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Conserved domains on  [gi|489177405|ref|WP_003086922|]
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MULTISPECIES: RNA polymerase sigma factor [Pseudomonas]

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]; ...
 16-172 7.27e-29

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: 105.08  E-value: 7.27e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  16 RHYEELVDHVRRRFGDRGMAREVVHDVCVQLLERDEK-EDVHTPLALLRKISHDAAVSRYRSDRRRTAWVEAVAElpEVA 94
Cdd:COG1595   25 RYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSfRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAE--ELP 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489177405  95 CMAATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACRERLGRGEA 172
Cdd:COG1595  103 DEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGA 180
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 16-172 7.27e-29

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: 105.08  E-value: 7.27e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  16 RHYEELVDHVRRRFGDRGMAREVVHDVCVQLLERDEK-EDVHTPLALLRKISHDAAVSRYRSDRRRTAWVEAVAElpEVA 94
Cdd:COG1595   25 RYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSfRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAE--ELP 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489177405  95 CMAATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACRERLGRGEA 172
Cdd:COG1595  103 DEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGA 180
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 11-167 7.44e-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: 96.65  E-value: 7.44e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405   11 LSTLVRHYEELVDHV-RRRFGDRGMAREVVHDVCVQLLERDEK-EDVHTPLALLRKISHDAAVSRYRSDRRRTAWVEAVA 88
Cdd:TIGR02937   3 FEELYERYLPLVYRYaRRYLGDDADAEDLVQEAFLKLLEALDRfDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489177405   89 ELPEvacMAATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACRERL 167
Cdd:TIGR02937  83 ELLD---SDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 16-172 6.20e-20

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 81.36  E-value: 6.20e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  16 RHYEELVDHVRRRFGDRGMAREVVHDVCVQLLERDEKEDVHTPLALLRKISHDAAVSRYRSDR-RRTAWVEAVAElpEVA 94
Cdd:PRK12527   3 NYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRvRQAEPLEVLDE--EER 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489177405  95 CMAATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACRERLGRGEA 172
Cdd:PRK12527  81 LHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQWES 158
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 110-163 1.18e-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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 54.00  E-value: 1.18e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 489177405  110 FQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAAC 163
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 111-164 8.67e-06

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: 41.32  E-value: 8.67e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489177405 111 QALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACR 164
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
RpoE COG1595
DNA-directed RNA polymerase specialized sigma subunit, sigma24 family [Transcription]; ...
 16-172 7.27e-29

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: 105.08  E-value: 7.27e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  16 RHYEELVDHVRRRFGDRGMAREVVHDVCVQLLERDEK-EDVHTPLALLRKISHDAAVSRYRSDRRRTAWVEAVAElpEVA 94
Cdd:COG1595   25 RYRPRLYRYARRLLGDRADAEDLVQETFLRLWRKLDSfRGRGSFRAWLYRIARNLAIDHLRKRRRRRELLDELAE--ELP 102

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489177405  95 CMAATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACRERLGRGEA 172
Cdd:COG1595  103 DEAADPEEALEAEELLEALLAALERLPPRQREVLVLRYLEGLSYAEIAEILGISEGTVKSRLSRARKKLREALEEEGA 180
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 11-167 7.44e-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: 96.65  E-value: 7.44e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405   11 LSTLVRHYEELVDHV-RRRFGDRGMAREVVHDVCVQLLERDEK-EDVHTPLALLRKISHDAAVSRYRSDRRRTAWVEAVA 88
Cdd:TIGR02937   3 FEELYERYLPLVYRYaRRYLGDDADAEDLVQEAFLKLLEALDRfDPEGSFKAWLFRIARNLILDYLRRKRRLRRELDLLE 82

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 489177405   89 ELPEvacMAATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACRERL 167
Cdd:TIGR02937  83 ELLD---SDPSPEEELEQEEEREALREALEKLPEREREVLVLRYLEGLSYKEIAEILGISVGTVKRRLKRARKKLRELL 158
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 15-167 3.91e-25

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: 94.94  E-value: 3.91e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405   15 VRHYEELVDHVRRRFGDRGMAREVVHDVCVQLLE-RDEKEDVHTPLALLRKISHDAAVSRYRSDRRRTAWVEAVAELPEV 93
Cdd:TIGR02985   8 RRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWEnRETLEISESIKAYLFTIVKNRCLNYLRHKQVEEKYQEELAEIEER 87

