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Conserved domains on  [gi|1088640828|gb|OHE54611|]
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MAG: hypothetical protein A2558_09250 [Tenericutes bacterium RIFOXYD2_FULL_35_11]

Protein Classification

RNA polymerase sigma factor( domain architecture ID 11446377)

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-156 2.26e-35

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: 120.87  E-value: 2.26e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   1 MEFNETYYKFKSMVTGICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLV--- 77
Cdd:COG1595    17 AAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELlde 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  78 FSNEMIASTRAFDD--EKSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLE 155
Cdd:COG1595    97 LAEELPDEAADPEEalEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALE 176


                  .
gi 1088640828 156 K 156
Cdd:COG1595   177 E 177
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-156 2.26e-35

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: 120.87  E-value: 2.26e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   1 MEFNETYYKFKSMVTGICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLV--- 77
Cdd:COG1595    17 AAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELlde 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  78 FSNEMIASTRAFDD--EKSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLE 155
Cdd:COG1595    97 LAEELPDEAADPEEalEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALE 176


                  .
gi 1088640828 156 K 156
Cdd:COG1595   177 E 177
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 19-156 3.67e-31

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 110.22  E-value: 3.67e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  19 YTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLVFSNEMIASTRAFDDE------ 92
Cdd:PRK09415   34 YSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSWHNKKVIVTEDIFTYMESQKESveeevi 113

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088640828  93 KSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLEK 156
Cdd:PRK09415  114 QNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 1-151 1.72e-27

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: 100.11  E-value: 1.72e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   1 MEFNETYYKFKSMVTGICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLVFSN 80
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1088640828  81 EMIASTRAFDDEKS----DNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:TIGR02937  81 LEELLDSDPSPEEEleqeEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLR 155
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 103-150 4.65e-12

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: 57.47  E-value: 4.65e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1088640828 103 MVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAI 150
Cdd:pfam08281   7 ALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 100-151 8.03e-12

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: 56.73  E-value: 8.03e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1088640828 100 VFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:cd06171     4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 1-156 2.26e-35

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: 120.87  E-value: 2.26e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   1 MEFNETYYKFKSMVTGICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLV--- 77
Cdd:COG1595    17 AAFEELYERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELlde 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  78 FSNEMIASTRAFDD--EKSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLE 155
Cdd:COG1595    97 LAEELPDEAADPEEalEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALE 176


                  .
gi 1088640828 156 K 156
Cdd:COG1595   177 E 177
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 19-156 3.67e-31

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 110.22  E-value: 3.67e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  19 YTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLVFSNEMIASTRAFDDE------ 92
Cdd:PRK09415   34 YSYVKNKEVAEDLTQEIFVKCYKSLHTYKGKSSLKTWLYRIAINHCKDYLKSWHNKKVIVTEDIFTYMESQKESveeevi 113

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1088640828  93 KSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLEK 156
Cdd:PRK09415  114 QNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLEE 177
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 1-151 1.72e-27

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: 100.11  E-value: 1.72e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   1 MEFNETYYKFKSMVTGICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLVFSN 80
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDL 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1088640828  81 EMIASTRAFDDEKS----DNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:TIGR02937  81 LEELLDSDPSPEEEleqeEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLR 155
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 21-155 9.79e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 80.79  E-value: 9.79e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  21 YTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLVFSNEMIASTRAFDDE-------K 93
Cdd:PRK11924   33 QLGDRALAEDAVQEAFLRAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRREKAVLSDDALEPEFAETAEtpeaallA 112

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1088640828  94 SDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLE 155
Cdd:PRK11924  113 KDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 1-156 2.62e-17

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 74.22  E-value: 2.62e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   1 MEFNETYYKFKSMVTGICYTYTKNISDTEDLVQDIFMKLYteKQDFQSVDHLKHWLIRVSINESKNYVKSA--WKKRL-- 76
Cdd:PRK09639    3 ETFEDLFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLY--RSDFKGIENEKGWLIKSARNVAYNYLRSEkrRRARIlg 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  77 VFSNEMIASTRAFDDE--KSDNAQNVFNMVHNLPNKYKNIIILYYyEDLQIKEISQILGISENSIKKRLERARTAIRVGL 154
Cdd:PRK09639   81 EFQWQEVDNEPSPEEIwiRKEEITKVQEVLAKMTERDRTVLLLRF-SGYSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159


