4.68e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 80.93  E-value: 4.68e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  38 TLLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDpDKASPIGWLMMLTHRRAVDRV 117
Cdd:PRK12515   11 MLLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFE-GRSQVSTWLLSIARFKALSAL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 118 RAEQsatsrdlvfghtHLGRDHDSVA---------EEVTQRLDEQSV-QDCLDTMTDLQREAVALAYYSGRTYVEVSETL 187
Cdd:PRK12515   90 RRRK------------HEEIDDEAAAaiedgadtpEVALQKSDTSAAlRACLAKLSPAHREIIDLVYYHEKSVEEVGEIV 157

                         170       180
                  ....*....|....*....|....
gi 2760432372 188 AVPLPTVKSRIRDGLKRLENCLTG 211
Cdd:PRK12515  158 GIPESTVKTRMFYARKKLAELLKA 181
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 39-196 1.24e-17

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 77.00  E-value: 1.24e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  39 LLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIGWLMMLTHRRAVDRVR 118
Cdd:PRK05602   10 LLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEARFDTWLHRVVLNLCYDRLR 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2760432372 119 AEQSATSRDLvfghTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKS 196
Cdd:PRK05602   90 RRREVPVEDA----PDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALES 163
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 38-205 1.56e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 77.04  E-value: 1.56e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  38 TLLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPdKASPIGWLMMLTHRRAVDRV 117
Cdd:PRK12513   15 ALMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQP-RARFRTWLYQIARNLLIDHW 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 118 RAE--QSATSRDLVFGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVK 195
Cdd:PRK12513   94 RRHgaRQAPSLDADEQLHALADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVK 173

                         170
                  ....*....|
gi 2760432372 196 SRIRDGLKRL 205
Cdd:PRK12513  174 SRLRYALQKL 183
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 45-207 2.28e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 76.31  E-value: 2.28e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  45 SGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKaSPIGWLMMLTHR------------- 111
Cdd:PRK12543    3 SGDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR-PFRFWLIGLVIKqihswrrkrwrrf 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 112 RAVDRVRAEQSATSRDLvfghthlgrDHDSVAEEVTQRLdEQSVQDcldtMTDLQREAVALAYYSGRTYVEVSETLAVPL 191
Cdd:PRK12543   82 RIFEKAEEQRKPVSIDF---------SEDVLSKESNQEL-IELIHK----LPYKLRQVIILRYLHDYSQEEIAQLLQIPI 147

                         170
                  ....*....|....*.
gi 2760432372 192 PTVKSRIRDGLKRLEN 207
Cdd:PRK12543  148 GTVKSRIHAALKKLRQ 163
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 49-205 1.30e-16

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: 73.75  E-value: 1.30e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  49 TAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKaSPIGWLMMLTHRRAVDRVRaeqsatsrdl 128
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISE-SIKAYLFTIVKNRCLNYLR---------- 69

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 129 vfgHTHLGRDH-DSVAEEVTQRLDEQS-------------VQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTV 194
Cdd:TIGR02985  70 ---HKQVEEKYqEELAEIEERELSEADpeeeleakeleeiIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTV 146

                         170
                  ....*....|.
gi 2760432372 195 KSRIRDGLKRL 205
Cdd:TIGR02985 147 EYHITKALKFL 157
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 44-205 4.10e-15

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: 69.73  E-value: 4.10e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  44 ASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSlAGDYDPDKASPIGWLmmlthRRAVDRVRAEQSA 123
Cdd:TIGR02983   1 RSATEEEFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYV-RWDRIRDPDAPDAYV-----RRVLVNLARSRWR 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 124 TSRDLVFGHTHLGRDHdsVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLK 203
Cdd:TIGR02983  75 RRRLLELPTRELPDAA--APDPAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALA 152


                  ..
gi 2760432372 204 RL 205
Cdd:TIGR02983 153 RL 154
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 51-205 1.16e-14

