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Conserved domains on  [gi|639234871|ref|WP_024565864|]
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MULTISPECIES: RNA polymerase sigma factor [Elizabethkingia]

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]; ...
 2-158 5.38e-37

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: 125.11  E-value: 5.38e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   2 YDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSqKGRFYTWMINIARNTAIDYLKSKGFQNELKNQSIPDF 81
Cdd:COG1595   23 YERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRG-RGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAEEL 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 639234871  82 VYNSTALSTSNNTSDFIG-FNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLKDYQ 158
Cdd:COG1595  102 PDEAADPEEALEAEELLEaLLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEG 179
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 2-158 5.38e-37

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: 125.11  E-value: 5.38e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   2 YDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSqKGRFYTWMINIARNTAIDYLKSKGFQNELKNQSIPDF 81
Cdd:COG1595   23 YERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRG-RGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAEEL 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 639234871  82 VYNSTALSTSNNTSDFIG-FNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLKDYQ 158
Cdd:COG1595  102 PDEAADPEEALEAEELLEaLLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEG 179
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 1-157 1.60e-35

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 121.71  E-value: 1.60e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHqYDSQKGRFYTWMINIARNTAIDYLKSKG--------FQNE 72
Cdd:PRK12519  34 LYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSS-YDPKRGSLSSYLLTLTRSRAIDRLRSRRsrqrllerWQQE 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  73 LKNQSIPDFVYNSTALstsNNTSDFIgfNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKD 152
Cdd:PRK12519 113 LLGEASEDTPLEQASL---AERSQRV--QTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187


                 ....*
gi 639234871 153 LLKDY 157
Cdd:PRK12519 188 LLQDL 192
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 1-154 9.16e-29

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: 103.58  E-value: 9.16e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871    1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDsQKGRFYTWMINIARNTAIDYLKSKGFQNELKNQSIPD 80
Cdd:TIGR02937   6 LYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFD-PEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEEL 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 639234871   81 FVYNSTALSTSNNTSDFIGFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLL 154
Cdd:TIGR02937  85 LDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 1-68 2.23e-15

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: 66.46  E-value: 2.23e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 639234871    1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKG-RFYTWMINIARNTAIDYLKSKG 68
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGvSFSTWLYTIIRNAIIDYLRKQR 69
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 102-151 2.87e-09

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 50.18  E-value: 2.87e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 639234871 102 NVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLK 151
Cdd:cd06171    6 EALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 121-151 7.36e-06

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 41.36  E-value: 7.36e-06
                           10        20        30
                   ....*....|....*....|....*....|.
gi 639234871   121 QGYTQNEISEQLKIPLGTVKTKMRNALMKLK 151
Cdd:smart00421  17 EGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 2-158 5.38e-37

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: 125.11  E-value: 5.38e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   2 YDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSqKGRFYTWMINIARNTAIDYLKSKGFQNELKNQSIPDF 81
Cdd:COG1595   23 YERYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSFRG-RGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAEEL 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 639234871  82 VYNSTALSTSNNTSDFIG-FNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLKDYQ 158
Cdd:COG1595  102 PDEAADPEEALEAEELLEaLLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEG 179
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 1-157 1.60e-35

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 121.71  E-value: 1.60e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHqYDSQKGRFYTWMINIARNTAIDYLKSKG--------FQNE 72
Cdd:PRK12519  34 LYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSS-YDPKRGSLSSYLLTLTRSRAIDRLRSRRsrqrllerWQQE 112

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  73 LKNQSIPDFVYNSTALstsNNTSDFIgfNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKD 152
Cdd:PRK12519 113 LLGEASEDTPLEQASL---AERSQRV--QTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187


                 ....*
gi 639234871 153 LLKDY 157
Cdd:PRK12519 188 LLQDL 192
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 1-154 9.16e-29

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: 103.58  E-value: 9.16e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871    1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDsQKGRFYTWMINIARNTAIDYLKSKGFQNELKNQSIPD 80
Cdd:TIGR02937   6 LYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFD-PEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLEEL 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 639234871   81 FVYNSTALSTSNNTSDFIGFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLL 154
Cdd:TIGR02937  85 LDSDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
1-154 5.58e-28

