NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|2537604820|ref|WP_294122708|]
View 

MULTISPECIES: sigma-70 family RNA polymerase sigma factor [unclassified Pseudoalteromonas]

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
PRK12514 super family cl30921
RNA polymerase sigma factor; Provisional
 1-172 3.46e-50

RNA polymerase sigma factor; Provisional


The actual alignment was detected with superfamily member PRK12514:

Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 159.60  E-value: 3.46e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   1 MDNDDLLPLLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVR 80
Cdd:PRK12514    1 TQPDDIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIAR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  81 YRSLDSLRYHKVRKEQ-----SLGDDEYENECIDVNYDEETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLG 155
Cdd:PRK12514   81 NHAIDRLRARKAVAVDideahDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLN 160

                         170
                  ....*....|....*..
gi 2537604820 156 TVKSWIRRGLMQLQRCL 172
Cdd:PRK12514  161 TMRTWLRRSLLKLRECL 177
 
Name Accession Description Interval E-value
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 1-172 3.46e-50

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 159.60  E-value: 3.46e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   1 MDNDDLLPLLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVR 80
Cdd:PRK12514    1 TQPDDIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIAR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  81 YRSLDSLRYHKVRKEQ-----SLGDDEYENECIDVNYDEETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLG 155
Cdd:PRK12514   81 NHAIDRLRARKAVAVDideahDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLN 160

                         170
                  ....*....|....*..
gi 2537604820 156 TVKSWIRRGLMQLQRCL 172
Cdd:PRK12514  161 TMRTWLRRSLLKLRECL 177
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-173 8.11e-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: 130.50  E-value: 8.11e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   1 MDNDDLLplLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNaSKGTVISWMISIVR 80
Cdd:COG1595     1 MSSDEEL--LERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFR-GRGSFRAWLYRIAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  81 YRSLDSLRYHKVRKE------QSLGDDEYENECIDVNYDEETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPL 154
Cdd:COG1595    78 NLAIDHLRKRRRRRElldelaEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                         170
                  ....*....|....*....
gi 2537604820 155 GTVKSWIRRGLMQLQRCLT 173
Cdd:COG1595   158 GTVKSRLSRARKKLREALE 176
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 19-172 1.96e-28

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: 103.20  E-value: 1.96e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  19 NAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNaSKGTVISWMISIVRYRSLDSLRyhKVRKEQSL 98
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFD-PEGSFKAWLFRIARNLILDYLR--RKRRLRRE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  99 GDDEYENECIDVNYDEET-------KLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQRC 171
Cdd:TIGR02937  78 LDLLEELLDSDPSPEEELeqeeereALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157


                  .
gi 2537604820 172 L 172
Cdd:TIGR02937 158 L 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 24-91 1.34e-09

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


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 51.82  E-value: 1.34e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2537604820  24 LYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGT-VISWMISIVRYRSLDSLRYHK 91
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVsFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 116-169 2.40e-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: 48.25  E-value: 2.40e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2537604820 116 TKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQ 169
Cdd:cd06171     2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 1-172 3.46e-50

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 159.60  E-value: 3.46e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   1 MDNDDLLPLLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVR 80
Cdd:PRK12514    1 TQPDDIEKLIVRVSLGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIAR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  81 YRSLDSLRYHKVRKEQ-----SLGDDEYENECIDVNYDEETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLG 155
Cdd:PRK12514   81 NHAIDRLRARKAVAVDideahDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLN 160

                         170
                  ....*....|....*..
gi 2537604820 156 TVKSWIRRGLMQLQRCL 172
Cdd:PRK12514  161 TMRTWLRRSLLKLRECL 177
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 2-172 1.32e-46

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 150.59  E-value: 1.32e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   2 DNDDLLPLLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVRY 81
Cdd:PRK12534    8 DDDETGRLLTATAGGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLAMIARN 87

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  82 RSLDSLRYHKVRKEQSLGDDEYENECIDVNYDEET-------KLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPL 154
Cdd:PRK12534   88 KAIDHLRANAPQRRNVALDDAGELRAADASPLERTerastrrRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPI 167

                         170
                  ....*....|....*...
gi 2537604820 155 GTVKSWIRRGLMQLQRCL 172
Cdd:PRK12534  168 GTVKSWIRRGLAKLKACL 185
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 10-173 3.35e-44