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 68.82  E-value: 1.16e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  51 FAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQ----AWSlagdydpDKASPIGWLMMLTHRRAVDRVRAEQSATSR 126
Cdd:PRK09639    5 FEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRlyrsDFK-------GIENEKGWLIKSARNVAYNYLRSEKRRRAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 127 DL-VFGHTHLgrDHDSVAEEVTQRLDE-QSVQDCLDTMTDLQReAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKR 204
Cdd:PRK09639   78 ILgEFQWQEV--DNEPSPEEIWIRKEEiTKVQEVLAKMTERDR-TVLLLRFSGYSYKEIAEALGIKESSVGTTLARAKKK 154


                  .
gi 2760432372 205 L 205
Cdd:PRK09639  155 F 155
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 38-211 2.13e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 68.76  E-value: 2.13e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  38 TLLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIGWLMMLTHRRAVDRV 117
Cdd:PRK12524   15 ALLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEARVSTWLYRVVCNLCTDRL 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 118 RAEQSATSRDLvfGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSR 197
Cdd:PRK12524   95 RRRRRASVDLD--DAPEPADAAPGAEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESL 172

                         170
                  ....*....|....
gi 2760432372 198 IRDGLKRLENCLTG 211
Cdd:PRK12524  173 TARGKRALAALLAG 186
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 28-207 3.94e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 65.59  E-value: 3.94e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  28 PDRAVQARLVTLLGEVA-SGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIGWLM 106
Cdd:PRK12526   16 TDEQVPTELSQWLILVAiSRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGAATTWVY 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 107 MLTHRRAVD---RVRAEQSATSRDLVFGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEV 183
Cdd:PRK12526   96 TVMRNAAFDmlrKIKAKKEQNLGDDIWPIEQALAESQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQL 175

                         170       180
                  ....*....|....*....|....
gi 2760432372 184 SETLAVPLPTVKSRIRDGLKRLEN 207
Cdd:PRK12526  176 AQQLNVPLGTVKSRLRLALAKLKV 199
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 16-209 5.59e-13

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 65.19  E-value: 5.59e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  16 ADPAPACPATAGPDRAVQArlvtllGEVASGDrtafaEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYD 95
Cdd:PRK09647    6 VEPSDELTGTAVFDATGDK------ATMPSWE-----ELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQ 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  96 PDKASpiGWLMMLTHRRAVDRVRAEQSATsrdlvfgHTHLGRDHDSV-AEEVT-------QRLDEqSVQDCLDTMTDLQR 167
Cdd:PRK09647   75 PGTFE--GWLHRITTNLFLDMVRRRARIR-------MEALPEDYDRVpGDEPNpeqiyhdARLDP-DLQAALDSLPPEFR 144

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 2760432372 168 EAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRLENCL 209
Cdd:PRK09647  145 AAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 54-121 1.08e-12

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: 61.06  E-value: 1.08e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2760432372  54 FYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKA-SPIGWLMMLTHRRAVDRVRAEQ 121
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGvSFSTWLYTIIRNAIIDYLRKQR 69
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 53-206 2.45e-12

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 62.59  E-value: 2.45e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  53 EFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPigWLMMLTHRRAVDRVRAEQsatsRDLVFGH 132
Cdd:PRK09644    5 EIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQKVKP--WLFKVAYHTFIDFVRKEK----KVSFVGT 78

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2760432372 133 THLGRDH-DSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRLE 206
Cdd:PRK09644   79 DEIEAIQaESTEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLK 153
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 40-205 5.66e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 62.26  E-value: 5.66e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  40 LGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIGWLMMLTHRRAVDRVRA 119
Cdd:PRK12531   18 MEKVKSRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKSALSTWIYTIIRNLCFDLLRK 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 120 EQsatSRDLvfgHTHLGR------------DHDSVAEEVtqrLDEQsVQDCLDTMTDLQREAVALAYYSGRTYVEVSETL 187
Cdd:PRK12531   98 QK---GKDL---HIHADDiwpsdyyppdlvDHYSPEQDM---LKEQ-VMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMF 167

