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Conserved domains on  [gi|517910544|ref|WP_019080752|]
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MULTISPECIES: RNA polymerase sigma factor [Yersinia]

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]; ...
 13-176 1.30e-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: 127.80  E-value: 1.30e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  13 YQNTYGQLVSFFRKRLDNASDATDLSHDVF-TLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRAAGKQRMALaqshedDD 91
Cdd:COG1595   23 YERYRPRLYRYARRLLGDRADAEDLVQETFlRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELL------DE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  92 AEQEMAPSGADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCKRHVA 171
Cdd:COG1595   97 LAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALE 176


                 ....*
gi 517910544 172 EQGSE 176
Cdd:COG1595  177 EEGAL 181
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-176 1.30e-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: 127.80  E-value: 1.30e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  13 YQNTYGQLVSFFRKRLDNASDATDLSHDVF-TLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRAAGKQRMALaqshedDD 91
Cdd:COG1595   23 YERYRPRLYRYARRLLGDRADAEDLVQETFlRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELL------DE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  92 AEQEMAPSGADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCKRHVA 171
Cdd:COG1595   97 LAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALE 176


                 ....*
gi 517910544 172 EQGSE 176
Cdd:COG1595  177 EEGAL 181
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 14-167 1.00e-36

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 124.89  E-value: 1.00e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  14 QNTYGQLVSFFRKRLDNASDATDLSHDVFTLWLKRAKQTPVEHSRAFLFKIAHRVLID-HWRAAGKQRMALaqsHEDDDA 92
Cdd:PRK12527   2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDrHRRHRVRQAEPL---EVLDEE 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 517910544  93 EQEMAPSgadPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCK 167
Cdd:PRK12527  79 ERLHSPS---PQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCR 150
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 13-170 2.26e-26

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: 98.19  E-value: 2.26e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544   13 YQNTYGQLVSFFRKRLDNASDATDLSHDVF-TLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRaagKQRMALAQSHEDDD 91
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFlKLLEALDRFDPEGSFKAWLFRIARNLILDYLR---RKRRLRRELDLLEE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 517910544   92 AEQEMApsgaDPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCKRHV 170
Cdd:TIGR02937  84 LLDSDP----SPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 115-166 1.33e-13

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: 62.09  E-value: 1.33e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 517910544  115 RLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHC 166
Cdd:pfam08281   3 ALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 115-167 9.32e-10

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


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 52.11  E-value: 9.32e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 517910544 115 RLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCK 167
Cdd:cd06171    3 RLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 120-163 5.46e-03

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 33.65  E-value: 5.46e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 517910544   120 LNSLSPRRRE--AFLMhrfDGLSQIEVAERMGISVSMVEKHIAGAL 163
Cdd:smart00421   1 LASLTPREREvlRLLA---EGLTNKEIAERLGISEKTVKTHLSNIM 43
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 13-176 1.30e-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: 127.80  E-value: 1.30e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  13 YQNTYGQLVSFFRKRLDNASDATDLSHDVF-TLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRAAGKQRMALaqshedDD 91
Cdd:COG1595   23 YERYRPRLYRYARRLLGDRADAEDLVQETFlRLWRKLDSFRGRGSFRAWLYRIARNLAIDHLRKRRRRRELL------DE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  92 AEQEMAPSGADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCKRHVA 171
Cdd:COG1595   97 LAEELPDEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALE 176


                 ....*
gi 517910544 172 EQGSE 176
Cdd:COG1595  177 EEGAL 181
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 14-167 1.00e-36

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 124.89  E-value: 1.00e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  14 QNTYGQLVSFFRKRLDNASDATDLSHDVFTLWLKRAKQTPVEHSRAFLFKIAHRVLID-HWRAAGKQRMALaqsHEDDDA 92
Cdd:PRK12527   2 ENYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDrHRRHRVRQAEPL---EVLDEE 78

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 517910544  93 EQEMAPSgadPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCK 167
Cdd:PRK12527  79 ERLHSPS---PQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCR 150
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 13-170 2.26e-26

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: 98.19  E-value: 2.26e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544   13 YQNTYGQLVSFFRKRLDNASDATDLSHDVF-TLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRaagKQRMALAQSHEDDD 91
Cdd:TIGR02937   7 YERYLPLVYRYARRYLGDDADAEDLVQEAFlKLLEALDRFDPEGSFKAWLFRIARNLILDYLR---RKRRLRRELDLLEE 83

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 517910544   92 AEQEMApsgaDPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCKRHV 170
Cdd:TIGR02937  84 LLDSDP----SPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 1-167 1.21e-25

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 96.96  E-value: 1.21e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544   1 MDKPPSNKVSLAYQNTYGQLVSFFRKRLDNASDATDLSHDVFT-LWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRAAGKQ 79
Cdd:PRK11924   7 DATGDKEAFSELFRPHAPDLLRYARRQLGDRALAEDAVQEAFLrAWRKADLFNGKGSARTWLLTIARNVCYDLLRRRRRE 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  80 RMALaqshEDDDAEQEMAPSGADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHI 159
Cdd:PRK11924  87 KAVL----SDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRL 162