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 144.15  E-value: 3.35e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  10 LCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVRYRSLDSLRY 89
Cdd:PRK12537   14 LLACARGDRRALQALYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSARGWIYSVTRHLALNVLRD 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  90 HkvRKEQSLGDDEYENECIDVNYDEE-------TKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIR 162
Cdd:PRK12537   94 T--RREVVLDDDAEETAQTLHEIIDDfdlwansGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIK 171

                         170
                  ....*....|.
gi 2537604820 163 RGLMQLQRCLT 173
Cdd:PRK12537  172 RSLKALRECMG 182
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
2-172 2.76e-41

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 137.11  E-value: 2.76e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   2 DNDDLLPLLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVRY 81
Cdd:PRK09646   13 ESPDLDALLRRVARGDQDAFAELYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARGSALAWLLTLAHR 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  82 RSLDslryhKVRKEQSLGDDE--YENECIDVNYDEETKLV----------NCIEQLEPQQKQAIHLAYYKGLSHSELVDH 149
Cdd:PRK09646   93 RAVD-----RVRSEQAASQREvrYGARNVDPAFDQVAEEVearlerervrDCLDALTDTQRESVTLAYYGGLTYREVAER 167

                         170       180
                  ....*....|....*....|...
gi 2537604820 150 IETPLGTVKSWIRRGLMQLQRCL 172
Cdd:PRK09646  168 LAVPLGTVKTRMRDGLIRLRDCL 190
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-173 8.11e-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: 130.50  E-value: 8.11e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   1 MDNDDLLplLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNaSKGTVISWMISIVR 80
Cdd:COG1595     1 MSSDEEL--LERLRAGDEAAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFR-GRGSFRAWLYRIAR 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  81 YRSLDSLRYHKVRKE------QSLGDDEYENECIDVNYDEETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPL 154
Cdd:COG1595    78 NLAIDHLRKRRRRRElldelaEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISE 157

                         170
                  ....*....|....*....
gi 2537604820 155 GTVKSWIRRGLMQLQRCLT 173
Cdd:COG1595   158 GTVKSRLSRARKKLREALE 176
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 9-172 3.57e-36

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 123.54  E-value: 3.57e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   9 LLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNaSKGTVISWMISIVRYRSLDSLR 88
Cdd:PRK11924    3 LMPVDATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLFN-GKGSARTWLLTIARNVCYDLLR 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  89 YHKVRKEQSLGDDEYENECIDVNYDEETKLVN--------CIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSW 160
Cdd:PRK11924   82 RRRREKAVLSDDALEPEFAETAETPEAALLAKddlaridrCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSR 161

                         170
                  ....*....|..
gi 2537604820 161 IRRGLMQLQRCL 172
Cdd:PRK11924  162 LRRARQLLRECL 173
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 9-172 1.65e-33

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 117.47  E-value: 1.65e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   9 LLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASeYNASKGTVISWMISIVRYRSLDSLR 88
Cdd:PRK12519   19 LFSALKAGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSS-YDPKRGSLSSYLLTLTRSRAIDRLR 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  89 YHKVRK------EQSLGDDEYENECID-VNYDEETKLV-NCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSW 160
Cdd:PRK12519   98 SRRSRQrllerwQQELLGEASEDTPLEqASLAERSQRVqTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKAR 177

                         170
                  ....*....|..
gi 2537604820 161 IRRGLMQLQRCL 172
Cdd:PRK12519  178 ARQGLLKLRELL 189
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 9-172 7.80e-33

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 115.40  E-value: 7.80e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   9 LLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVRYRSLDSLR 88
Cdd:PRK13919   13 LLALVARGEEEALRALFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLLALAHHAAVDHVR 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  89 YHKVRKeQSLGDDEYENECIDV---NYDEE-----TKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSW 160
Cdd:PRK13919   93 RRAARP-QPLEPDEREPEAFDLpgpGLDEEghldrTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTR 171

                         170
                  ....*....|..
gi 2537604820 161 IRRGLMQLQRCL 172
Cdd:PRK13919  172 ARRALSRLKEVL 183
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 19-172 1.96e-28