                         170
                  ....*....|....*...
gi 2760432372 188 AVPLPTVKSRIRDGLKRL 205
Cdd:PRK12531  168 DIPLGTVKSRLRLAVEKL 185
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 46-205 1.70e-11

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 60.42  E-value: 1.70e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  46 GDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPD-KASPigWLMMLTHRRAVDRVRAEQSAT 124
Cdd:PRK09638   15 GDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRsKFST--WLISIASRLYKDHLRKQKREK 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 125 SRDlvfghthlgrdhDSVAEEVTQRLDEQSVQ---DCLDTMTDLQ------REAVALAYYSGRTYVEVSETLAVPLPTVK 195
Cdd:PRK09638   93 LRL------------QRAKEETLRKEKWEAAIkgaEWSEMLDALSkldpefRAPVILKHYYGYTYEEIAKMLNIPEGTVK 160

                         170
                  ....*....|
gi 2760432372 196 SRIRDGLKRL 205
Cdd:PRK09638  161 SRVHHGIKQL 170
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 62-212 2.64e-11

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 60.15  E-value: 2.64e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  62 VFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDpDKASPIGWLMMLTHRRAVDRVRaeqSATSRDLVFGH---THLGRD 138
Cdd:PRK09415   29 VLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYK-GKSSLKTWLYRIAINHCKDYLK---SWHNKKVIVTEdifTYMESQ 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2760432372 139 HDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRLENCLTGG 212
Cdd:PRK09415  105 KESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEEE 178
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 46-198 1.42e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 57.81  E-value: 1.42e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  46 GDRTAFAEFYRATSPRVFGLALRVVRNHgAAEDITQEVFLQAW-SLAGDYDPDKASPigWLMMLTHRRAVDRVRaeQSAT 124
Cdd:PRK12518    8 GDRQSFRQLYRRYQQKVRSTLYQLCGRE-LLDDLVQEVFLRVWkGLPKLRNPAYFST--WLYRITWNVATDARR--QFAQ 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2760432372 125 SRDLVFGHTHLGRDHDSVAEEVTQRLD-EQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRI 198
Cdd:PRK12518   83 RPSRIQDDSLNDQPSRPSDTPDLMQLHyQDLVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRL 157
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 39-205 1.61e-10

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 58.18  E-value: 1.61e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  39 LLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDkASPIGWLMMLTHRRAVDRVR 118
Cdd:PRK09643   17 LLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRGD-AAVSSWLHRIVVNACLDRLR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 119 AEQS--ATSRDLVFGHTHLGRDHdsvAEEVTQRLDeqsVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKS 196
Cdd:PRK09643   96 RAKArpTVPLDDVYPVAQLERDP---TARVETALA---VQRALMRLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKS 169


                  ....*....
gi 2760432372 197 RIRDGLKRL 205
Cdd:PRK09643  170 RCARGRARL 178
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 63-211 5.23e-10

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 56.53  E-value: 5.23e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  63 FGLALRV-----VRNHGAAEDITQEVFLQAWSLAGDYDpDKASPIGWLMMLTHRRAVD--RVRAEQSATSRDLVFghthl 135
Cdd:PRK09637   10 YKAQLKAflhsrVSNEADVDDLLQEVLIKTHSNLHSLK-DGSSIKSWLYQIANNTIIDfyRKKNRSEELPDDLLF----- 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2760432372 136 grdHDS-VAEEVTQRLdEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRLENCLTG 211
Cdd:PRK09637   84 ---EDEeREENAKKEL-APCLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 153-205 1.07e-09