                 ....*...
gi 517910544 160 AGALLHCK 167
Cdd:PRK11924 163 RRARQLLR 170
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 2-166 2.56e-25

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 95.69  E-value: 2.56e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544   2 DKPPSNKVSLAYQNTYGQLVSFFRKRLDNASDATDLSHDVFTLWLKRAK-QTPVEhSRAFLFKIAHRVLIDHWRAAGKQR 80
Cdd:PRK12523   5 QSPHSELVGALYRDHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPElPTPRE-PRAFLAAVAKGLMFDHFRRAALEQ 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  81 MALAQSHEDDDAEQemaPSGADPQHVLEQQQRLSRLeqaLNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIA 160
Cdd:PRK12523  84 AYLAELALVPEAEQ---PSPEEQHLILEDLKAIDRL---LGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLA 157


                 ....*.
gi 517910544 161 GALLHC 166
Cdd:PRK12523 158 QGLRQC 163
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 5-166 6.42e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 86.82  E-value: 6.42e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544   5 PSNKVSLAYQNTYGQLVSFFRKRLDNASDATDLSHDVFTLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRAAGKQRM--- 81
Cdd:PRK12528   2 HSATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLERAyle 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  82 ALAQSHEdddaeqEMAPSGADPQHVLEQqqrLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAG 161
Cdd:PRK12528  82 ALAQLPE------RVAPSEEERAIILET---LVELDQLLDGLPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYLNK 152


                 ....*
gi 517910544 162 ALLHC 166
Cdd:PRK12528 153 AAMRC 157
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 1-172 7.56e-22

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 86.92  E-value: 7.56e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544   1 MDKPPSNKVSLAYQNTYGQLVSFFRKRLDNASDATDLSHDVFTLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRAAGKQR 80
Cdd:PRK12525   3 QGSIKNTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASIREPRALLTTIARRLMYEGWRRQDLER 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  81 MALAQSHEdddAEQEMAPSGADPQHVLEQQQRLSRLeqaLNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIA 160
Cdd:PRK12525  83 AYLQSLAE---APEAVQPSPEEQWMVIETLLAIDRL---LDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMV 156

                        170
                 ....*....|..
gi 517910544 161 GALLHCKRHVAE 172
Cdd:PRK12525 157 EAFKCCYQGFQE 168
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 13-174 2.14e-21

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 85.63  E-value: 2.14e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  13 YQNTYGQLVSFFRKRLDNASDATDLSHDVFTLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRaagkqRMALAQSHEDDDA 92
Cdd:PRK09651  16 YGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFR-----RNALEKAYLEMLA 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  93 E--QEMAPSGADPQHVLEQQQRLSRLeqaLNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCKRHV 170
Cdd:PRK09651  91 LmpEGGAPSPEERESQLETLQLLDSM---LDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCLLFR 167


                 ....
gi 517910544 171 AEQG 174
Cdd:PRK09651 168 LEYG 171
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 19-167 6.23e-17

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 73.95  E-value: 6.23e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  19 QLVSFFRKRLDNASDATDLSHDVFTLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRaagkqRMALAQSHEDDDAEQEMAP 98
Cdd:PRK07037  10 MLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPVAYLFRIVRNLAIDHYR-----RQALENKYHGDEEDGLDVP 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  99 S-GADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCK 167
Cdd:PRK07037  85 SpEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCR 154
PRK09637 PRK09637
RNA polymerase sigma factor SigZ; Provisional
 13-153 2.96e-14

RNA polymerase sigma factor SigZ; Provisional


Pssm-ID: 236601 [Multi-domain]  Cd Length: 181  Bit Score: 66.93  E-value: 2.96e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  13 YQNTYGQLVSFFRKRLDNASDATDLSHDVFtlwLKRAKQTP----VEHSRAFLFKIAHRVLIDHWRAAGKQRMALAQ-SH 87
Cdd:PRK09637   7 WSEYKAQLKAFLHSRVSNEADVDDLLQEVL---IKTHSNLHslkdGSSIKSWLYQIANNTIIDFYRKKNRSEELPDDlLF 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 517910544  88 EDDDAEQEMapsgadpqhvleqQQRLSR-LEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVS 153
Cdd:PRK09637  84 EDEEREENA-------------KKELAPcLRPFIDALPEKYAEALRLTELEGLSQKEIAEKLGLSLS 137
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 115-166 1.33e-13

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: 62.09  E-value: 1.33e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 517910544  115 RLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHC 166
Cdd:pfam08281   3 ALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 8-166 1.36e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 62.65  E-value: 1.36e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544   8 KVSLAYQNTYGQLVSFFRKRLDNASD--ATDLSHDVFTLWL--KRAKQTP-VEHSRAFLFKIAHRVLIDhWRAagKQRMA 82
Cdd:PRK12529  14 KVATLYRENHAWLRNWLAYRLRSWGRgvADDLAHDIFLRILasRDGGQREaIRQPRAYLARIANCVLVS-WRR--RQSLE 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  83 LAQSHEDDDAEQEMAPSGADPQHVLEQqqrLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGA 162
Cdd:PRK12529  91 LAWLEALATLPEPLHPSPEQQSVILET---LHEIDALLDTLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQA 167