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: 103.20  E-value: 1.96e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  19 NAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNaSKGTVISWMISIVRYRSLDSLRyhKVRKEQSL 98
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFD-PEGSFKAWLFRIARNLILDYLR--RKRRLRRE 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  99 GDDEYENECIDVNYDEET-------KLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQRC 171
Cdd:TIGR02937  78 LDLLEELLDSDPSPEEELeqeeereALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLREL 157


                  .
gi 2537604820 172 L 172
Cdd:TIGR02937 158 L 158
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 17-169 1.59e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 91.79  E-value: 1.59e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  17 DKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVRYRSLDSLRYHKVRKEQ 96
Cdd:PRK12526   36 DKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKGAATTWVYTVMRNAAFDMLRKIKAKKEQ 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  97 SLGDD----------EYENECIDVNYDEETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLM 166
Cdd:PRK12526  116 NLGDDiwpieqalaeSQSESEEFSDHLMDKQILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALA 195


                  ...
gi 2537604820 167 QLQ 169
Cdd:PRK12526  196 KLK 198
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 13-170 1.80e-20

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 83.32  E-value: 1.80e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  13 TAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNAsKGTVISWMISIVRYRSLDSLRYHKV 92
Cdd:PRK09652    4 VQRGDRAAFALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRG-GAAFYTWLYRIARNTAINYLRKQGR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  93 RKEQSLGD-DEYENECI-DVNYDEET------------KLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVK 158
Cdd:PRK09652   83 RPPASDVDaEEAEDFDLaDALRDISTpenellsaeleqRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVR 162

                         170
                  ....*....|..
gi 2537604820 159 SWIRRGLMQLQR 170
Cdd:PRK09652  163 SRIFRAREALRA 174
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 9-159 4.81e-19

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 79.78  E-value: 4.81e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   9 LLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNAsKGTVISWMISIVRYRSLDSLR 88
Cdd:PRK12515   12 LLARIAQGDRTAMQTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEG-RSQVSTWLLSIARFKALSALR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  89 YhkvRKEQSLgDDEYENECIDVNYDEETK---------LVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKS 159
Cdd:PRK12515   91 R---RKHEEI-DDEAAAAIEDGADTPEVAlqksdtsaaLRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKT 166
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 19-168 2.94e-18

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: 76.83  E-value: 2.94e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  19 NAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKgTVISWMISIVRYRSLDSLRYHKVRKE--- 95
Cdd:TIGR02985   1 EAFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISE-SIKAYLFTIVKNRCLNYLRHKQVEEKyqe 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2537604820  96 --QSLGDDEYENECI--DVNYDE-ETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQL 168
Cdd:TIGR02985  80 elAEIEERELSEADPeeELEAKElEEIIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFL 157
PRK09643 PRK09643
RNA polymerase sigma factor SigM; Reviewed
 9-173 1.49e-17

RNA polymerase sigma factor SigM; Reviewed


Pssm-ID: 236604 [Multi-domain]  Cd Length: 192  Bit Score: 75.90  E-value: 1.49e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   9 LLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNAsKGTVISWMISIVRYRSLDSLR 88
Cdd:PRK09643   17 LLAAHVAGDRYAFGELFRRHHRRLWAVARRTSGTREDAADALQDAMLSAHRAAGSFRG-DAAVSSWLHRIVVNACLDRLR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  89 YHKVRKEQSLgDDEYENECIDVNYDEETKLVNCIEQ----LEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRG 164
Cdd:PRK09643   96 RAKARPTVPL-DDVYPVAQLERDPTARVETALAVQRalmrLPVEQRAALVAVDMQGYSVADAARMLGVAEGTVKSRCARG 174


                  ....*....
gi 2537604820 165 LMQLQRCLT 173
Cdd:PRK09643  175 RARLAELLG 183
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 2-172 1.94e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 73.74  E-value: 1.94e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   2 DNDDLLPLLcatAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVRY 81
Cdd:PRK12538   49 EDEELLDRL---ATDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRAKFSTWLYRVVSN 125

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  82 RSLDSLRYHKVRKEQSLGD--DEYENECIDVNYDEETKLV-NCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVK 158
Cdd:PRK12538  126 RCIDLRRKPRTENVDAVPEvaDGKPDAVSVIERNELSDLLeAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVE 205

                         170
                  ....*....|....
gi 2537604820 159 SWIRRGLMQLQRCL 172
Cdd:PRK12538  206 SLLKRGRQQLRDLL 219
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 9-172 2.43e-16