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: 52.49  E-value: 1.07e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2760432372 153 QSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRL 205
Cdd:cd06171     2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKL 54
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 1-211 1.45e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 56.02  E-value: 1.45e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372   1 MTNSPGAAPIRLRAVADPAPACPAtagPDRAVQARLVTLLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDIT 80
Cdd:PRK12538   18 TAPSPIVAEAPDAASVSIVPDPPP---VADAVFDEDEELLDRLATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVV 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  81 QEVFLQAWSLAGDYDPDKASPIGWLMMLTHRRAVDRVR----------AEQSATSRDLVfghTHLGRDHDS-VAEEVTQR 149
Cdd:PRK12538   95 QDTMLKVWTHRGRWQHGRAKFSTWLYRVVSNRCIDLRRkprtenvdavPEVADGKPDAV---SVIERNELSdLLEAAMQR 171

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2760432372 150 LDEQsvqdcldtmtdlQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRLENCLTG 211
Cdd:PRK12538  172 LPEQ------------QRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRR 221
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 158-205 7.04e-09

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 50.12  E-value: 7.04e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2760432372 158 CLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRL 205
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKL 48
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 153-205 1.55e-08

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: 49.38  E-value: 1.55e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2760432372 153 QSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRL 205
Cdd:pfam08281   2 EALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 52-209 2.43e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 51.89  E-value: 2.43e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  52 AEFYR---ATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPD---KAspigWLMMLTHRRAVDRVRAE-QSAT 124
Cdd:PRK12516   10 PPFKRellAALPSLRAFAVSLIGRHDRADDLVQDTIMKAWAKQDHFEVGtnmKA----WLFTILRNEFYSQMRKRgREVQ 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 125 SRDLVFGhthlgrdhDSVAEEVTQ--RLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGL 202
Cdd:PRK12516   86 DTDGMFT--------EQLAVHPSQygTLDLQDFRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRAR 157


                  ....*..
gi 2760432372 203 KRLENCL 209
Cdd:PRK12516  158 QRLQEIL 164
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 25-202 3.41e-08

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 51.58  E-value: 3.41e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  25 TAGPDRAVQArlvtLLGEVASGDRTAFAEFYRATSPRVFGLaLRVVRNHGAAEDITQEVFLQAWSLAGDYDpDKASPIGW 104
Cdd:PRK09649    4 TASDDEAVTA----LALSAAKGNGRALEAFIKATQQDVWRF-VAYLSDVGSADDLTQETFLRAIGAIPRFS-ARSSARTW 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 105 LMMLTHRRAVDRVRAEQsATSRDLVFGHTHLGRDHDSVAEEVTqrlDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVS 184
Cdd:PRK09649   78 LLAIARHVVADHIRHVR-SRPRTTRGARPEHLIDGDRHARGFE---DLVEVTTMIADLTTDQREALLLTQLLGLSYADAA 153

                         170       180
                  ....*....|....*....|.
gi 2760432372 185 ETLAVPLPTVKSRI---RDGL 202
Cdd:PRK09649  154 AVCGCPVGTIRSRVaraRDAL 174
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 39-198 4.69e-08

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 51.34  E-value: 4.69e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  39 LLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASpIGWLMMLT------HRR 112
Cdd:PRK11923   10 LVERVQRGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAF-YTWLYRIAintaknHLV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 113 AVDRVRAEQSATSRDL-VFGHTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPL 191
Cdd:PRK11923   89 SRGRRPPDSDVSSEDAeFYDGDHALKDIESPERALLRDEIEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPV 168