                 ....
gi 517910544 163 LLHC 166
Cdd:PRK12529 168 YVTC 171
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 14-172 6.01e-12

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 60.98  E-value: 6.01e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  14 QNTYGQLVSFFRKRLD--------NASDATDLSHDVF-TLWLK------RAKqtpvehSRAFLFKIAHRVLIDHWRAAGK 78
Cdd:PRK09652   9 RAAFALLVRRYQPRVKrllsrltrDPADAEDLVQETFiKAYRAlhsfrgGAA------FYTWLYRIARNTAINYLRKQGR 82

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  79 QRMALAQSHEDDDAEQ--EMAPSGADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVE 156
Cdd:PRK09652  83 RPPASDVDAEEAEDFDlaDALRDISTPENELLSAELEQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVR 162

                        170
                 ....*....|....*.
gi 517910544 157 KHIAGALLHCKRHVAE 172
Cdd:PRK09652 163 SRIFRAREALRAKLQP 178
PRK12513 PRK12513
RNA polymerase sigma factor; Provisional
 20-174 9.84e-12

RNA polymerase sigma factor; Provisional


Pssm-ID: 183566 [Multi-domain]  Cd Length: 194  Bit Score: 60.47  E-value: 9.84e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  20 LVSFFRKRLDNASDATDLSHDVftlWLK----RAKQTPVEHSRAFLFKIAHRVLIDHWRAAGKQRmalAQSHEDDDAEQE 95
Cdd:PRK12513  39 LYRFLLRLARDRALAEDIFQET---WLRviraRAQYQPRARFRTWLYQIARNLLIDHWRRHGARQ---APSLDADEQLHA 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 517910544  96 MAPSGADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCKRHVAEQG 174
Cdd:PRK12513 113 LADDGAAPEQQLSLFRDRRRLQAALETLPDEQREVFLLREHGDLELEEIAELTGVPEETVKSRLRYALQKLRELLAEEV 191
PRK12534 PRK12534
RNA polymerase sigma factor; Provisional
 13-167 2.75e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 183576 [Multi-domain]  Cd Length: 187  Bit Score: 56.60  E-value: 2.75e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  13 YQNTYGQLVSFFRKRLDNASDATDLSHDVFTLWLKRAKQTPVEHSRA--FLFKIAHRVLIDHWRAAGKQRMALAQshedD 90
Cdd:PRK12534  31 YRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRARGltWLAMIARNKAIDHLRANAPQRRNVAL----D 106

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 517910544  91 DAeQEMAPSGADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCK 167
Cdd:PRK12534 107 DA-GELRAADASPLERTERASTRRRIDHCLAELEPPRSELIRTAFFEGITYEELAARTDTPIGTVKSWIRRGLAKLK 182
PRK06930 PRK06930
positive control sigma-like factor; Validated
 74-172 3.35e-10

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 55.89  E-value: 3.35e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  74 RAAGKQRMAL-------AQSHEDDDAEQEMApsgaDPQHVLEQQQRLsRLEQALNSLSPRRREAFLMHRFDGLSQIEVAE 146
Cdd:PRK06930  64 RRAAYQREVIcdplliqRYFRSMEDLEWDIE----EPESVISEWDKI-RIEDALSVLTEREKEVYLMHRGYGLSYSEIAD 138

                         90       100
                 ....*....|....*....|....*.
gi 517910544 147 RMGISVSMVEKHIAGALLHCKRHVAE 172
Cdd:PRK06930 139 YLNIKKSTVQSMIERAEKKIARQINE 164
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 115-167 9.32e-10

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


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 52.11  E-value: 9.32e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 517910544 115 RLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCK 167
Cdd:cd06171    3 RLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 9-153 1.37e-09

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 55.74  E-value: 1.37e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544   9 VSLAYQNTYGQLVSFFRKRLDNASDATDLSHDVFtLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRAAG--KQRMALAQS 86
Cdd:PRK09635   7 VSAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAF-SRLLRAPVGDIDDERGWLIVVTSRLCLDHIKSAStrRERPQDIAA 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 517910544  87 HEDDDAeqemAPSGADPQH--VLEQQQRLSRLEqALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVS 153
Cdd:PRK09635  86 WHDGDA----SVSSVDPADrvTLDDEVRLALLI-MLERLGPAERVVFVLHEIFGLPYQQIATTIGSQAS 149
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 75-172 4.75e-09

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: 53.67  E-value: 4.75e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  75 AAGKQRMALAQSHEDDDAEQEMAPSGaDPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSM 154
Cdd:COG1191  140 ANAYQLLSLDEPLEDGDDLLDLLESG-DPEEELEHEELREALAEAIEQLPERERLVLSLYYFEELTLKEIAEVLGVSESR 218