                  ..
gi 1088640828 155 EK 156
Cdd:PRK09639  160 EQ 161
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 3-154 4.33e-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: 70.67  E-value: 4.33e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   3 FNETYYKFKSmvtgICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLV---FS 79
Cdd:TIGR02985   7 YRRYYPKLCA----FARRYVKDEEDAEDIVQDVFLKLWENRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYqeeLA 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1088640828  80 NEMIASTRAFDDEKSDNAQNVFNMVH----NLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGL 154
Cdd:TIGR02985  83 EIEERELSEADPEEELEAKELEEIIEeaieKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 10-155 1.77e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 69.51  E-value: 1.77e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  10 FKSMVTGICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYV--KSAWKKRLV--FSNE---- 81
Cdd:PRK12522   12 YKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVENYKKWITTICVRTFYDFYrkKKRWKDRILdlFHKEdgge 91

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1088640828  82 -MIASTRAFDDE--KSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLE 155
Cdd:PRK12522   92 iEFADDVNISEEfiQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREHLE 168
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 23-156 6.11e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 69.22  E-value: 6.11e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  23 KNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLVFSNEMIASTRAFDDEKSDNA----- 97
Cdd:PRK11922   52 RNDAEAEDVVQEAYLRAFRALGTFRGDASLSTWLSRIVLNEALGRLRRRRRLVNLAEMVMASTIAGGERTPLADPaedpe 131

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1088640828  98 ---------QNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLEK 156
Cdd:PRK11922  132 raaarreirALLERAIDALPDAFRAVFVLRVVEELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 1-152 8.56e-15

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 67.60  E-value: 8.56e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   1 MEFNETYYKFKSMVTGICYTYTKNISDTEDLVQDIFMK--LYTEKQDFQSVdhlKHWLIRVSINESKNYVKSAwKKRLVF 78
Cdd:PRK09644    1 MEIEEIYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRayIYLEDYDNQKV---KPWLFKVAYHTFIDFVRKE-KKVSFV 76

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1088640828  79 SNEMIASTRAFDDEKSDNAQNVF----NMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRV 152
Cdd:PRK09644   77 GTDEIEAIQAESTEEYVVAKNSYekliQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 2-155 1.30e-14

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: 67.03  E-value: 1.30e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   2 EFNETYYKFKSMVTGICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKnyvkSAW--KKRLVFS 79
Cdd:TIGR02983   7 EFTAFVAARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRWDRIRDPDAPDAYVRRVLVNLAR----SRWrrRRLLELP 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1088640828  80 NEMIASTRAFD-DEKSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLE 155
Cdd:TIGR02983  83 TRELPDAAAPDpAPDVALRAALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELLE 159
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 3-151 4.05e-14

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 65.98  E-value: 4.05e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   3 FNETYYKFKSMVTGICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYV--KSAWKKRLVFSN 80
Cdd:PRK09652   12 FALLVRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRGGAAFYTWLYRIARNTAINYLrkQGRRPPASDVDA 91

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  81 EMIASTRAFDDEKSDN-----------AQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTA 149
Cdd:PRK09652   92 EEAEDFDLADALRDIStpenellsaelEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREA 171


                  ..
gi 1088640828 150 IR 151
Cdd:PRK09652  172 LR 173
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 10-156 5.86e-14

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 65.87  E-value: 5.86e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  10 FKSMVTGICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKsawKKRLVFSNE-------- 81
Cdd:PRK09641   27 YKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINRKFSTWLYRIATNLTIDRLR---KRKPDYYLDaevagteg 103

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  82 -----MIASTRAFDDE---KSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVG 153
Cdd:PRK09641  104 ltmysQLAADDALPEEqvvSLELQETIQEAILQLPEKYRTVIVLKYIEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183


                  ...
gi 1088640828 154 LEK 156
Cdd:PRK09641  184 LRH 186
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 24-151 1.10e-13

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 65.01  E-value: 1.10e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  24 NISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSawKKRlvfSNEMIASTRAFDDEKSDN-----AQ 98
Cdd:PRK09637   24 NEADVDDLLQEVLIKTHSNLHSLKDGSSIKSWLYQIANNTIIDFYRK--KNR---SEELPDDLLFEDEEREENakkelAP 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1088640828  99 NVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:PRK09637   99 CLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLK 151
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 23-151 2.82e-13

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 63.60  E-value: 2.82e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  23 KNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKK-RLVFSNEMIASTRAFDDEKS----DNA 97
Cdd:PRK12543   29 EDKQDVDDVVNEIYIQLWESLRKYDSNRPFRFWLIGLVIKQIHSWRRKRWRRfRIFEKAEEQRKPVSIDFSEDvlskESN 108