                  ....*..
gi 2760432372 192 PTVKSRI 198
Cdd:PRK11923  169 GTVRSRI 175
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 62-211 6.75e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 50.64  E-value: 6.75e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  62 VFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDpDKASPIGWLMMLTHRRAVDRVRAEQSATSRDLVFGHTHLGRD--- 138
Cdd:PRK12522   16 IYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLS-YVENYKKWITTICVRTFYDFYRKKKRWKDRILDLFHKEDGGEief 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2760432372 139 HDSV--AEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRLENCLTG 211
Cdd:PRK12522   95 ADDVniSEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 25-198 7.71e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 50.67  E-value: 7.71e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  25 TAGPDRAVQARLVTLLGEVASGDRTAFAEFYRATSPRVFGLaLRVVRNHGAAEDITQEVFLQAWSLAGDYdPDKASPIGW 104
Cdd:PRK12535    1 TMKSSERDDAHVTDLALAAGRGDRAALTEFIRETQDDVWRL-LAHLGGHDIADDLTQETYLRVMSALPRF-AARSSARTW 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 105 LMMLTHRRAVDRVRAE-----QSATSRDLVFGHTHLGRDHDSVAEEVtqrldeqSVQDCLDTMTDLQREAVALAYYSGRT 179
Cdd:PRK12535   79 LLSLARRVWVDNIRHDmarprKSATEYEDAAATTASNETTGSWSEWI-------DVRTLIDALPPERREALILTQVLGYT 151

                         170
                  ....*....|....*....
gi 2760432372 180 YVEVSETLAVPLPTVKSRI 198
Cdd:PRK12535  152 YEEAAKIADVRVGTIRSRV 170
Sig70_famx2 TIGR02952
RNA polymerase sigma-70 factor, TIGR02952 family; This group of sigma factors are members of ...
 39-187 7.35e-07

RNA polymerase sigma-70 factor, TIGR02952 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 a limited number of Gram-positive bacterial lineages.


Pssm-ID: 131997 [Multi-domain]  Cd Length: 170  Bit Score: 47.49  E-value: 7.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  39 LLGEVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIGWLMMLTHRRAVD--R 116
Cdd:TIGR02952   1 LLERAQDREEDAFARIYETYSDRVYRYIYYRVGCKYTAEDLTSEVFERVLRKIDSFKEQKNSFEAWLFTIARNVVNDyfR 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2760432372 117 VRAEQSATSRDLVfghTHLGRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETL 187
Cdd:TIGR02952  81 GSKRHPLFSLDVF---KELLSNEPNPEEAILKEEANEKLLKALKILTPKQQHVIALRFGQNLPIAEVARIL 148
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 60-209 9.39e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 47.18  E-value: 9.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  60 PRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPD---KAspigWLMMLTHRRAVDRVRAE-QSATSRDLVFghthl 135
Cdd:PRK12547   17 PALRAFAVSLSSKHDKAEDLVQDTLMKAWAKQDSFEMGtnlKA----WLFTILRNEFYSQMRKRgREVQDSDGVF----- 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2760432372 136 gRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRLENCL 209
Cdd:PRK12547   88 -TARVAVHPAQYGSLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELL 160
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 66-207 1.31e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 47.09  E-value: 1.31e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  66 ALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIgWLMMLTHRRAVDRVRAEQSATSRDLVFGHthLGRDHDSVAEE 145
Cdd:PRK12511   21 ARSLTRDSAEAEDLVHDALVRALERRASFRSGGNLRT-WLMSILHNAFIDELRRRRVEARRADELAV--LADASLPAAQE 97

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2760432372 146 VTQRLdeQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRI---RDGLKRLEN 207
Cdd:PRK12511   98 HAVRL--AQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIgraRAALRAFEE 160
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 23-197 1.82e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 46.88  E-value: 1.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  23 PATAGPDRAVQARlvtllgeVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDkASPI 102
Cdd:PRK11922   11 PLSAASDRELVAR-------VLAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFRGD-ASLS 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 103 GWLMMLTHRRAVDRVR-----------AEQSATSRDLVFGHTHLGRD-HDSVAEEVTQRLDEQSVqdclDTMTDLQREAV 170
Cdd:PRK11922   83 TWLSRIVLNEALGRLRrrrrlvnlaemVMASTIAGGERTPLADPAEDpERAAARREIRALLERAI----DALPDAFRAVF 158