                         90
                 ....*....|....*...
gi 517910544 155 VEKHIAGALLHCKRHVAE 172
Cdd:COG1191  219 VSRLHKKALARLREYLKE 236
PRK09639 PRK09639
RNA polymerase sigma factor SigX; Provisional
 13-169 5.06e-09

RNA polymerase sigma factor SigX; Provisional


Pssm-ID: 236602 [Multi-domain]  Cd Length: 166  Bit Score: 52.64  E-value: 5.06e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  13 YQNTYGQLVSFFRKRLDNASDATDLSHDVFtlwLKRAKQTP--VEHSRAFLFKIAHRVLIDHWRAAGKQRmalaqSHEDD 90
Cdd:PRK09639   9 FEQYYPDVVQQIFYIVKDRTQAEDLAQEVF---LRLYRSDFkgIENEKGWLIKSARNVAYNYLRSEKRRR-----ARILG 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 517910544  91 DAEQEMAPSGADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMhRFDGLSQIEVAERMGISVSMVEKHIAGALLHCKRH 169
Cdd:PRK09639  81 EFQWQEVDNEPSPEEIWIRKEEITKVQEVLAKMTERDRTVLLL-RFSGYSYKEIAEALGIKESSVGTTLARAKKKFRKI 158
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 28-156 1.94e-08

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 51.58  E-value: 1.94e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  28 LDNASDATDLSHDVFT-LWLKRAKQTPVEHS-RAFLFKIAHRVLIDHWRaagKQRMALaqshEDDDAEQEMAPSGADPQH 105
Cdd:PRK05602  41 LGDPAEAEDVAQETFLrIWKQAPSWRPGEARfDTWLHRVVLNLCYDRLR---RRREVP----VEDAPDVPDPAPGPDAGL 113

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 517910544 106 VLEQQQRlsRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVE 156
Cdd:PRK05602 114 EARQRAR--RVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALE 162
PRK09047 PRK09047
RNA polymerase factor sigma-70; Validated
 33-163 2.00e-08

RNA polymerase factor sigma-70; Validated


Pssm-ID: 236367 [Multi-domain]  Cd Length: 161  Bit Score: 51.12  E-value: 2.00e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  33 DATDLSHDVFTLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRaagKQRM-----ALAQSHEDDDAEQEM---------AP 98
Cdd:PRK09047   6 AALDIVQDAMIKLAEKYGDRPAAEWPPLFQRILQNRIHDWFR---RQKVrntwvSLFSSFSDDDDDDDFdpletldsaDE 82

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 517910544  99 SGADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGAL 163
Cdd:PRK09047  83 GAESPADKLERAQVLQLIEEAIQKLPARQREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRAT 147
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 15-168 2.39e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 51.21  E-value: 2.39e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  15 NTYGQLVsfFR---KRLDNASDATDLSHDVF-TLWlKRAKQTPVEHS-RAFLFKIAHRVLIDHWRAAGKQRMALAQSHED 89
Cdd:PRK12519  36 DRHAGLV--YGlalKILGNSQEAEDLTQEIFlSLW-RKSSYDPKRGSlSSYLLTLTRSRAIDRLRSRRSRQRLLERWQQE 112

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 517910544  90 DDAEqemaPSGADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCKR 168
Cdd:PRK12519 113 LLGE----ASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187
PRK13919 PRK13919
putative RNA polymerase sigma E protein; Provisional
 25-172 6.37e-08

putative RNA polymerase sigma E protein; Provisional


Pssm-ID: 184395 [Multi-domain]  Cd Length: 186  Bit Score: 49.91  E-value: 6.37e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  25 RKRLDNASdATDLSHDVFT-LWLKRAKQTPVEHS-RAFLFKIAHRVLIDHWRaagkQRMALAQSHEDDDAEQE---MAPS 99
Cdd:PRK13919  42 RMGLDGAA-AEDVVQEVFIrVWKKAKEFDPRRGSaRAWLLALAHHAAVDHVR----RRAARPQPLEPDEREPEafdLPGP 116

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 517910544 100 GADPQHVLEQqqrlSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCKRHVAE 172
Cdd:PRK13919 117 GLDEEGHLDR----TRLGRALKALSPEERRVIEVLYYQGYTHREAAQLLGLPLGTLKTRARRALSRLKEVLRE 185
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 119-168 1.05e-06

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: 43.57  E-value: 1.05e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 517910544  119 ALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCKR 168
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 28-156 1.28e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 46.42  E-value: 1.28e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  28 LDNASDATDLSHDVFTLWLKRAKQTPVEHSR--AFLFKIAHRVLIDHWRAAGKQRMALaqsheddDAEQEMAPSGADPQH 105
Cdd:PRK12524  47 LGDRAEAEDVTQEAMLRLWRIAPDWRQGEARvsTWLYRVVCNLCTDRLRRRRRASVDL-------DDAPEPADAAPGAEE 119