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 102.44  E-value: 5.58e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGRFYTWMINIARNTAIDYLKSKGFQNE------LK 74
Cdd:PRK09646  35 LYDRTSSRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARGSALAWLLTLAHRRAVDRVRSEQAASQrevrygAR 114

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  75 NQSIP-DFVynSTALSTSNNTSDFIGfnnVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDL 153
Cdd:PRK09646 115 NVDPAfDQV--AEEVEARLERERVRD---CLDALTDTQRESVTLAYYGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189


                 .
gi 639234871 154 L 154
Cdd:PRK09646 190 L 190
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 1-155 6.56e-28

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 102.06  E-value: 6.56e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGRFYTWMINIARNTAIDYLKSKGFQNelKNQSIPD 80
Cdd:PRK12534  30 LYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGLTWLAMIARNKAIDHLRANAPQR--RNVALDD 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 639234871  81 F----VYNSTALSTSNNTSDFIGFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLK 155
Cdd:PRK12534 108 AgelrAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAKLKACLE 186
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 1-154 1.07e-25

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 96.43  E-value: 1.07e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGRFYTWMINIARNTAIDYLKSKGFQNELKNQS--I 78
Cdd:PRK12514  24 LYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSGLSPMTWLITIARNHAIDRLRARKAVAVDIDEAhdL 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 639234871  79 PDFVYNSTALSTSNNTSDFIgfNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLL 154
Cdd:PRK12514 104 ADPSPGPEAEVIAGDEGQRI--DACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRECL 177
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 2-158 1.82e-24

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 92.95  E-value: 1.82e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   2 YDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSqKGRFYTWMINIARNTAIDYL-KSKGFQNELKNQSIPD 80
Cdd:PRK09652  16 VRRYQPRVKRLLSRLTRDPADAEDLVQETFIKAYRALHSFRG-GAAFYTWLYRIARNTAINYLrKQGRRPPASDVDAEEA 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  81 FVYNSTALSTSNNTSDFIGF--------NNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKD 152
Cdd:PRK09652  95 EDFDLADALRDISTPENELLsaeleqrvRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174


                 ....*.
gi 639234871 153 LLKDYQ 158
Cdd:PRK09652 175 KLQPLL 180
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 1-156 2.16e-24

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 93.05  E-value: 2.16e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGRFYTWMINIARNTAIDYLKSKgfqnELKNQSI-P 79
Cdd:PRK13919  28 LFRRYAGAFLALARRMGLDGAAAEDVVQEVFIRVWKKAKEFDPRRGSARAWLLALAHHAAVDHVRRR----AARPQPLeP 103

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  80 D------FVYNSTALSTSNNTsDFIGFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDL 153
Cdd:PRK13919 104 DerepeaFDLPGPGLDEEGHL-DRTRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEV 182


                 ...
gi 639234871 154 LKD 156
Cdd:PRK13919 183 LRE 185
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 9-156 8.00e-23

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 88.87  E-value: 8.00e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   9 LYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQY-DSQKGRfyTWMINIARNTAIDYLKSKGFQNELKNQSIPDFVYNSTA 87
Cdd:PRK11924  26 LLRYARRQLGDRALAEDAVQEAFLRAWRKADLFnGKGSAR--TWLLTIARNVCYDLLRRRRREKAVLSDDALEPEFAETA 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 639234871  88 LSTSNNTSDFIgFNNV----LESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLKD 156
Cdd:PRK11924 104 ETPEAALLAKD-DLARidrcLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQLLRECLEA 175
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 1-154 1.40e-20

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 82.90  E-value: 1.40e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGRFYTWMINIARNTAIDYLKSKGFQNELKNQSIPD 80
Cdd:PRK12537  28 LYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTGAASFDPARGSARGWIYSVTRHLALNVLRDTRREVVLDDDAEET 107

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 639234871  81 FVYNSTALSTSNNTSDFIGFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLL 154
Cdd:PRK12537 108 AQTLHEIIDDFDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALRECM 181
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 1-151 1.01e-19