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489177405   94 ACMAATPMGRHEAErEFQALV-DAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACRERL 167
Cdd:TIGR02985  88 ELSEADPEEELEAK-ELEEIIeEAIEKLPEQCREIFILSRFEGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 161
PRK12527 PRK12527
RNA polymerase sigma factor; Reviewed
 16-172 6.20e-20

RNA polymerase sigma factor; Reviewed


Pssm-ID: 171560 [Multi-domain]  Cd Length: 159  Bit Score: 81.36  E-value: 6.20e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  16 RHYEELVDHVRRRFGDRGMAREVVHDVCVQLLERDEKEDVHTPLALLRKISHDAAVSRYRSDR-RRTAWVEAVAElpEVA 94
Cdd:PRK12527   3 NYYRELVRFLSARLGNRQAAEDVAHDAYLRVLERSSSAQIEHPRAFLYRTALNLVVDRHRRHRvRQAEPLEVLDE--EER 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 489177405  95 CMAATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACRERLGRGEA 172
Cdd:PRK12527  81 LHSPSPQTRLDLGQRLALLQRALAELPPACRDSFLLRKLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQWES 158
PRK11924 PRK11924
RNA polymerase sigma factor; Provisional
 4-171 1.25e-17

RNA polymerase sigma factor; Provisional


Pssm-ID: 183384 [Multi-domain]  Cd Length: 179  Bit Score: 75.78  E-value: 1.25e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405   4 DPAKPTLLSTLVR-HYEELVDHVRRRFGDRGMAREVVHDVCVQLLERDEK-EDVHTPLALLRKISHDAAVSRYRSDRRRT 81
Cdd:PRK11924   8 ATGDKEAFSELFRpHAPDLLRYARRQLGDRALAEDAVQEAFLRAWRKADLfNGKGSARTWLLTIARNVCYDLLRRRRREK 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  82 AWVEAVAELPEVACMAATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLA 161
Cdd:PRK11924  88 AVLSDDALEPEFAETAETPEAALLAKDDLARIDRCLDALPVKQREVFLLRYVEGLSYREIAEILGVPVGTVKSRLRRARQ 167

                        170
                 ....*....|
gi 489177405 162 ACRERLGRGE 171
Cdd:PRK11924 168 LLRECLEAQW 177
PRK07037 PRK07037
extracytoplasmic-function sigma-70 factor; Validated
 11-171 7.28e-15

extracytoplasmic-function sigma-70 factor; Validated


Pssm-ID: 180803 [Multi-domain]  Cd Length: 163  Bit Score: 68.17  E-value: 7.28e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  11 LSTLVRHYEELVDHVRRRFGDRGMAREVVHDVCVQLLERDEKEDVHTPLALLRKISHDAAVSRYRSDRRRTAWVEAVAEL 90
Cdd:PRK07037   1 LDVFVDNRSMLVKIAARIVGCRSRAEDVVQDAFVKLVEAPNQDAVKQPVAYLFRIVRNLAIDHYRRQALENKYHGDEEDG 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  91 PEVACMAATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACRERLGRG 170
Cdd:PRK07037  81 LDVPSPEASPEAALINRDTLRHVADALSELPARTRYAFEMYRLHGETQKDIARELGVSPTLVNFMIRDALVHCRKCLDAC 160


                 .
gi 489177405 171 E 171
Cdd:PRK07037 161 H 161
SigE-fam_strep TIGR02983
RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors ...
 15-168 2.84e-12

RNA polymerase sigma-70 factor, sigma-E family; This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.


Pssm-ID: 132028 [Multi-domain]  Cd Length: 162  Bit Score: 61.25  E-value: 2.84e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405   15 VRHYEELVDHVRRRFGDRGMAREVVHDVCVQLLER-DEKEDVHTPLALLRKISHDAAVSRYRSDRRRTAwveAVAELPEv 93
Cdd:TIGR02983  13 AARYPRLLRTAYLLTGDPHEAEDLVQEALVRTYVRwDRIRDPDAPDAYVRRVLVNLARSRWRRRRLLEL---PTRELPD- 88