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 517910544 106 VLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVE 156
Cdd:PRK12524 120 ALIEGDRMRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVE 170
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
100-170 6.03e-06

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 44.94  E-value: 6.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544 100 GADPQHVLEQ-----QQRLSRLE-----QALNSLSPRRREAFLMHRFDGLSQIEVAERMGIS---VSMVEKhiaGALLHC 166
Cdd:PRK08215 177 GGDPIYVMDQisdekNKDENWLEeialkEAMKKLNDREKLILNLRFFQGKTQMEVAEEIGISqaqVSRLEK---AALKHM 253


                 ....
gi 517910544 167 KRHV 170
Cdd:PRK08215 254 RKYI 257
PRK12511 PRK12511
RNA polymerase sigma factor; Provisional
 18-150 6.17e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237123 [Multi-domain]  Cd Length: 182  Bit Score: 44.39  E-value: 6.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  18 GQLVS---FFRKRLDNASDATDLSHDVFTLWL-KRAKQTPVEHSRAFLFKIAHRVLIDHWRaagkQRMALAQSHedDDAE 93
Cdd:PRK12511  12 DQLVPlrrYARSLTRDSAEAEDLVHDALVRALeRRASFRSGGNLRTWLMSILHNAFIDELR----RRRVEARRA--DELA 85

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 517910544  94 QEMAPSGADPQhvlEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGI 150
Cdd:PRK12511  86 VLADASLPAAQ---EHAVRLAQIRDAFFDLPEEQRAALHLVAIEGLSYQEAAAVLGI 139
Sigma70_ECF pfam07638
ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the ...
 17-169 7.15e-06

ECF sigma factor; These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545.


Pssm-ID: 254323 [Multi-domain]  Cd Length: 185  Bit Score: 44.33  E-value: 7.15e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544   17 YGQLVSFFRKRLDNAS-----DATDLSHDVFtLWLKRAKQTPVEHSRAFLFKIA----HRVLIDHWRAAGKQ-RMALAQS 86
Cdd:pfam07638  27 YDELRRLAGSKLQNERrghtlQPTALVHEAF-VRLVDTEDFPDWSGRGHFFAAAaeamRRILIDHARRRQRQkRGGDVQR 105

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544   87 HE-DDDAEQEMAPsgaDPQHVLEQQQRLSRLEqalnSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLH 165
Cdd:pfam07638 106 RElDEVVDNGDSP---NPDLLLDLDEALEQLF----SLSPRQARLVELRFFAGLSNDEIAERLGVSERTVERNWALARAW 178


                  ....
gi 517910544  166 CKRH 169
Cdd:pfam07638 179 LHRE 182
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 107-159 8.94e-06

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 44.53  E-value: 8.94e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 517910544 107 LEQQQRLsRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHI 159
Cdd:PRK07408 189 LAQEDRI-RLQQALAQLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRV 240
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 36-155 1.17e-05

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 43.55  E-value: 1.17e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  36 DLSHDVFtlwLKRAKQTPVEHSRAF----LFKIAHRVLIDHWRAAGKQRMALaqsHEDDDAEQEMAPSGADPQHVLEQQQ 111
Cdd:PRK12518  39 DLVQEVF---LRVWKGLPKLRNPAYfstwLYRITWNVATDARRQFAQRPSRI---QDDSLNDQPSRPSDTPDLMQLHYQD 112

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 517910544 112 RLSrleQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMV 155
Cdd:PRK12518 113 LVQ---QGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNIPVGTV 153
PRK12539 PRK12539
RNA polymerase sigma factor SigF;
18-155 1.23e-05

RNA polymerase sigma factor SigF;


Pssm-ID: 237132 [Multi-domain]  Cd Length: 184  Bit Score: 43.57  E-value: 1.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  18 GQLVSFFRKRLD----NASDATDLSHD-VFTLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRAagkQRMALAQShEDDDA 92
Cdd:PRK12539  32 GHLRAYYKGKLArigrGAEEAEDLVQEaLMAIHTRRHTYDPEQPLTPWVYAIARYKLIDHLRR---TRASLADV-PIDDA 107

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 517910544  93 EQEMApsgADPQHVLEQQQRLSRLeqaLNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMV 155
Cdd:PRK12539 108 DELVA---HDDHAAVESTLDLGRL---LARLPEKMRLAIQAVKLEGLSVAEAATRSGMSESAV 164
PRK09647 PRK09647
RNA polymerase sigma factor SigE; Reviewed
 30-159 2.72e-05

RNA polymerase sigma factor SigE; Reviewed


Pssm-ID: 236606 [Multi-domain]  Cd Length: 203  Bit Score: 42.85  E-value: 2.72e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  30 NASDATDLSHDVFTLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRAAGKQRM-ALAqshedDDAEQeMAPSGADPQHVLE 108
Cdd:PRK09647  51 NQHDAEDLTQETFIRVFRSLQNYQPGTFEGWLHRITTNLFLDMVRRRARIRMeALP-----EDYDR-VPGDEPNPEQIYH 124