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: 80.30  E-value: 1.01e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871    1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKgRFYTWMINIARNTAIDYLKSKGFQNELKNQSIPD 80
Cdd:TIGR02985   6 LYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRETLEISE-SIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAEI 84

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 639234871   81 FVynsTALSTSNNTSDFIG------FNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLK 151
Cdd:TIGR02985  85 EE---RELSEADPEEELEAkeleeiIEEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLR 158
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
1-157 7.20e-19

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 78.20  E-value: 7.20e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGRFYTWMINIARNTAIDYLKSKGFQNELKNQSiPD 80
Cdd:PRK09645  14 LYDEHAAPLWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADTGRSARAWLFTVARNLVIDERRSARARPVEGGDD-VL 92

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 639234871  81 FVYNSTALSTSNNTSDFIGFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLKDY 157
Cdd:PRK09645  93 GVPEQSAPDEVDRALDRLLVADALAQLSPEHRAVLVRSYYRGWSTAQIAADLGIPEGTVKSRLHYALRALRLALQER 169
PRK12526 PRK12526
RNA polymerase sigma factor; Provisional
 25-156 2.28e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 237127 [Multi-domain]  Cd Length: 206  Bit Score: 77.92  E-value: 2.28e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  25 EIIQDVFVKIWNSVHQYDSQKGRFYTWMINIARNTAIDYLKSKGFQNElknQSIPDFVYN-STALSTSNNTSDFIG---- 99
Cdd:PRK12526  67 ELVQETMSNVWRKAHLYNGDKGAATTWVYTVMRNAAFDMLRKIKAKKE---QNLGDDIWPiEQALAESQSESEEFSdhlm 143

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871 100 ---FNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLKD 156
Cdd:PRK12526 144 dkqILSYIEKLPEAQQTVVKGVYFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMGE 203
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 1-155 4.53e-18

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 76.69  E-value: 4.53e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSqKGRFYTWMINIARNTAIDYLKSKGFQnELKNQ---S 77
Cdd:PRK12515  27 LYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEG-RSQVSTWLLSIARFKALSALRRRKHE-EIDDEaaaA 104

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 639234871  78 IPDFVYNSTALSTSNNTSDFIgfNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLK 155
Cdd:PRK12515 105 IEDGADTPEVALQKSDTSAAL--RACLAKLSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 4-156 7.61e-17

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 73.13  E-value: 7.61e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   4 NYSgALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYdSQKGRFYTWMINIARNTAIDYLKSKGfQNELKNQSIPDFVY 83
Cdd:PRK09638  27 HYS-FLYKYLLKLTLDPDLAEDLVQETMLKAIENLSSF-QGRSKFSTWLISIASRLYKDHLRKQK-REKLRLQRAKEETL 103

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 639234871  84 NSTALSTSNNTSDFIGFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLKD 156
Cdd:PRK09638 104 RKEKWEAAIKGAEWSEMLDALSKLDPEFRAPVILKHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKEWGQ 176
Sig70_famx3 TIGR02954
RNA polymerase sigma-70 factor, TIGR02954 family; This group of sigma factors are members of ...
 9-155 6.29e-16

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


Pssm-ID: 213752 [Multi-domain]  Cd Length: 169  Bit Score: 70.51  E-value: 6.29e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871    9 LYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKgRFYTWMINIARNTAIDYLKSKGfQNELKNQSIPDfvynsTAL 88
Cdd:TIGR02954  29 LYKTAFIYVKNEHDALDVIQETVYKAYLSIDKLKHPK-YFNTWLTRILINECIDLLKKKK-KVIPFDPNTSI-----EKG 101

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 639234871   89 STSNNTSDFIGFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLK 155
Cdd:TIGR02954 102 ECETHADSRLDLYKAIDTLNDKYQTAIILRYYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKKRLE 168
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 2-139 1.10e-15