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 72.80  E-value: 2.43e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   9 LLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNaSKGTVISWMISIVRYRSLDSLR 88
Cdd:PRK12513   16 LMLRYRAGDAAAFEALYARHRTGLYRFLLRLARDRALAEDIFQETWLRVIRARAQYQ-PRARFRTWLYQIARNLLIDHWR 94

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  89 YHKVRKEQSLGDDEYENECIDVNYDEETKLVNC---------IEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKS 159
Cdd:PRK12513   95 RHGARQAPSLDADEQLHALADDGAAPEQQLSLFrdrrrlqaaLETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKS 174

                         170
                  ....*....|...
gi 2537604820 160 WIRRGLMQLQRCL 172
Cdd:PRK12513  175 RLRYALQKLRELL 187
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 1-173 4.16e-16

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 71.99  E-value: 4.16e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   1 MDNDDLLPLLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVR 80
Cdd:PRK05602    2 MDADPDEELLARVAAGDPAAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEARFDTWLHRVVL 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  81 YRSLDSLRYHKVRKEQSLGDDEYENECIDVNY--DEETKLVN-CIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTV 157
Cdd:PRK05602   82 NLCYDRLRRRREVPVEDAPDVPDPAPGPDAGLeaRQRARRVEqALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDAL 161

                         170
                  ....*....|....*.
gi 2537604820 158 KSWIRRGLMQLQRCLT 173
Cdd:PRK05602  162 ESLLARGRRALRAQLA 177
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 17-169 1.29e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 70.73  E-value: 1.29e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  17 DKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVRYRSLDSLRYHKVRKEQ 96
Cdd:PRK12531   25 DKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKSALSTWIYTIIRNLCFDLLRKQKGKDLH 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  97 SLGDD-----EYENECIDvNYDEETKL-----VNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLM 166
Cdd:PRK12531  105 IHADDiwpsdYYPPDLVD-HYSPEQDMlkeqvMKFLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVE 183


                  ...
gi 2537604820 167 QLQ 169
Cdd:PRK12531  184 KLR 186
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 15-164 3.30e-15

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 69.72  E-value: 3.30e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  15 QGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKgTVISWMISIVRYRSLDSLRyhKVRK 94
Cdd:PRK09641   14 KGDQNAFAELVDLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR-KFSTWLYRIATNLTIDRLR--KRKP 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  95 EQSLGDDEYENECIDVnYDE--------ETKLVNC---------IEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTV 157
Cdd:PRK09641   91 DYYLDAEVAGTEGLTM-YSQlaaddalpEEQVVSLelqetiqeaILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTV 169


                  ....*..
gi 2537604820 158 KSWIRRG 164
Cdd:PRK09641  170 KTRIHRG 176
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
23-172 2.57e-14

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 67.03  E-value: 2.57e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  23 SLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVRYRSLDSLRYHKVRKEQSlGDDE 102
Cdd:PRK09645   13 ALYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERRSARARPVEG-GDDV 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2537604820 103 YENECIDVNYDEETKL-----VNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQRCL 172
Cdd:PRK09645   92 LGVPEQSAPDEVDRALdrllvADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 9-164 1.20e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 65.68  E-value: 1.20e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   9 LLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVRYRSLDSLR 88
Cdd:PRK12524   16 LLVLYANGDPAAARALTLRLAPRALAVATRVLGDRAEAEDVTQEAMLRLWRIAPDWRQGEARVSTWLYRVVCNLCTDRLR 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  89 YHKVRKEQSLGDDEYEN-----ECIDVNYDEETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRR 163
Cdd:PRK12524   96 RRRRASVDLDDAPEPADaapgaEEALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVESLTAR 175


                  .
gi 2537604820 164 G 164
Cdd:PRK12524  176 G 176
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 15-170 2.28e-13

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 64.66  E-value: 2.28e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  15 QGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNA-SKGTviSWMISIVRYRSLDSLRYHKvr 93
Cdd:PRK09638   14 KGDDAALTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGrSKFS--TWLISIASRLYKDHLRKQK-- 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  94 KEQSLgDDEYENECIDVNYDEE-------TKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLM 166
Cdd:PRK09638   90 REKLR-LQRAKEETLRKEKWEAaikgaewSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIK 168