                         170       180
                  ....*....|....*....|....*..
gi 2760432372 171 ALAYYSGRTYVEVSETLAVPLPTVKSR 197
Cdd:PRK11922  159 VLRVVEELSVEETAQALGLPEETVKTR 185
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 50-205 2.24e-06

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: 45.77  E-value: 2.24e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  50 AFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKaSPIGWLMMLthrrAVDRVRAEQSATSRD-L 128
Cdd:TIGR02989   2 AFVRLLTRHERALRAFVRSLVADRDDVDDVLQETFVVAWRKFDQFDPGT-NFVAWARGI----ARNKVLNYRRKLGRDrL 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 129 VFG---HTHLGRDHDSVAEEvTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTyvevSETLAVPLPTVKSRIRDGLKRL 205
Cdd:TIGR02989  77 VFDddlLEALAAEAEPTEAE-RLSDDRQALEGCLEKLPERQRELLDLRYQRGQK----ATALAEQTGRTVNAVYKALQRI 151
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 47-213 2.82e-05

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 43.39  E-value: 2.82e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  47 DRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDpDKASPIGWLMMLTHRRAVDRVRAE------ 120
Cdd:PRK09640   24 VTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFE-GKSKFKTWLYSITYNECITQYRKErrkrrl 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 121 QSATSRDLVfghthlgrdhDSVAEEVTQRLDEQSVQD-CLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIR 199
Cdd:PRK09640  103 MDALSLDPL----------EEASEEKAPKPEERGGLDrWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYK 172

                         170
                  ....*....|....
gi 2760432372 200 DGLKRLENCLTGGN 213
Cdd:PRK09640  173 RALDKLREKFAGLA 186
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 42-211 5.20e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 42.35  E-value: 5.20e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  42 EVASGDRTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAW-SLAGDYDPDKASPIGWLMMLTHRRAVDRVRAE 120
Cdd:PRK12542    2 KVTNNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYkNLEKLHSLNTQELKRYILRVAKNKAIDSYRKN 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 121 QsatsRDLVFGHTHLGRDHDSVAEEVTQ----RLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKS 196
Cdd:PRK12542   82 K----RHETFLEEYERESIEAVDENIEEwekrKMSEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRK 157

                         170
                  ....*....|....*
gi 2760432372 197 RIRDGLKRLENCLTG 211
Cdd:PRK12542  158 QFERARKRVQNMIGG 172
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 52-199 8.87e-05

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 42.26  E-value: 8.87e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  52 AEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQ-AWSLAGDYDpdkaSPIGWLMMLTHRRAVDRVRAEQSATSRDLVF 130
Cdd:PRK09635    8 SAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRlLRAPVGDID----DERGWLIVVTSRLCLDHIKSASTRRERPQDI 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2760432372 131 GHTHLGRDHDSV---AEEVTqrLDEQ---SVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIR 199
Cdd:PRK09635   84 AAWHDGDASVSSvdpADRVT--LDDEvrlALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAH 156
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 60-205 1.31e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 41.36  E-value: 1.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  60 PRVFGLALRVVRNHGAAEDITQEVFLQAWSlagdyDPDKASP----IGWLMMLTHRR--AVDRVRAEQSATSRDLVFGHT 133
Cdd:PRK12546   18 PALRAFAISLTRNVAVADDLVQDTIVKAWT-----NFDKFQEgtnlRAWLFTILRNTfySDRRKHKREVPDPEGVHAASL 92