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 70.35  E-value: 1.10e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   2 YDNYSGALYGVIFRI---VQSKEYTEEIIQDVFVKIWNSVHQYDSQKGRFYTWMINIARNTAIDYLKSKGFQNELknQSI 78
Cdd:PRK06811  24 VDTYGNLVKKIVHKVlgtVNYSQLIEECVNDIFLSIWNNIDKFDEEKGSFKKWIAAISKYKAIDYKRKLTKNNEI--DSI 101

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 639234871  79 PDFVynstaLSTSNNTSDFIGFNNVLESL--------ETDKQELInMAYYQGYTQNEISEQLKIPLGTV 139
Cdd:PRK06811 102 DEFI-----LISEESIENEIILKENKEEIlklindleKLDREIFI-RRYLLGEKIEEIAKKLGLTRSAI 164
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 2-156 1.35e-15

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 70.01  E-value: 1.35e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   2 YDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSqKGRFYTWMINIARNTAIDYLKSKGFQNELKnqsiPDF 81
Cdd:PRK09637   7 WSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKD-GSSIKSWLYQIANNTIIDFYRKKNRSEELP----DDL 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 639234871  82 VYNSTAlSTSNNTSDFIG-FNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLKD 156
Cdd:PRK09637  82 LFEDEE-REENAKKELAPcLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEG 156
PRK09415 PRK09415
RNA polymerase factor sigma C; Reviewed
 3-155 1.67e-15

RNA polymerase factor sigma C; Reviewed


Pssm-ID: 181835 [Multi-domain]  Cd Length: 179  Bit Score: 69.78  E-value: 1.67e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   3 DNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYdSQKGRFYTWMINIARNTAIDYLKSKGFQNELKNQSIPDF- 81
Cdd:PRK09415  23 NEYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTY-KGKSSLKTWLYRIAINHCKDYLKSWHNKKVIVTEDIFTYm 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 639234871  82 -VYNSTALSTSNNTSDFIGFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLK 155
Cdd:PRK09415 102 eSQKESVEEEVIQNAEDERLASAVMSLPIKYREVIYLFYYEELSIKEIAEVTGVNENTVKTRLKKAKELLKKGLE 176
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 1-68 2.23e-15

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: 66.46  E-value: 2.23e-15
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 639234871    1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKG-RFYTWMINIARNTAIDYLKSKG 68
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGvSFSTWLYTIIRNAIIDYLRKQR 69
PRK12531 PRK12531
RNA polymerase sigma factor; Provisional
 1-151 3.13e-15

RNA polymerase sigma factor; Provisional


Pssm-ID: 105726 [Multi-domain]  Cd Length: 194  Bit Score: 69.19  E-value: 3.13e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGRFYTWMINIARNTAIDYL-KSKGFQNELKNQSI- 78
Cdd:PRK12531  32 VFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKSALSTWIYTIIRNLCFDLLrKQKGKDLHIHADDIw 111

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 639234871  79 PDFVYNSTALSTSNNTSDFIGFNNV--LESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLK 151
Cdd:PRK12531 112 PSDYYPPDLVDHYSPEQDMLKEQVMkfLDRLPKAQRDVLQAVYLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLR 186
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 9-157 1.14e-14

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 67.79  E-value: 1.14e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   9 LYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQkGRFYTWMINIARNTAIDYLKSKGFQNELKNQSIPDFvynsTAL 88
Cdd:PRK12513  39 LYRFLLRLARDRALAEDIFQETWLRVIRARAQYQPR-ARFRTWLYQIARNLLIDHWRRHGARQAPSLDADEQL----HAL 113

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 639234871  89 STSNNTSD--FIGFNN------VLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLKDY 157
Cdd:PRK12513 114 ADDGAAPEqqLSLFRDrrrlqaALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAEE 190
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 1-155 3.85e-13

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 63.04  E-value: 3.85e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGrfyTWMINIARNTAIDYLKS---------KGFQ- 70
Cdd:PRK09639   8 LFEQYYPDVVQQIFYIVKDRTQAEDLAQEVFLRLYRSDFKGIENEK---GWLIKSARNVAYNYLRSekrrrarilGEFQw 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  71 NELKNQSIPDfvynSTALSTSNNTSDFigfnNVLESLETDKQELINMAyYQGYTQNEISEQLKIPLGTVKTKMRNALMKL 150
Cdd:PRK09639  85 QEVDNEPSPE----EIWIRKEEITKVQ----EVLAKMTERDRTVLLLR-FSGYSYKEIAEALGIKESSVGTTLARAKKKF 155