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489177405   94 acMAATPMGRHEAERefQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACRERLG 168
Cdd:TIGR02983  89 --AAAPDPAPDVALR--AALARALRRLPARQRAVVVLRYYEDLSEAQVAEALGISVGTVKSRLSRALARLRELLE 159
PRK12529 PRK12529
RNA polymerase sigma factor; Provisional
 26-163 4.04e-11

RNA polymerase sigma factor; Provisional


Pssm-ID: 183574 [Multi-domain]  Cd Length: 178  Bit Score: 58.41  E-value: 4.04e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  26 RRRFGDRGMAREVVHDVCVQLL---ERDEKEDVHTPLALLRKISHDAAVSRYRSDRRRTAWVEAVAELPEVacMAATPMG 102
Cdd:PRK12529  33 RLRSWGRGVADDLAHDIFLRILasrDGGQREAIRQPRAYLARIANCVLVSWRRRQSLELAWLEALATLPEP--LHPSPEQ 110

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489177405 103 RH---EAEREFQALVDaiaTLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAAC 163
Cdd:PRK12529 111 QSvilETLHEIDALLD---TLRPRVKQAFLMATLDGMKQKDIAQALDIALPTVKKYIHQAYVTC 171
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 110-163 1.18e-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.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 54.00  E-value: 1.18e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 489177405  110 FQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAAC 163
Cdd:pfam08281   1 LEALLRALEELPPRQREVFLLRYLEGLSYAEIAELLGISEGTVKSRLSRARKKL 54
PRK12528 PRK12528
RNA polymerase sigma factor; Provisional
 17-156 2.17e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 171561 [Multi-domain]  Cd Length: 161  Bit Score: 53.69  E-value: 2.17e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  17 HYEELVDHVRRRFGDRGMAREVVHDVCVQLLERDEKEDVHTPLALLRKISHDAAVSRYRSDRRRTAWVEAVAELPE-VAC 95
Cdd:PRK12528  13 HHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQIIEPRAFLTTIAKRVLCNHYRRQDLERAYLEALAQLPErVAP 92

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 489177405  96 MAATPMGRHEAEREFQALVDAiatLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHL 156
Cdd:PRK12528  93 SEEERAIILETLVELDQLLDG---LPPLVKRAFLLAQVDGLGYGEIATELGISLATVKRYL 150
PRK12525 PRK12525
RNA polymerase sigma factor; Provisional
 18-163 3.60e-09

RNA polymerase sigma factor; Provisional


Pssm-ID: 139037 [Multi-domain]  Cd Length: 168  Bit Score: 53.03  E-value: 3.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  18 YEELVDHVRRRFGDRGMAREVVHDVCVQLLERDEKEDVHTPLALLRKISHDAAVSRYRSDRRRTAWVEAVAELPEVacMA 97
Cdd:PRK12525  19 YDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASIREPRALLTTIARRLMYEGWRRQDLERAYLQSLAEAPEA--VQ 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 489177405  98 ATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAAC 163
Cdd:PRK12525  97 PSPEEQWMVIETLLAIDRLLDGLSGKARAAFLMSQLEGLTYVEIGERLGVSLSRIHQYMVEAFKCC 162
PRK12523 PRK12523
RNA polymerase sigma factor; Reviewed
 10-163 7.20e-09

RNA polymerase sigma factor; Reviewed


Pssm-ID: 183572 [Multi-domain]  Cd Length: 172  Bit Score: 52.16  E-value: 7.20e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  10 LLSTLVR-HYEELVDHVRRRFGDRGMAREVVHDVCVQLLERDEKEDVHTPLALLRKISHDAAVSRYRSDRRRTAWVEAVA 88
Cdd:PRK12523  11 LVGALYRdHRGWLLAWLRRNVACRQRAEDLSQDTFVRLLGRPELPTPREPRAFLAAVAKGLMFDHFRRAALEQAYLAELA 90

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 489177405  89 ELPEVacMAATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAAC 163
Cdd:PRK12523  91 LVPEA--EQPSPEEQHLILEDLKAIDRLLGKLSSKARAAFLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGLRQC 163
PRK12524 PRK12524
RNA polymerase sigma factor; Provisional
 4-171 2.29e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 183573 [Multi-domain]  Cd Length: 196  Bit Score: 48.35  E-value: 2.29e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405   4 DPAKPTLLStlVRHYEELVDHVRRRFGDRGMAREVVHDVCVQL--LERDEKEDVHTPLALLRKISHDAAVSRYRSDRRRT 81
Cdd:PRK12524  24 DPAAARALT--LRLAPRALAVATRVLGDRAEAEDVTQEAMLRLwrIAPDWRQGEARVSTWLYRVVCNLCTDRLRRRRRAS 101