                  ....
gi 2537604820 167 QLQR 170
Cdd:PRK09638  169 QLRK 172
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 24-169 8.84e-12

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 59.89  E-value: 8.84e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  24 LYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKgtVISWMISIVRYRSLDSLRYHKvrKEQSLGDDEY 103
Cdd:PRK09644    6 IYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQK--VKPWLFKVAYHTFIDFVRKEK--KVSFVGTDEI 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2537604820 104 EN------ECIDVNYDEETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQ 169
Cdd:PRK09644   82 EAiqaestEEYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLK 153
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 16-169 1.20e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 60.13  E-value: 1.20e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  16 GDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKgTVISWMISIV-----RYRSLDSLRYH 90
Cdd:PRK12543    4 GDQEAFSEIYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNR-PFRFWLIGLVikqihSWRRKRWRRFR 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  91 KVRKEQSLGDDE-YENECIDVNYDEETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQ 169
Cdd:PRK12543   83 IFEKAEEQRKPVsIDFSEDVLSKESNQELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLR 162
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 21-168 7.92e-10

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 54.96  E-value: 7.92e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  21 FSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTvisWMISIVRYRSLDSLRYHKVRKEQSLGD 100
Cdd:PRK09639    5 FEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFKGIENEKG---WLIKSARNVAYNYLRSEKRRRARILGE 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2537604820 101 DEYENECID------VNYDEETKLV-NCIEQLEPQQKQAIHLAyYKGLSHSELVDHIETPLGTVKSWIRRGLMQL 168
Cdd:PRK09639   82 FQWQEVDNEpspeeiWIRKEEITKVqEVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVGTTLARAKKKF 155
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 16-169 1.14e-09

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 54.56  E-value: 1.14e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  16 GDKNAFSSLYQQTSGKLFAI---SLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVRYRSLDSLRyhKV 92
Cdd:PRK06811   15 KNEKALEFIVDTYGNLVKKIvhkVLGTVNYSQLIEECVNDIFLSIWNNIDKFDEEKGSFKKWIAAISKYKAIDYKR--KL 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  93 RKEQSLGD-DEY--------ENECIDVNYDEEtkLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRR 163
Cdd:PRK06811   93 TKNNEIDSiDEFiliseesiENEIILKENKEE--ILKLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSR 170


                  ....*.
gi 2537604820 164 GLMQLQ 169
Cdd:PRK06811  171 GRKKLQ 176
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 24-91 1.34e-09

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


Pssm-ID: 427998 [Multi-domain]  Cd Length: 71  Bit Score: 51.82  E-value: 1.34e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2537604820  24 LYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKGT-VISWMISIVRYRSLDSLRYHK 91
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVsFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 117-168 5.54e-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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 49.76  E-value: 5.54e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2537604820 117 KLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQL 168
Cdd:pfam08281   3 ALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 23-164 1.51e-08

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 51.52  E-value: 1.51e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  23 SLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNaSKGTVISWMISIVRYRSLDSlrYHKVRKEQSLGDDE 102
Cdd:PRK09637    5 SIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLK-DGSSIKSWLYQIANNTIIDF--YRKKNRSEELPDDL 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2537604820 103 -YENECIDVNYDEEtkLVNCIE----QLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRG 164
Cdd:PRK09637   82 lFEDEEREENAKKE--LAPCLRpfidALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRG 146
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 116-169 2.40e-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: 48.25  E-value: 2.40e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2537604820 116 TKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQ 169
Cdd:cd06171     2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 14-172 6.36e-08

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 50.17  E-value: 6.36e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  14 AQGDKNAFSS---LYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNAskGTVISWMISIVRYRSLDSLRYH 90
Cdd:PRK09647   20 ATGDKATMPSweeLVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQP--GTFEGWLHRITTNLFLDMVRRR 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  91 -KVRKEqSLGDDeYEN--------ECI--DVNYDEEtkLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKS 159
Cdd:PRK09647   98 aRIRME-ALPED-YDRvpgdepnpEQIyhDARLDPD--LQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRS 173

                         170
                  ....*....|...
gi 2537604820 160 WIRRGLMQLQRCL 172
Cdd:PRK09647  174 RIHRGRQQLRAAL 186
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 2-164 7.42e-08