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1088640828  98 QNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:PRK12543  109 QELIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLR 162
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 103-150 4.65e-12

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: 57.47  E-value: 4.65e-12
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1088640828 103 MVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAI 150
Cdd:pfam08281   7 ALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 3-156 6.82e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 60.12  E-value: 6.82e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   3 FNETYYKFKSMVTGICYTYTkNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAwKKRLVFSNEM 82
Cdd:PRK12518   13 FRQLYRRYQQKVRSTLYQLC-GRELLDDLVQEVFLRVWKGLPKLRNPAYFSTWLYRITWNVATDARRQF-AQRPSRIQDD 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  83 IASTRAFDDEKSDNAQN------VFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLEK 156
Cdd:PRK12518   91 SLNDQPSRPSDTPDLMQlhyqdlVQQGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQ 170
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 100-151 8.03e-12

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: 56.73  E-value: 8.03e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1088640828 100 VFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:cd06171     4 LEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK09640 PRK09640
RNA polymerase sigma factor SigX; Reviewed
 3-151 1.56e-11

RNA polymerase sigma factor SigX; Reviewed


Pssm-ID: 236603 [Multi-domain]  Cd Length: 188  Bit Score: 59.18  E-value: 1.56e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   3 FNETYYKFKSMVTGICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLVFSNEM 82
Cdd:PRK09640   28 YEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGKSKFKTWLYSITYNECITQYRKERRKRRLMDALS 107

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1088640828  83 IASTRAFDDEKS---DNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:PRK09640  108 LDPLEEASEEKApkpEERGGLDRWLVHVNPIDREILVLRFVAELEFQEIADIMHMGLSATKMRYKRALDKLR 179
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 3-156 1.39e-10

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 56.57  E-value: 1.39e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   3 FNETYYKFKSMVTGICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSawKKRLVFSNEM 82
Cdd:PRK09638   20 LTTLFQQHYSFLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSFQGRSKFSTWLISIASRLYKDHLRK--QKREKLRLQR 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  83 IASTRAfDDEKSDNAQ------NVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLEK 156
Cdd:PRK09638   98 AKEETL-RKEKWEAAIkgaewsEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWGQ 176
Sig-70_gvs1 TIGR02989
RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma ...
 19-151 2.65e-10

RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).


Pssm-ID: 274379 [Multi-domain]  Cd Length: 159  Bit Score: 55.40  E-value: 2.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  19 YTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLVFSNEMIA-----STRAFDDEK 93
Cdd:TIGR02989  19 RSLVADRDDVDDVLQETFVVAWRKFDQFDPGTNFVAWARGIARNKVLNYRRKLGRDRLVFDDDLLEalaaeAEPTEAERL 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1088640828  94 SDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:TIGR02989  99 SDDRQALEGCLEKLPERQRELLDLRYQRGQKATALAEQTGRTVNAVYKALQRIRVSLR 156
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 3-150 5.23e-09

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 52.50  E-value: 5.23e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   3 FNETYYKFKSMVTGICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSawKKRLVFSNEM 82
Cdd:PRK11923   22 FDLLVLKYQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSAFYTWLYRIAINTAKNHLVS--RGRRPPDSDV 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  83 IASTRAF---DDEKSDNA------------QNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERAR 147
Cdd:PRK11923  100 SSEDAEFydgDHALKDIEsperallrdeieGTVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIFRAR 179


                  ...
gi 1088640828 148 TAI 150
Cdd:PRK11923  180 EAI 182
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 9-73 7.03e-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: 49.51  E-value: 7.03e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1088640828   9 KFKSMVTGICYTYTKNISDTEDLVQDIFMKLYT--EKQDFQSVDHLKHWLIRVSINESKNYVKSAWK 73
Cdd:pfam04542   4 RYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRaiERFDPERGVSFSTWLYTIIRNAIIDYLRKQRR 70
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 26-156 2.68e-08

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 50.42  E-value: 2.68e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  26 SDTEDLVQDIFMKLYTEKQDFQS-VDHLKHWLIRVSINESKNYVKsawKKRLVFSNEM--IASTRAFDDEK---SDNAQN 99
Cdd:PRK05602   45 AEAEDVAQETFLRIWKQAPSWRPgEARFDTWLHRVVLNLCYDRLR---RRREVPVEDApdVPDPAPGPDAGleaRQRARR 121