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 517910544 109 QQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHI 159
Cdd:PRK09647 125 DARLDPDLQAALDSLPPEFRAAVVLCDIEGLSYEEIAATLGVKLGTVRSRI 175
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 13-78 8.44e-05

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: 39.11  E-value: 8.44e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 517910544   13 YQNTYGQLVSFFRKRLDNASDATDLSHDVFTLWLKRAKQTPVEHS---RAFLFKIAHRVLIDHWRAAGK 78
Cdd:pfam04542   2 VERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGvsfSTWLYTIIRNAIIDYLRKQRR 70
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
100-157 1.05e-04

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 41.47  E-value: 1.05e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544 100 GADPQHVLEQQQR---LSRLEQALNSLSPRRREAFLMhRFdGL------SQIEVAERMGIS---VSMVEK 157
Cdd:PRK05803 150 GSEEDDVIEQVELkmeVEKLYKKIDILDEREKEVIEM-RY-GLgngkekTQREIAKALGISrsyVSRIEK 217
PRK12541 PRK12541
RNA polymerase sigma factor; Provisional
 34-156 1.26e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 183580 [Multi-domain]  Cd Length: 161  Bit Score: 40.69  E-value: 1.26e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  34 ATDLSHDVFTLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRAAGKQRMAlaqsheddDAEQEMAPSGADPQHVLEQQQRL 113
Cdd:PRK12541  32 AEDLMQETFYRMLVHIDYYKGEEIRPWLFTIAYNAFIDWYRKEKKYKTT--------TIEEFHLPNVPSTEHEYFIKHEI 103

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 517910544 114 SRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVE 156
Cdd:PRK12541 104 ASWLDSLSSLPLERRNVLLLRDYYGFSYKEIAEMTGLSLAKVK 146
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
116-159 1.69e-04

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 40.73  E-value: 1.69e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 517910544 116 LEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGIS---VSMVEKHI 159
Cdd:PRK05572 196 LKEAIRELDERERLIVYLRYFKDKTQSEVAKRLGISqvqVSRLEKKI 242
PRK09646 PRK09646
ECF RNA polymerase sigma factor SigK;
59-163 2.24e-04

ECF RNA polymerase sigma factor SigK;


Pssm-ID: 182015 [Multi-domain]  Cd Length: 194  Bit Score: 40.04  E-value: 2.24e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  59 AFLFKIAHRVLIDHWRAAgkqrmalaQSHEDDDAEQEMAPSGADPQHVLEQQQRL---SRLEQALNSLSPRRREAFLMHR 135
Cdd:PRK09646  84 AWLLTLAHRRAVDRVRSE--------QAASQREVRYGARNVDPAFDQVAEEVEARlerERVRDCLDALTDTQRESVTLAY 155

                         90       100
                 ....*....|....*....|....*...
gi 517910544 136 FDGLSQIEVAERMGISVSMVEKHIAGAL 163
Cdd:PRK09646 156 YGGLTYREVAERLAVPLGTVKTRMRDGL 183
PRK12544 PRK12544
RNA polymerase factor sigma-70;
58-153 2.31e-04

RNA polymerase factor sigma-70;


Pssm-ID: 183583 [Multi-domain]  Cd Length: 206  Bit Score: 40.17  E-value: 2.31e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  58 RAFLFKIAHRVLIDHWRAagKQRMALAQSHEDDDAEQEM---------------APSGAD-PQHVLEQQQRLSRLEQALN 121
Cdd:PRK12544  70 KTWVFAILKNKIIDLLRQ--KKRHVSASSLLRDEEEEEDfeelfdesghwqkdeRPQAWGnPEESLEQEQFWRIFEACLD 147

                         90       100       110
                 ....*....|....*....|....*....|..
gi 517910544 122 SLSPRRREAFLMHRFDGLSQIEVAERMGISVS 153
Cdd:PRK12544 148 GLPAKYARVFMMREFIELETNEICHAVDLSVS 179
PRK12532 PRK12532
RNA polymerase sigma factor; Provisional
 19-153 3.20e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 171564 [Multi-domain]  Cd Length: 195  Bit Score: 39.53  E-value: 3.20e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  19 QLVSFFRKRL-DNASDATDLSHDVFTLWLKRAKQTPVEHS-RAFLFKIAHRVLIDHWRAAGKQR--MALAQSHEDDDAEQ 94
Cdd:PRK12532  17 LLLHFARLQLpDHPDLAEDLVQETLLSAYSAGDSFQGRALvNSWLFAILKNKIIDALRQIGRQRkvFTLLDDELLDEAFE 96