                 ....*
gi 639234871 151 KDLLK 155
Cdd:PRK09639 156 RKIYE 160
PRK09641 PRK09641
RNA polymerase sigma factor SigW; Provisional
 3-149 4.64e-12

RNA polymerase sigma factor SigW; Provisional


Pssm-ID: 182012 [Multi-domain]  Cd Length: 187  Bit Score: 60.87  E-value: 4.64e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   3 DNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKgRFYTWMINIARNTAIDYLKSKGfqnelknqsiPDFV 82
Cdd:PRK09641  25 DLYKDKIYQLCYRMLGNRHEAEDAAQEAFIRAYVNIDSYDINR-KFSTWLYRIATNLTIDRLRKRK----------PDYY 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  83 YNSTALST------SNNTSDFIGFNNVLESLETDK--QELIN-----------MAYYQGYTQNEISEQLKIPLGTVKTKM 143
Cdd:PRK09641  94 LDAEVAGTegltmySQLAADDALPEEQVVSLELQEtiQEAILqlpekyrtvivLKYIEDLSLKEISEILDLPVGTVKTRI 173


                 ....*....
gi 639234871 144 ---RNALMK 149
Cdd:PRK09641 174 hrgREALRK 182
PRK12543 PRK12543
RNA polymerase sigma factor; Provisional
 1-151 1.02e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183582 [Multi-domain]  Cd Length: 179  Bit Score: 59.75  E-value: 1.02e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGrFYTWMINIARNTAIDY----------LKSKGFQ 70
Cdd:PRK12543  12 IYDVTIQEVYKTVHFLVEDKQDVDDVVNEIYIQLWESLRKYDSNRP-FRFWLIGLVIKQIHSWrrkrwrrfriFEKAEEQ 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  71 NELKNQSIPDfvynsTALSTSNNTSdfigFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKL 150
Cdd:PRK12543  91 RKPVSIDFSE-----DVLSKESNQE----LIELIHKLPYKLRQVIILRYLHDYSQEEIAQLLQIPIGTVKSRIHAALKKL 161


                 .
gi 639234871 151 K 151
Cdd:PRK12543 162 R 162
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 103-152 1.23e-10

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


Pssm-ID: 461347 [Multi-domain]  Cd Length: 50  Bit Score: 53.59  E-value: 1.23e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 639234871  103 VLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKD 152
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12522 PRK12522
RNA polymerase sigma factor; Provisional
 1-155 1.44e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183571 [Multi-domain]  Cd Length: 173  Bit Score: 56.42  E-value: 1.44e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKgRFYTWMINIARNTAID-YLKSKGFQNELKN---- 75
Cdd:PRK12522   8 LIDIYKQQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE-NYKKWITTICVRTFYDfYRKKKRWKDRILDlfhk 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  76 --QSIPDFVYNSTALSTSNNTSDFIGFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDL 153
Cdd:PRK12522  87 edGGEIEFADDVNISEEFIQKVEAEMIREVIQLLNEKYKTVLVLYYYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166


                 ..
gi 639234871 154 LK 155
Cdd:PRK12522 167 LE 168
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 21-149 3.23e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 55.49  E-value: 3.23e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  21 EYTEEIIQDVFVKIWNSVHQYdSQKGRFYTWMINIARNTAIDYLKSKGFQNELKNQSIpdfvyNSTALSTSNNTSDF--I 98
Cdd:PRK12518  35 ELLDDLVQEVFLRVWKGLPKL-RNPAYFSTWLYRITWNVATDARRQFAQRPSRIQDDS-----LNDQPSRPSDTPDLmqL 108

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 639234871  99 GFNNV----LESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKM---RNALMK 149
Cdd:PRK12518 109 HYQDLvqqgLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTVKSRLfyaRRQLRK 166
algU PRK11923
RNA polymerase sigma factor AlgU; Provisional
 5-156 1.32e-09