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  82 AWVEAVAELPEVACMAATPMgrHEAEReFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVE-------K 154
Cdd:PRK12524 102 VDLDDAPEPADAAPGAEEAL--IEGDR-MRALDAALAALPERQRQAVVLRHIEGLSNPEIAEVMEIGVEAVEsltargkR 178

                        170
                 ....*....|....*..
gi 489177405 155 HLRLGLAACRERLGRGE 171
Cdd:PRK12524 179 ALAALLAGQRAELGYGE 195
PRK12519 PRK12519
RNA polymerase sigma factor; Provisional
 70-168 1.72e-06

RNA polymerase sigma factor; Provisional


Pssm-ID: 237125 [Multi-domain]  Cd Length: 194  Bit Score: 45.82  E-value: 1.72e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  70 AVSRYRSDRRRTAWVEAVAELPEVACMAATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISV 149
Cdd:PRK12519  92 AIDRLRSRRSRQRLLERWQQELLGEASEDTPLEQASLAERSQRVQTALAQLPESQRQVLELAYYEGLSQSEIAKRLGIPL 171

                         90
                 ....*....|....*....
gi 489177405 150 KTVEKHLRLGLAACRERLG 168
Cdd:PRK12519 172 GTVKARARQGLLKLRELLQ 190
PRK09652 PRK09652
RNA polymerase sigma factor RpoE; Provisional
 13-168 5.70e-06

RNA polymerase sigma factor RpoE; Provisional


Pssm-ID: 236608 [Multi-domain]  Cd Length: 182  Bit Score: 44.41  E-value: 5.70e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  13 TLVRHYEELVDHVRRRFG-DRGMAREVVHDVCVQLLERDEKEDVHTPL-ALLRKISHDAAVSRYRSDRRRTAWVEAVAEL 90
Cdd:PRK09652  14 LLVRRYQPRVKRLLSRLTrDPADAEDLVQETFIKAYRALHSFRGGAAFyTWLYRIARNTAINYLRKQGRRPPASDVDAEE 93

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  91 PEVACMAATPMGRHEAEREF------QALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACR 164
Cdd:PRK09652  94 AEDFDLADALRDISTPENELlsaeleQRVRAAIESLPEELRTAITLREIEGLSYEEIAEIMGCPIGTVRSRIFRAREALR 173


                 ....
gi 489177405 165 ERLG 168
Cdd:PRK09652 174 AKLQ 177
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 111-164 8.67e-06

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: 41.32  E-value: 8.67e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 489177405 111 QALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACR 164
Cdd:cd06171    2 ERLEEALDKLPEREREVILLRFGEGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 116-165 1.32e-05

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: 40.49  E-value: 1.32e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 489177405  116 AIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACRE 165
Cdd:pfam04545   1 ALASLPPRERQVLVLRYGEGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
sigI PRK09635
RNA polymerase sigma factor SigI; Provisional
 16-151 4.55e-05

RNA polymerase sigma factor SigI; Provisional


Pssm-ID: 182008 [Multi-domain]  Cd Length: 290  Bit Score: 42.65  E-value: 4.55e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  16 RHYEELVDHVRRRFGDRGMAREVVHDVCVQLLeRDEKEDVHTPLALLRKISHDAAVSRYRSDRRRTAWVEAVAELPEVAC 95
Cdd:PRK09635  13 AHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLL-RAPVGDIDDERGWLIVVTSRLCLDHIKSASTRRERPQDIAAWHDGDA 91

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489177405  96 MAAT--PMGRHEAEREFQ-ALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKT 151
Cdd:PRK09635  92 SVSSvdPADRVTLDDEVRlALLIMLERLGPAERVVFVLHEIFGLPYQQIATTIGSQAST 150
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 106-172 4.47e-04

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 39.52  E-value: 4.47e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 489177405 106 AEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHLRLGLAACRERLGRGEA 172
Cdd:PRK07408 190 AQEDRIRLQQALAQLEERTREVLEFVFLHDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQPEDD 256
PRK09651 PRK09651
RNA polymerase sigma factor FecI; Provisional
 5-156 5.09e-04