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 49.65  E-value: 7.42e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   2 DNDDLLPLLCATAQGDKNAFSSLYQQTSGKLFAIsLNMLTNRAHAEEALQDAFIKIWhNASEYNASKGTVISWMISIVRY 81
Cdd:PRK09649    7 DDEAVTALALSAAKGNGRALEAFIKATQQDVWRF-VAYLSDVGSADDLTQETFLRAI-GAIPRFSARSSARTWLLAIARH 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  82 RSLDSLRYHKVRKEQSLgdDEYENECIDVN-----YDEETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGT 156
Cdd:PRK09649   85 VVADHIRHVRSRPRTTR--GARPEHLIDGDrhargFEDLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGT 162


                  ....*...
gi 2537604820 157 VKSWIRRG 164
Cdd:PRK09649  163 IRSRVARA 170
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 15-163 1.39e-07

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 49.03  E-value: 1.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  15 QGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNaSKGTVISWMISIvryrSLDSLRYHKVRK 94
Cdd:PRK11923   16 RGDKRAFDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFR-GDSAFYTWLYRI----AINTAKNHLVSR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  95 -------EQSLGDDEY---ENECIDVNYDE--------ETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGT 156
Cdd:PRK11923   91 grrppdsDVSSEDAEFydgDHALKDIESPErallrdeiEGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGT 170


                  ....*..
gi 2537604820 157 VKSWIRR 163
Cdd:PRK11923  171 VRSRIFR 177
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
1-168 7.91e-07

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 47.03  E-value: 7.91e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   1 MDNDDLLPLLCATAQGDKNAFSSLYQQTSGKLFAISLNML----TNRAHAEEALQDAFIKIWHNASEYNASKgTVISWMI 76
Cdd:PRK12539    3 SQENELKALMLASLDGDAAAHRALLERLSGHLRAYYKGKLarigRGAEEAEDLVQEALMAIHTRRHTYDPEQ-PLTPWVY 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  77 SIVRYRSLDSLRyhkvRKEQSLGD---DEYENECI-DVNYDEETK--LVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHI 150
Cdd:PRK12539   82 AIARYKLIDHLR----RTRASLADvpiDDADELVAhDDHAAVESTldLGRLLARLPEKMRLAIQAVKLEGLSVAEAATRS 157

                         170
                  ....*....|....*...
gi 2537604820 151 ETPLGTVKSWIRRGLMQL 168
Cdd:PRK12539  158 GMSESAVKVSVHRGLKAL 175
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 42-170 1.67e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 45.93  E-value: 1.67e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  42 NRAHAEEALQDAFIKiwhnASEYNAS---KGTVISWMISIVRYRSLDSLRYHKVRKEQSLGDDEYENECIDVNYDEETKL 118
Cdd:PRK12511   27 DSAEAEDLVHDALVR----ALERRASfrsGGNLRTWLMSILHNAFIDELRRRRVEARRADELAVLADASLPAAQEHAVRL 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2537604820 119 V---NCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQR 170
Cdd:PRK12511  103 AqirDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157
PRK12546 PRK12546
RNA polymerase sigma factor; Provisional
 33-169 2.40e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139055 [Multi-domain]  Cd Length: 188  Bit Score: 45.60  E-value: 2.40e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  33 FAISLNmlTNRAHAEEALQDAFIKIWHNASEYNAskGTVI-SWMISIVRYRSLDSLRYHKVRKEQSLGDdeyENECIDVN 111
Cdd:PRK12546   23 FAISLT--RNVAVADDLVQDTIVKAWTNFDKFQE--GTNLrAWLFTILRNTFYSDRRKHKREVPDPEGV---HAASLAVK 95

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2537604820 112 YDEETKLV-----NCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRG------LMQLQ 169
Cdd:PRK12546   96 PAHDGRLAmsdfrAAFAQLPDEQREALILVGASGFSYEEAAEMCGVAVGTVKSRANRArarlaeLLQLE 164
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 38-164 2.51e-06

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 45.51  E-value: 2.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  38 NMLTNRAHAEEALQDAFIKIWHNASEYNaSKGTVISWMISIVRYRSLDSLRYHKVRKEQSLGDDEYEN-------ECIDV 110
Cdd:PRK09415   35 SYVKNKEVAEDLTQEIFVKCYKSLHTYK-GKSSLKTWLYRIAINHCKDYLKSWHNKKVIVTEDIFTYMesqkesvEEEVI 113