RNA polymerase sigma factor AlgU; Provisional


Pssm-ID: 171347 [Multi-domain]  Cd Length: 193  Bit Score: 54.42  E-value: 1.32e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   5 YSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGrFYTWMINIARNTAIDYLKSKGFQNELKNQSIPD--FV 82
Cdd:PRK11923  29 YQHKILGLIVRFVHDTAEAQDVAQEAFIKAYRALGNFRGDSA-FYTWLYRIAINTAKNHLVSRGRRPPDSDVSSEDaeFY 107

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  83 YNSTALSTSNN-----TSDFIG--FNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKM---RNALMK-LK 151
Cdd:PRK11923 108 DGDHALKDIESperalLRDEIEgtVHRTIQQLPEDLRTALTLREFDGLSYEDIASVMQCPVGTVRSRIfraREAIDKaLQ 187


                 ....*
gi 639234871 152 DLLKD 156
Cdd:PRK11923 188 PLLQE 192
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 102-151 2.87e-09

Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplasmic stress and pathogenesis. Ec sigmaE SR4 also contacts the -35 element, but recognizes a different consensus (a 7-base-pair GGAACTT). Plant SFs recognize sigma70 type promoters and direct transcription of the major plastid RNA polymerase, plastid-encoded RNA polymerase (PEP).


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 50.18  E-value: 2.87e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 639234871 102 NVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLK 151
Cdd:cd06171    6 EALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK09644 PRK09644
RNA polymerase sigma factor SigM; Provisional
 1-156 1.11e-08

RNA polymerase sigma factor SigM; Provisional


Pssm-ID: 170033 [Multi-domain]  Cd Length: 165  Bit Score: 51.42  E-value: 1.11e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGRfyTWMINIARNTAIDYLKSKGFQNELKNQSIPD 80
Cdd:PRK09644   6 IYKMYINDVYRYLFSLTKSHHAAEDLLQETFYRAYIYLEDYDNQKVK--PWLFKVAYHTFIDFVRKEKKVSFVGTDEIEA 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 639234871  81 FVYNSTAlSTSNNTSDFIGFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLKD 156
Cdd:PRK09644  84 IQAESTE-EYVVAKNSYEKLIQIIHTLPVIEAQAILLCDVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 104-150 1.87e-08

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


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 48.22  E-value: 1.87e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 639234871  104 LESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKL 150
Cdd:pfam08281   8 LEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12538 PRK12538
RNA polymerase sigma factor; Provisional
 10-155 3.80e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 139048 [Multi-domain]  Cd Length: 233  Bit Score: 47.93  E-value: 3.80e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  10 YGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGRFYTWMINIARNTAIDYLKSKGFQNELKNQSIPDFVYNSTALS 89
Cdd:PRK12538  77 YAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRAKFSTWLYRVVSNRCIDLRRKPRTENVDAVPEVADGKPDAVSVI 156

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 639234871  90 TSNNTSDFIgfNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLK 155
Cdd:PRK12538 157 ERNELSDLL--EAAMQRLPEQQRIAVILSYHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 8-65 8.79e-07

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 46.18  E-value: 8.79e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 639234871   8 ALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGRFYTWMINIARNTAIDYLK 65
Cdd:PRK05602  32 RLLALATRMLGDPAEAEDVAQETFLRIWKQAPSWRPGEARFDTWLHRVVLNLCYDRLR 89
PRK12547 PRK12547
RNA polymerase sigma factor; Provisional
 16-155 3.55e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 139056 [Multi-domain]  Cd Length: 164  Bit Score: 44.48  E-value: 3.55e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  16 IVQSKEYTEEIIQDVFVKIWNsvhQYDS-QKG-RFYTWMINIARNTAIDYLKSKGFQNELKNQSipdFVYNSTALSTSNN 93
Cdd:PRK12547  26 LSSKHDKAEDLVQDTLMKAWA---KQDSfEMGtNLKAWLFTILRNEFYSQMRKRGREVQDSDGV---FTARVAVHPAQYG 99