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1088640828 100 VFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLEK 156
Cdd:PRK05602  122 VEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLLARGRRALRAQLAD 178
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 19-156 3.50e-08

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 50.55  E-value: 3.50e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  19 YTYTKNISDTEDLVQDIFMKLYTEKQDFQSvDHLKHWLIRVSINESKNYVKSAWKKRL---------VFSNEMiASTRAF 89
Cdd:PRK09647   46 YRLSGNQHDAEDLTQETFIRVFRSLQNYQP-GTFEGWLHRITTNLFLDMVRRRARIRMealpedydrVPGDEP-NPEQIY 123

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1088640828  90 DDEKSDNAqnVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLEK 156
Cdd:PRK09647  124 HDARLDPD--LQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 107-151 6.82e-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. 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: 46.27  E-value: 6.82e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1088640828 107 LPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:pfam04545   5 LPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLR 49
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 92-150 7.96e-08

DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440804 [Multi-domain]  Cd Length: 236  Bit Score: 49.82  E-value: 7.96e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1088640828  92 EKSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISEnsikKRLERARTAI 150
Cdd:COG1191   172 EHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSE----SRVSRLHKKA 226
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 92-139 1.95e-07

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 48.92  E-value: 1.95e-07
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1088640828  92 EKSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSI 139
Cdd:PRK06288  198 EREEIKRVIVEAIKTLPEREKKVLILYYYEDLTLKEIGKVLGVTESRI 245
PRK12516 PRK12516
RNA polymerase sigma factor; Provisional
 29-151 3.41e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183568 [Multi-domain]  Cd Length: 187  Bit Score: 47.65  E-value: 3.41e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  29 EDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINEsknyVKSAWKKR---LVFSNEMIASTRAFDDEK--SDNAQNVFNM 103
Cdd:PRK12516   38 DDLVQDTIMKAWAKQDHFEVGTNMKAWLFTILRNE----FYSQMRKRgreVQDTDGMFTEQLAVHPSQygTLDLQDFRAA 113

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1088640828 104 VHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:PRK12516  114 LDQLPDDQREAIILVGASGFAYEEAAEICGCAVGTIKSRVNRARQRLQ 161
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 20-151 4.76e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 47.09  E-value: 4.76e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  20 TYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVsineSKNYVKSAWKKRLVFSNEMIASTRAFDD------EK 93
Cdd:PRK12511   23 SLTRDSAEAEDLVHDALVRALERRASFRSGGNLRTWLMSI----LHNAFIDELRRRRVEARRADELAVLADAslpaaqEH 98

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1088640828  94 SDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:PRK12511   99 AVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGIPIGTLMSRIGRARAALR 156
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 22-147 5.74e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 47.03  E-value: 5.74e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  22 TKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIrvSINESKNYvkSAWKKRlvfSNEMI--ASTRAFDD-------- 91
Cdd:PRK12515   43 VRDEQTAEDLVSEVFLDVWRQAGQFEGRSQVSTWLL--SIARFKAL--SALRRR---KHEEIddEAAAAIEDgadtpeva 115

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1088640828  92 -EKSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERAR 147
Cdd:PRK12515  116 lQKSDTSAALRACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYAR 172
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 22-148 8.51e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 46.02  E-value: 8.51e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  22 TKNISDTEDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESknYVKSAWKKRLVFSNEMIASTRAF---DDEKSDNAQ 98
Cdd:PRK12547   27 SSKHDKAEDLVQDTLMKAWAKQDSFEMGTNLKAWLFTILRNEF--YSQMRKRGREVQDSDGVFTARVAvhpAQYGSLDLQ 104

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1088640828  99 NVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERART 148
Cdd:PRK12547  105 DFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARN 154
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 81-154 1.94e-06

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 45.76  E-value: 1.94e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1088640828  81 EMIASTRA---FDD-EKSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGL 154
Cdd:PRK05911  176 ERIADERAetgYDVvDKKEFSSILAEAILALEEKERKVMALYYYEELVLKEIGKILGVSESRVSQIHSKALLKLRATL 253
PRK12542 PRK12542
RNA polymerase sigma factor; Provisional
 2-151 2.08e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183581 [Multi-domain]  Cd Length: 185  Bit Score: 45.43  E-value: 2.08e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828   2 EFNETYYKFKSMVTGICYTYTKNISDTEDLVQDIFMKLYT--EKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLVFS 79
Cdd:PRK12542   10 KMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKnlEKLHSLNTQELKRYILRVAKNKAIDSYRKNKRHETFLE 89