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2537604820 111 NYDEETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRG 164
Cdd:PRK09415  114 QNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKA 167
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 17-169 3.11e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 45.43  E-value: 3.11e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  17 DKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASE-YNASKGTVISWMISIVRYRSLDSLRYHKvRKE 95
Cdd:PRK12542    7 DYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKlHSLNTQELKRYILRVAKNKAIDSYRKNK-RHE 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  96 QSLGDDEYEN-ECIDVNYDE-------ETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQ 167
Cdd:PRK12542   86 TFLEEYERESiEAVDENIEEwekrkmsEVQIDTLLKELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKR 165


                  ..
gi 2537604820 168 LQ 169
Cdd:PRK12542  166 VQ 167
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 29-172 8.31e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 44.19  E-value: 8.31e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  29 SGKLFAISLnmlTNRAH-AEEALQDAFIKIWhnASEYNASKGTVI-SWMISIVRYRSLDSLRyhKVRKEQSLGDDEYeNE 106
Cdd:PRK12516   22 SLRAFAVSL---IGRHDrADDLVQDTIMKAW--AKQDHFEVGTNMkAWLFTILRNEFYSQMR--KRGREVQDTDGMF-TE 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2537604820 107 CIDVNYDEETKL-----VNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQRCL 172
Cdd:PRK12516   94 QLAVHPSQYGTLdlqdfRAALDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 32-169 1.60e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 42.93  E-value: 1.60e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  32 LFAISLNMLTNRAHAEEALQDAFIKIWHNASEYNASKgTVISWMISIVRYRSLDSLRYHKVRKEQSLG-----DDEYENE 106
Cdd:PRK12522   16 IYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE-NYKKWITTICVRTFYDFYRKKKRWKDRILDlfhkeDGGEIEF 94

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820 107 CIDVNYDEET-------KLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQ 169
Cdd:PRK12522   95 ADDVNISEEFiqkveaeMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMR 164
PRK06759 PRK06759
RNA polymerase factor sigma-70; Validated
 43-169 2.83e-05

RNA polymerase factor sigma-70; Validated


Pssm-ID: 235857 [Multi-domain]  Cd Length: 154  Bit Score: 42.11  E-value: 2.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  43 RAHAEEALQDAFIKIWHNASEYNASKGTVISWMISIVRYRSLDSLRYHKVRKEQSLGDDEYENECIDVnyDEETKLVNCI 122
Cdd:PRK06759   27 YQDYEEYYQCGLIGLWHAYERYDEKKGSFPAYAVVTVRGYILERLKKEFAVQEKCVCVGEYEDHFHFE--DVEMKVKDFM 104

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2537604820 123 EQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQ 169
Cdd:PRK06759  105 SVLDEKEKYIIFERFFVGKTMGEIALETEMTYYQVRWIYRQALEKMR 151
PRK12540 PRK12540
RNA polymerase sigma factor; Provisional
 31-172 6.97e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183579 [Multi-domain]  Cd Length: 182  Bit Score: 41.49  E-value: 6.97e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  31 KLFAISLNMLTNRAhaEEALQDAFIKIWHNASEYNASKgTVISWMISIVR--YRSldslRYHKVRKEQSLGDDEYEnECI 108
Cdd:PRK12540   19 RAFAISLSGNGDRA--DDLVQETLLRALANIDSFQPGS-NLPAWLFTILRnlFRS----DYRKRRREVEDADGSYA-KTL 90

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2537604820 109 DVNYDEETKL-----VNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQRCL 172
Cdd:PRK12540   91 KSQPGQNAHLefeefRAALDKLPQDQREALILVGASGFSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 9-168 8.10e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 41.19  E-value: 8.10e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   9 LLCATAQGDKNAFSSLYQQTSGKLFAISLNMLTNR-AHAEEALQDAFIKIwHNASEYNASKGTVISWMISIVRYRSLDSL 87
Cdd:PRK12536   11 LLLRGLAGDAAAYRQFLSELAAHLRGFLRRRLPQLpDEVEDLVQEILLAV-HNARHTYRADQPLTAWVHAIARYKLMDFL 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  88 RYHKVRKEQSLG-DDEYE--NECIDVNYDEETKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRG 164
Cdd:PRK12536   90 RSRARREALHDPlDDESElfATSDDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVKVGIHRG 169