RNA polymerase sigma factor FecI; Provisional


Pssm-ID: 182018 [Multi-domain]  Cd Length: 172  Bit Score: 38.64  E-value: 5.09e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405   5 PAKPTLLSTLVRHYEELVDHVRRRFGDRGMAREVVHDVCVQLLERDEKEDVHTPLALLRKISHDAAVSRYRSDRRRTAWV 84
Cdd:PRK09651   7 TASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVSETLSTIRDPRSFLCTIAKRVMVDLFRRNALEKAYL 86

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489177405  85 EAVAELPEVacMAATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHL 156
Cdd:PRK09651  87 EMLALMPEG--GAPSPEERESQLETLQLLDSMLDGLNGKTREAFLLSQLDGLTYSEIAHKLGVSVSSVKKYV 156
PRK12518 PRK12518
RNA polymerase sigma factor; Provisional
 69-167 8.50e-04

RNA polymerase sigma factor; Provisional


Pssm-ID: 237124 [Multi-domain]  Cd Length: 175  Bit Score: 38.16  E-value: 8.50e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  69 AAVSRYRSDRRRTAWVEAVAELPEVACMAATPMGRheaeREFQALVD-AIATLPPRCQAVFVMHKIHEVPQAQVADRLGI 147
Cdd:PRK12518  73 ATDARRQFAQRPSRIQDDSLNDQPSRPSDTPDLMQ----LHYQDLVQqGLQTLSLEHRAVLVLHDLEDLPQKEIAEILNI 148

                         90       100
                 ....*....|....*....|
gi 489177405 148 SVKTVEKHLRLGLAACRERL 167
Cdd:PRK12518 149 PVGTVKSRLFYARRQLRKFL 168
PRK06930 PRK06930
positive control sigma-like factor; Validated
 104-156 8.85e-04

positive control sigma-like factor; Validated


Pssm-ID: 180757 [Multi-domain]  Cd Length: 170  Bit Score: 38.17  E-value: 8.85e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 489177405 104 HEAEREF-----QALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHL 156
Cdd:PRK06930  94 EEPESVIsewdkIRIEDALSVLTEREKEVYLMHRGYGLSYSEIADYLNIKKSTVQSMI 151
PRK05602 PRK05602
RNA polymerase sigma factor; Reviewed
 77-169 1.24e-03

RNA polymerase sigma factor; Reviewed


Pssm-ID: 235530 [Multi-domain]  Cd Length: 186  Bit Score: 37.71  E-value: 1.24e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  77 DRRRTAWVEAVAELPEVACMAATPMGRHEAEREFQALVDAIATLPPRCQAVFVMHKIHEVPQAQVADRLGISVKTVEKHL 156
Cdd:PRK05602  86 DRLRRRREVPVEDAPDVPDPAPGPDAGLEARQRARRVEQALAALPERQREAIVLQYYQGLSNIEAAAVMDISVDALESLL 165

                         90
                 ....*....|...
gi 489177405 157 RLGLAACRERLGR 169
Cdd:PRK05602 166 ARGRRALRAQLAD 178
PRK11922 PRK11922
RNA polymerase sigma factor; Provisional
 70-169 1.95e-03

RNA polymerase sigma factor; Provisional


Pssm-ID: 237024 [Multi-domain]  Cd Length: 231  Bit Score: 37.64  E-value: 1.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489177405  70 AVSRYRSDRRRTAWVE-AVAELPEVACMAATPMG-----RHEAEREFQALVD-AIATLPPRCQAVFVMHKIHEVPQAQVA 142
Cdd:PRK11922  93 ALGRLRRRRRLVNLAEmVMASTIAGGERTPLADPaedpeRAAARREIRALLErAIDALPDAFRAVFVLRVVEELSVEETA 172

                         90       100
                 ....*....|....*....|....*..
gi 489177405 143 DRLGISVKTVEKHLRLGLAACRERLGR 169
Cdd:PRK11922 173 QALGLPEETVKTRLHRARRLLRESLAR 199
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 103-155 7.56e-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: 35.46  E-value: 7.56e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 489177405 103 RHEAEREFQALVDAIATLPPRCQAVFV------MHKihevpqaQVADRLGISVKTVEKH 155
Cdd:COG4566  121 RRAERARRAELRARLASLTPREREVLDlvvaglSNK-------QIARELGISPRTVEVH 172
 
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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