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 517910544  95 EMAPSGA------------DPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVS 153
Cdd:PRK12532  97 SHFSQNGhwtpegqpqhwnTPEKSLNNNEFQKILQSCLYNLPENTARVFTLKEILGFSSDEIQQMCGISTS 167
PRK09191 PRK09191
two-component response regulator; Provisional
 101-162 3.89e-04

two-component response regulator; Provisional


Pssm-ID: 236402 [Multi-domain]  Cd Length: 261  Bit Score: 39.83  E-value: 3.89e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 517910544 101 ADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGA 162
Cdd:PRK09191  67 AGANDPEPGSPFEARAERRLAGLTPLPRQAFLLTALEGFSVEEAAEILGVDPAEAEALLDDA 128
PRK09649 PRK09649
RNA polymerase sigma factor SigC; Reviewed
 19-162 5.27e-04

RNA polymerase sigma factor SigC; Reviewed


Pssm-ID: 137458 [Multi-domain]  Cd Length: 185  Bit Score: 38.87  E-value: 5.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  19 QLVSFFRKRLDNASDATDLSHDVFTLWLKRAKQTPVEHS-RAFLFKIAHRVLIDHWRAAgkqrmalaqshedddAEQEMA 97
Cdd:PRK09649  35 QDVWRFVAYLSDVGSADDLTQETFLRAIGAIPRFSARSSaRTWLLAIARHVVADHIRHV---------------RSRPRT 99

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 517910544  98 PSGADPQHVLEQQQR------LSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGA 162
Cdd:PRK09649 100 TRGARPEHLIDGDRHargfedLVEVTTMIADLTTDQREALLLTQLLGLSYADAAAVCGCPVGTIRSRVARA 170
PRK09638 PRK09638
RNA polymerase sigma factor SigY; Reviewed
 61-163 7.94e-04

RNA polymerase sigma factor SigY; Reviewed


Pssm-ID: 182010 [Multi-domain]  Cd Length: 176  Bit Score: 38.46  E-value: 7.94e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  61 LFKIAHRVLIDHWRAAGKQRMALAQ-SHEDDDAEQ-EMAPSGADPQHVLEqqqrlsrleqALNSLSPRRREAFLMHRFDG 138
Cdd:PRK09638  73 LISIASRLYKDHLRKQKREKLRLQRaKEETLRKEKwEAAIKGAEWSEMLD----------ALSKLDPEFRAPVILKHYYG 142

                         90       100
                 ....*....|....*....|....*
gi 517910544 139 LSQIEVAERMGISVSMVEKHIAGAL 163
Cdd:PRK09638 143 YTYEEIAKMLNIPEGTVKSRVHHGI 167
PRK09645 PRK09645
ECF RNA polymerase sigma factor SigL;
58-150 9.75e-04

ECF RNA polymerase sigma factor SigL;


Pssm-ID: 236605 [Multi-domain]  Cd Length: 173  Bit Score: 38.14  E-value: 9.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  58 RAFLFKIAHRVLIDHWRAAGKQRMALaqsheDDDAEQEMAPSGADpqhvlEQQQRLSRLE--QALNSLSPRRREAFLMHR 135
Cdd:PRK09645  62 RAWLFTVARNLVIDERRSARARPVEG-----GDDVLGVPEQSAPD-----EVDRALDRLLvaDALAQLSPEHRAVLVRSY 131

                         90
                 ....*....|....*
gi 517910544 136 FDGLSQIEVAERMGI 150
Cdd:PRK09645 132 YRGWSTAQIAADLGI 146
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 132-161 1.55e-03

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 36.15  E-value: 1.55e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 517910544 132 LMHRFDGLSQIEVAERMGISVSMVEKHIAG 161
Cdd:COG3620   24 LMRKELGLSQLPVAELVGVSQSDILRIESG 53
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 104-158 1.64e-03

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 37.39  E-value: 1.64e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 517910544 104 QHVLEQQQRLSRLEQALNSLSPRRRE--AFLMhrfDGLSQIEVAERMGISVSMVEKH 158
Cdd:COG4566  119 RARRAERARRAELRARLASLTPREREvlDLVV---AGLSNKQIARELGISPRTVEVH 172
PRK12514 PRK12514
RNA polymerase sigma factor; Provisional
 10-167 2.30e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 105710 [Multi-domain]  Cd Length: 179  Bit Score: 37.11  E-value: 2.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  10 SLAYQNTYGQLVSFFRKRLDNASDATDLSHDVFTLWLKRAKQTPV-EHS-RAFLFKIAHRVLIDHWRAAGKqrmalaqSH 87
Cdd:PRK12514  22 SSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVsGLSpMTWLITIARNHAIDRLRARKA-------VA 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  88 EDDDAEQEMAPSGADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALLHCK 167
Cdd:PRK12514  95 VDIDEAHDLADPSPGPEAEVIAGDEGQRIDACLEELEKDRAAAVRRAYLEGLSYKELAERHDVPLNTMRTWLRRSLLKLR 174
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
138-161 2.52e-03

Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 35.57  E-value: 2.52e-03
                         10        20
                 ....*....|....*....|....
gi 517910544 138 GLSQIEVAERMGISVSMVEKHIAG 161
Cdd:COG2522   28 GLSQSEIAKLLGITQAAVSQYLSG 51
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 88-151 2.58e-03

DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 37.34  E-value: 2.58e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  88 EDDDAEqemapsgaDPQHVLEQQQRLSRLEQALNSLSPRRREaFLMHRFdGLSQI------EVAERMGIS 151
Cdd:COG0568  180 EDEEAP--------SPEEALEEELLREELREALDTLTERERE-ILRLRF-GLDDGephtleEIGKEFGVS 239
PRK12537 PRK12537
RNA polymerase sigma factor; Provisional
 13-164 2.87e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 171568 [Multi-domain]  Cd Length: 182  Bit Score: 36.68  E-value: 2.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  13 YQNTYGQLVSFFRKRLDNASDATDLSHDVF-TLWLKRAKQTPVEHS-RAFLFKI----AHRVLIDHWRAAgkqrmalaqS 86
Cdd:PRK12537  29 YQQESARLLGVARRIVRDRALAEDIVHDAFiKIWTGAASFDPARGSaRGWIYSVtrhlALNVLRDTRREV---------V 99

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 517910544  87 HEDDDAEQEMAPSGADPQhvLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGALL 164
Cdd:PRK12537 100 LDDDAEETAQTLHEIIDD--FDLWANSGKIHRCLEQLEPARRNCILHAYVDGCSHAEIAQRLGAPLGTVKAWIKRSLK 175
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
11-162 3.19e-03

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 36.66  E-value: 3.19e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  11 LAYQNTYGQLVSFFRKRLDNASDATDLSHDVFTLWLKRAKQTPVEHSRAFLFKIAHRVLIDHWRAAGKQRMALAQSHEDD 90
Cdd:COG2771   16 LLLALLALLLLLLLAALLLLLALLLLAALLLLAAAAAALAAALAAALLLGLLLLLLIALLLLLLLLLALLLLLALLALLA 95

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 517910544  91 DAEQEMAPSGADPQHVLEQQQRLSRLEQALNSLSPRRREAfLMHRFDGLSQIEVAERMGISVSMVEKHIAGA 162
Cdd:COG2771   96 ALLARLAALLLALALAALLLAALARLLARAPGLTPREREV-LRLLAEGLTLKEIARILGISERTVRTHLKRI 166
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 84-163 3.41e-03

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 37.06  E-value: 3.41e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  84 AQSHEDDDAeQEMAPSGADPQHVLEQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIAGAL 163
Cdd:PRK07122 178 GGGSGDDDA-RAIADTLGDVDAGLDQIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVGISQMHVSRLLAKTL 256
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 108-160 5.03e-03

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 36.75  E-value: 5.03e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 517910544 108 EQQQRLSRLEQALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHIA 160
Cdd:COG3415    8 EERRDLEKLLRKTKDAREARRLRAVLLLAEGLSVREIAERLGVSRSTVYRWLK 60
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 120-163 5.46e-03

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 33.65  E-value: 5.46e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
gi 517910544   120 LNSLSPRRRE--AFLMhrfDGLSQIEVAERMGISVSMVEKHIAGAL 163
Cdd:smart00421   1 LASLTPREREvlRLLA---EGLTNKEIAERLGISEKTVKTHLSNIM 43
PRK12515 PRK12515
RNA polymerase sigma factor; Provisional
 64-172 7.19e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 183567 [Multi-domain]  Cd Length: 189  Bit Score: 35.86  E-value: 7.19e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  64 IAHRVLIDHWRAAGK-----------------QRMALAQSHEDDDAEQEMA---PSGAD-PQHVLEQQQRLSRLEQALNS 122
Cdd:PRK12515  52 LVSEVFLDVWRQAGQfegrsqvstwllsiarfKALSALRRRKHEEIDDEAAaaiEDGADtPEVALQKSDTSAALRACLAK 131

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 517910544 123 LSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHiagaLLHCKRHVAE 172
Cdd:PRK12515 132 LSPAHREIIDLVYYHEKSVEEVGEIVGIPESTVKTR----MFYARKKLAE 177
PRK06811 PRK06811
RNA polymerase factor sigma-70; Validated
 40-159 9.29e-03

RNA polymerase factor sigma-70; Validated


Pssm-ID: 180707 [Multi-domain]  Cd Length: 189  Bit Score: 35.30  E-value: 9.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 517910544  40 DVFT-LWLKRAKQTPVEHS-RAFLFKIAHRVLIDHWRAAGKQrmalaqsHEDDDAEQEMAPSGADPQHVLEQQQRLSRLE 117
Cdd:PRK06811  54 DIFLsIWNNIDKFDEEKGSfKKWIAAISKYKAIDYKRKLTKN-------NEIDSIDEFILISEESIENEIILKENKEEIL 126

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 517910544 118 QALNSLSPRRREAFLMHRFDGLSQIEVAERMGISVSMVEKHI 159
Cdd:PRK06811 127 KLINDLEKLDREIFIRRYLLGEKIEEIAKKLGLTRSAIDNRL 168
 
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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