                  ....
gi 2537604820 165 LMQL 168
Cdd:PRK12536  170 LKAL 173
PRK12544 PRK12544
RNA polymerase factor sigma-70;
40-172 9.27e-05

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 41.33  E-value: 9.27e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  40 LTNRAHAEEALQDAFIKIWHNASEYnASKGTVISWMISIVRYRSLDSLRyHKVR--KEQSLGDDEYENECIDVNYDE--- 114
Cdd:PRK12544   39 LSDLHLAEDAVQEALIGALKNADSF-AGRAAFKTWVFAILKNKIIDLLR-QKKRhvSASSLLRDEEEEEDFEELFDEsgh 116

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820 115 -------------ETKLVN---------CIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQRCL 172
Cdd:PRK12544  117 wqkderpqawgnpEESLEQeqfwrifeaCLDGLPAKYARVFMMREFIELETNEICHAVDLSVSNLNVLLYRARLRLRECL 196
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 23-99 1.60e-04

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 40.67  E-value: 1.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  23 SLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKiWHNASEynaskgTVI----SWMISIVRYRSLDSLRYHKVRKEQSL 98
Cdd:PRK09636    8 AEFEPLRPHLLSVAYRMLGSVADAEDIVQEAWLR-WNNADR------AQIrdprAWLTRVVTRLCLDRLRSARHRRETYV 80


                  .
gi 2537604820  99 G 99
Cdd:PRK09636   81 G 81
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 33-174 2.06e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 39.86  E-value: 2.06e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  33 FAISLNmlTNRAHAEEALQDAFIKIWhnASEYNASKGTVI-SWMISIVRYRSLDSLRyhKVRKEQSLGDDEYeNECIDVN 111
Cdd:PRK12547   22 FAVSLS--SKHDKAEDLVQDTLMKAW--AKQDSFEMGTNLkAWLFTILRNEFYSQMR--KRGREVQDSDGVF-TARVAVH 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2537604820 112 YDEETKL-----VNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQRCLTL 174
Cdd:PRK12547   95 PAQYGSLdlqdfKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLKV 162
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 2-163 2.27e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 39.88  E-value: 2.27e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820   2 DNDDLLPLLCATAQGDKNAFSSLYQQTSGKLFAIsLNMLTNRAHAEEALQDAFIKIWHNASEYnASKGTVISWMISIVRY 81
Cdd:PRK12535    8 DDAHVTDLALAAGRGDRAALTEFIRETQDDVWRL-LAHLGGHDIADDLTQETYLRVMSALPRF-AARSSARTWLLSLARR 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  82 RSLDSLRYHKVRKEQSLGddEYENECIDVNYDEETKLVN-------CIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPL 154
Cdd:PRK12535   86 VWVDNIRHDMARPRKSAT--EYEDAAATTASNETTGSWSewidvrtLIDALPPERREALILTQVLGYTYEEAAKIADVRV 163


                  ....*....
gi 2537604820 155 GTVKSWIRR 163
Cdd:PRK12535  164 GTIRSRVAR 172
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 14-88 6.47e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 38.79  E-value: 6.47e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2537604820  14 AQGDKNAFSSLYQQTSGKLFAISLNMLTNRAHAEEALQDAFIKIWHNASEY--NASKGTvisWMISIVRYRSLDSLR 88
Cdd:PRK11922   25 LAGDEAAFEALMRRHNRRLYRTARAILRNDAEAEDVVQEAYLRAFRALGTFrgDASLST---WLSRIVLNEALGRLR 98
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 32-169 2.25e-03

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 37.64  E-value: 2.25e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820  32 LFAISLNMLTNRAHAEEALQDAFIKIWHN-ASEYNASKGtvisWMISIVRYRSLDSLRYHKVRKEQSLGDDEYEN----- 105
Cdd:PRK09635   18 LVDLAFRMVGDIGVAEDMVQEAFSRLLRApVGDIDDERG----WLIVVTSRLCLDHIKSASTRRERPQDIAAWHDgdasv 93

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2537604820 106 ECID----VNYDEE--TKLVNCIEQLEPQQKQAIHLAYYKGLSHSELVDHIETPLGTVKSWIRRGLMQLQ 169
Cdd:PRK09635   94 SSVDpadrVTLDDEvrLALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQASTCRQLAHRARRKIN 163
 
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