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1088640828  80 NEMIASTRAFDDEKSDNAQNVFNMVH------NLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:PRK12542   90 EYERESIEAVDENIEEWEKRKMSEVQidtllkELNESNRQVFKYKVFYNLTYQEISSVMGITEANVRKQFERARKRVQ 167
PRK12533 PRK12533
RNA polymerase sigma factor; Provisional
 24-147 3.94e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237129 [Multi-domain]  Cd Length: 216  Bit Score: 44.72  E-value: 3.94e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  24 NISDTEDLVQDIFMKLYTEKQDFQSvDHLKHWLIRVSinesKNYVKSAWKKRlVFSNEMIASTRAFDDE----------- 92
Cdd:PRK12533   41 NASDADDVVQEACMRALRFFDSFRG-DNARPWLLAIV----RHTWYSEWRRR-ANAHEVAAPDTLDDADslddwqpaged 114

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088640828  93 ------KSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERAR 147
Cdd:PRK12533  115 plalllRAEDVRLVNAALAKLPVEYREVLVLRELEDMSYREIAAIADVPVGTVMSRLARAR 175
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 107-139 7.01e-06

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


Pssm-ID: 274153 [Multi-domain]  Cd Length: 224  Bit Score: 44.19  E-value: 7.01e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1088640828 107 LPNKYKNIIILYYYEDLQIKEISQILGISENSI 139
Cdd:TIGR02479 176 LSEREQLVLSLYYYEELNLKEIGEVLGLTESRV 208
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 92-139 1.14e-05

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 43.68  E-value: 1.14e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1088640828  92 EKSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSI 139
Cdd:PRK06986  170 EDEELREALVEAIESLPEREQLVLSLYYQEELNLKEIGAVLGVSESRV 217
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 29-154 1.32e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 43.14  E-value: 1.32e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  29 EDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVsineSKNYVKSAWKKR-----LVFSNEMIASTRAFDDEKSDNAQNVFNM 103
Cdd:PRK12513   54 EDIFQETWLRVIRARAQYQPRARFRTWLYQI----ARNLLIDHWRRHgarqaPSLDADEQLHALADDGAAPEQQLSLFRD 129

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1088640828 104 -------VHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGL 154
Cdd:PRK12513  130 rrrlqaaLETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187
PRK09642 PRK09642
RNA polymerase sigma factor;
10-151 7.64e-05

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 40.85  E-value: 7.64e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  10 FKSMVTGICYTYTKNISDTEDLVQDIFMKLYTEKQDFQsVDHLKHWLIRVSINESKNYVKSAWKKRLVFS-----NEMIA 84
Cdd:PRK09642    4 YRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQ-FRGLKTWMARIATNHAIDYKRKKARENEELSlcketEENIK 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1088640828  85 STRAFDDEKSDNAQNVF--NMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:PRK09642   83 SSHNIEDLLLTKEQKLLiaQKLRELPENYRDVVLAHYLEEKSYQEIALQEKIEVKTVEMKLYRARKWIK 151
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 29-155 8.71e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 40.68  E-value: 8.71e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  29 EDLVQDIFMKLYTEKQDFQSVDHLKHWLIRVSINESKNYVKSAWKKRLVFSNEMI-ASTRAFDDEKSDNA---------- 97
Cdd:PRK12532   34 EDLVQETLLSAYSAGDSFQGRALVNSWLFAILKNKIIDALRQIGRQRKVFTLLDDeLLDEAFESHFSQNGhwtpegqpqh 113

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1088640828  98 ---------QNVFNMV-----HNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLE 155
Cdd:PRK12532  114 wntpekslnNNEFQKIlqsclYNLPENTARVFTLKEILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 27-151 1.11e-04

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 40.31  E-value: 1.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  27 DTEDLVQDIFMKLYTEKQDFQS-VDHLKHWLIRVSINESKNYVKSAWKKRLV--FSNEMIASTRAFDDE--KSDNAQNVF 101
Cdd:PRK06811   47 LIEECVNDIFLSIWNNIDKFDEeKGSFKKWIAAISKYKAIDYKRKLTKNNEIdsIDEFILISEESIENEiiLKENKEEIL 126

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1088640828 102 NMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIR 151
Cdd:PRK06811  127 KLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQ 176
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 26-146 1.17e-04