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2760432372 134 HLGRDHDSvaeevtqRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRL 205
Cdd:PRK12546   93 AVKPAHDG-------RLAMSDFRAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRARARL 157
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 48-207 5.82e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 39.15  E-value: 5.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  48 RTAFAEFYRATSPRVFGLALRVVRNHGAAEDITQEVFLQAWSLAGDYDPDKASPigWLMMLTHRRAVDRVRAEQSATSRD 127
Cdd:PRK12541    4 KQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEEIRP--WLFTIAYNAFIDWYRKEKKYKTTT 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 128 LVFGHThlgRDHDSVAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKRLEN 207
Cdd:PRK12541   82 IEEFHL---PNVPSTEHEYFIKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 56-203 5.94e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 39.28  E-value: 5.94e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  56 RATSPRVFGLALRVVRNHGAAEDITQEVFLQAW-SLAGDYDpDKASPiGWLMMLTHRRAVDRVRAEQSatsrDLVFGHTH 134
Cdd:PRK12517   30 KALHADIYRYAYWLCKDKHIAEDLVQETFLRAWrSLDSLKD-EKAAK-AWLITILRRENARRFERKQF----DLVDIEDD 103

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2760432372 135 LGRDHDSVAEEvtQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRI---RDGLK 203
Cdd:PRK12517  104 SIEDDASHSSE--EEMEQEWLRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLfraRNQLK 173
PRK06930 PRK06930
positive control sigma-like factor; Validated
 110-207 1.48e-03

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 37.79  E-value: 1.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 110 HRRAVDRVRAEQSATSRD------LVFGHTHLGRDHDSVAEEVTQRlDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEV 183
Cdd:PRK06930   58 NRRGIDRRAAYQREVICDplliqrYFRSMEDLEWDIEEPESVISEW-DKIRIEDALSVLTEREKEVYLMHRGYGLSYSEI 136

                          90       100
                  ....*....|....*....|....
gi 2760432372 184 SETLAVPLPTVKSRIRDGLKRLEN 207
Cdd:PRK06930  137 ADYLNIKKSTVQSMIERAEKKIAR 160
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 75-204 2.09e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 37.62  E-value: 2.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  75 AAEDITQEVFLQAWSLagdydPDKAS---PIGWLMMLTHRRAVDRVRAE--QSATSRDLVFGHTHLgrdHDSvAEEVTQR 149
Cdd:PRK12525   35 SAEDIASETFLQVLAL-----PDPASirePRALLTTIARRLMYEGWRRQdlERAYLQSLAEAPEAV---QPS-PEEQWMV 105

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2760432372 150 LDE-QSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRIRDGLKR 204
Cdd:PRK12525  106 IETlLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKC 161
PRK12545 PRK12545
RNA polymerase factor sigma-70;
70-125 3.61e-03

RNA polymerase factor sigma-70;


Pssm-ID: 183584 [Multi-domain]  Cd Length: 201  Bit Score: 37.24  E-value: 3.61e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2760432372  70 VRNHGAAEDITQEVFLQAWSLAGDYDPDKASPIgWLMMLTHRRAVDRVRAEQSATS 125
Cdd:PRK12545   29 LRDADAAEDAVQEALAAAWSQAGRFAGQSAHKT-WVFGILRNKLIDTLRARQRTVN 83
PRK12512 PRK12512
RNA polymerase sigma factor; Provisional
 46-205 3.89e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171551 [Multi-domain]  Cd Length: 184  Bit Score: 36.98  E-value: 3.89e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372  46 GDRTAFAEFYRATSPRVFGLALRVVRNHGA----AEDITQEVFLQAWSLAGDYDPDkaSPIG-WLMMLTHRRAVD--RVR 118
Cdd:PRK12512   19 GDAAAYRRLLKAVTPVLRAAARRGLARAGQpadqAEDIVQEILLAVHLKRHTWDPG--APFApWLFAIARNKLIDalRRR 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2760432372 119 AEQSATSRDLVFGHTHlgrdhdsvAEEVTQRLDEQSVQDCLDTMTDLQREAVALAYYSGRTYVEVSETLAVPLPTVKSRI 198
Cdd:PRK12512   97 GRRVFVDIDDFAETLP--------AEPATETLPAGDVGRHLETLPPRQRDVVQSISVEGASIKETAAKLSMSEGAVRVAL 168


                  ....*..
gi 2760432372 199 RDGLKRL 205
Cdd:PRK12512  169 HRGLAAL 175
 
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