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 639234871  94 TSDFIGFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDLLK 155
Cdd:PRK12547 100 SLDLQDFKKALNLLSADQREAIILIGASGFSYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161
PRK09642 PRK09642
RNA polymerase sigma factor;
5-72 5.46e-06

RNA polymerase sigma factor;


Pssm-ID: 170031 [Multi-domain]  Cd Length: 160  Bit Score: 43.94  E-value: 5.46e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 639234871   5 YSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYdsQKGRFYTWMINIARNTAIDYLKSKGFQNE 72
Cdd:PRK09642   4 YRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNY--QFRGLKTWMARIATNHAIDYKRKKARENE 69
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 121-151 7.36e-06

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 41.36  E-value: 7.36e-06
                           10        20        30
                   ....*....|....*....|....*....|.
gi 639234871   121 QGYTQNEISEQLKIPLGTVKTKMRNALMKLK 151
Cdd:smart00421  17 EGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 109-151 6.74e-05

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 38.67  E-value: 6.74e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 639234871 109 TDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLK 151
Cdd:cd06170    2 TPREREVLRLLAEGKTNKEIADILGISEKTVKTHLRNIMRKLG 44
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
105-150 1.85e-04

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 39.69  E-value: 1.85e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 639234871 105 ESLETDKQELInmayYQGYTQNEISEQLKIPLGTVKTKMRNALMKL 150
Cdd:COG2909  124 EALAALRRRLL----AEGLSNKEIAERLFISVNTVKTHLRNIYRKL 165
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 1-153 3.42e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 38.76  E-value: 3.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871   1 MYDNYSGALYGVIFRIVQSKEYTEEIIQDVFVKIWNSVHQYDSQKGRfyTWMINIARNTAID-YLKSKGFqnelKNQSIP 79
Cdd:PRK12541  10 IYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYKGEEIR--PWLFTIAYNAFIDwYRKEKKY----KTTTIE 83

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 639234871  80 DFVYNSTAlSTSNN---TSDFIGFNNVLESLETDKQELINMAYYQGYTQNEISEQLKIPLGTVKTKMRNALMKLKDL 153
Cdd:PRK12541  84 EFHLPNVP-STEHEyfiKHEIASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159
GerE pfam00196
Bacterial regulatory proteins, luxR family;
120-151 5.07e-04

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 36.41  E-value: 5.07e-04
                          10        20        30
                  ....*....|....*....|....*....|..
gi 639234871  120 YQGYTQNEISEQLKIPLGTVKTKMRNALMKLK 151
Cdd:pfam00196  15 AAGKSNKEIADELGISEKTVKVHRSNIMRKLN 46
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 121-150 1.17e-03

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 36.79  E-value: 1.17e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 639234871 121 QGYTQNEISEQLKIPLGTVKTKMRNALMKL 150
Cdd:COG2197   83 EGLSNKEIAERLGISERTVKTHVSNILRKL 112
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
121-150 1.47e-03

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 37.43  E-value: 1.47e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 639234871 121 QGYTQNEISEQLKIPLGTVKTKMRNALMKL 150
Cdd:COG2771  141 EGLTLKEIARILGISERTVRTHLKRIYRKL 170
PRK12535 PRK12535
RNA polymerase sigma factor; Provisional
 50-146 6.03e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237130 [Multi-domain]  Cd Length: 196  Bit Score: 35.64  E-value: 6.03e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 639234871  50 TWMINIARNTAIDYLKSKGFQNELKNQSIPDFVYNSTALSTSNNTSDFIGFNNVLESLETDKQELINMAYYQGYTQNEIS 129
Cdd:PRK12535  77 TWLLSLARRVWVDNIRHDMARPRKSATEYEDAAATTASNETTGSWSEWIDVRTLIDALPPERREALILTQVLGYTYEEAA 156

                         90
                 ....*....|....*..
gi 639234871 130 EQLKIPLGTVKTKMRNA 146
Cdd:PRK12535 157 KIADVRVGTIRSRVARA 173
 
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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