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 40.18  E-value: 1.17e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  26 SDTEDLVQDIFMKLYTeKQDFQSVDHLKHWLI----RVSINE-SKNYVKSAWKKRLVFSNEMIASTRAFDDEKSDNAQNV 100
Cdd:PRK09651   35 FDADDIAQDTFLRVMV-SETLSTIRDPRSFLCtiakRVMVDLfRRNALEKAYLEMLALMPEGGAPSPEERESQLETLQLL 113

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1088640828 101 FNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERA 146
Cdd:PRK09651  114 DSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKA 159
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
115-147 5.63e-04

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 38.58  E-value: 5.63e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1088640828 115 IILYYYEDLQIKEISQILGISENSIKKRLERAR 147
Cdd:COG2771   135 VLRLLAEGLTLKEIARILGISERTVRTHLKRIY 167
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
29-155 7.07e-04

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 38.14  E-value: 7.07e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  29 EDLVQDIFMKLYTEKQDFQSVDH-LKHWLIRVSINESKNYVKSAWKKRLVFSNEMIAS-TRAFDDE--KSDNAQNVFNMV 104
Cdd:PRK09645   37 EDVVQETLLRAWQHPEVLADTGRsARAWLFTVARNLVIDERRSARARPVEGGDDVLGVpEQSAPDEvdRALDRLLVADAL 116

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1088640828 105 HNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLE 155
Cdd:PRK09645  117 AQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQ 167
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 107-156 9.39e-04

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 37.64  E-value: 9.39e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1088640828 107 LPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLEK 156
Cdd:PRK09047  107 LPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRATHALAKALEA 156
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 16-156 2.04e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 36.72  E-value: 2.04e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  16 GICYTYTKNISDTEDLVQDIFMKLYTEKQDFQSVDHLK-HWLIRVSINESKNYVKsAWKKrlvfSNEMIASTRAFDDEK- 93
Cdd:PRK12514   34 GICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPmTWLITIARNHAIDRLR-ARKA----VAVDIDEAHDLADPSp 108

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088640828  94 --------SDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLEK 156
Cdd:PRK12514  109 gpeaeviaGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECLSR 179
PRK12517 PRK12517
RNA polymerase sigma factor; Provisional
 29-156 3.96e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183569 [Multi-domain]  Cd Length: 188  Bit Score: 36.20  E-value: 3.96e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  29 EDLVQDIFMKLYtekqdfQSVDHL------KHWLIRVSINESKNYVKsawKKRLVFSN---EMIASTRAFDDEKSDNAQN 99
Cdd:PRK12517   51 EDLVQETFLRAW------RSLDSLkdekaaKAWLITILRRENARRFE---RKQFDLVDiedDSIEDDASHSSEEEMEQEW 121

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1088640828 100 VFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLEK 156
Cdd:PRK12517  122 LRRQIAKLDPEYREPLLLQVIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALEK 178
PRK12536 PRK12536
RNA polymerase sigma factor; Provisional
 26-140 4.03e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237131 [Multi-domain]  Cd Length: 181  Bit Score: 35.80  E-value: 4.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1088640828  26 SDTEDLVQDIFMKLYTEKQDFQS----------------VDHLKHWLIRVSINESknyvksawkkrLVFSNEMIASTraf 89
Cdd:PRK12536   47 DEVEDLVQEILLAVHNARHTYRAdqpltawvhaiaryklMDFLRSRARREALHDP-----------LDDESELFATS--- 112

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1088640828  90 DDEKSDNAQNVFNMVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIK 140
Cdd:PRK12536  113 DDEAAEARRDLGKLLEQLPDRQRLPIVHVKLEGLSVAETAQLTGLSESAVK 163
PRK09636 PRK09636
RNA polymerase sigma factor SigJ; Provisional
 15-75 6.12e-03

RNA polymerase sigma factor SigJ; Provisional


Pssm-ID: 236600 [Multi-domain]  Cd Length: 293  Bit Score: 35.67  E-value: 6.12e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1088640828  15 TGICYTYTKNISDTEDLVQDIFMKLYTEKQDfqSVDHLKHWLIRVSINESKNYVKSAWKKR 75
Cdd:PRK09636   18 LSVAYRMLGSVADAEDIVQEAWLRWNNADRA--QIRDPRAWLTRVVTRLCLDRLRSARHRR 76
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
103-156 6.67e-03

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 35.79  E-value: 6.67e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1088640828 103 MVHNLPNKYKNIIILYYYEDLQIKEISQILGISENSIKKRLERARTAIRVGLEK 156
Cdd:PRK07670  198 KIKQLSEKEQLVISLFYKEELTLTEIGQVLNLSTSRISQIHSKALFKLKKLLEK 251
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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