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Conserved domains on  [gi|1061915492|ref|WP_069221706|]
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sigma-70 family RNA polymerase sigma factor [Burkholderia multivorans]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 1000435)

sigma-70 family RNA polymerase sigma factor similar to RNA polymerase sigma factor RpoD/SigA, which is the primary sigma factor during exponential growth; preferentially transcribes genes associated with fast growth, such as ribosomal operons, other protein-synthesis related genes, rRNA- and tRNA-encoding genes and prfB

CATH:  1.10.601.10
Gene Ontology:  GO:0016987|GO:0006352|GO:0003700|GO:0003677|GO:0006355
SCOP:  4003741

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK05658 super family cl35358
RNA polymerase sigma factor RpoD; Validated
 27-599 9.33e-123

RNA polymerase sigma factor RpoD; Validated


The actual alignment was detected with superfamily member PRK05658:

Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 376.06  E-value: 9.33e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492  27 LIALGLSRGFVTRGDVIDALPDDDAHDAGIDAATAVLAELGIAVSDDAHAETDWSLDRHFRPPPLSRAAAESNSAFAAFD 106
Cdd:PRK05658   16 LIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADAQTDEDAEEEAAAALSSV 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 107 LLAP-RTTDPVRLYLREMGTVPLLTHDEEIAYAQRIERGRAASVAVLCGDPDALDALASIRREIAEGRAAASAYL-MFVD 184
Cdd:PRK05658   96 ESEIgRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGERRLRELIdGFVD 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 185 EGRHADAAAAVDPHGDAQHDDMRPGDPHVCDAALVR---------LSSLDALAR---DMRAAL----ASGGTASPAYRAA 248
Cdd:PRK05658  176 PNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAAdeselpekvLEKFKALAKqykKLRKAQekkvEGRLAQHKKYAKL 255

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 249 VHDAAALLRPLRLSARAVERIGAPLRGRARRHREQRARMTRVLHHAGIPSQTTWRCHDAHDDDhARWLAAGIAAHPECER 328
Cdd:PRK05658  256 REKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLRLVERLKMPRKDFLKLFQGNELD-ITWLEKEIASGKPWSE 334

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 329 ALIRSAPVLFDAREAIAADARASVLPPRTVALLDARLDAIERATHAAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEG 408
Cdd:PRK05658  335 FLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 414

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 409 NIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAGAAATPDELAAQMG 488
Cdd:PRK05658  415 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLG 494

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 489 EPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPEDAADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAG 568
Cdd:PRK05658  495 MPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMN 574

                         570       580       590
                  ....*....|....*....|....*....|.
gi 1061915492 569 EGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:PRK05658  575 TDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605
 
Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 27-599 9.33e-123

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 376.06  E-value: 9.33e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492  27 LIALGLSRGFVTRGDVIDALPDDDAHDAGIDAATAVLAELGIAVSDDAHAETDWSLDRHFRPPPLSRAAAESNSAFAAFD 106
Cdd:PRK05658   16 LIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADAQTDEDAEEEAAAALSSV 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 107 LLAP-RTTDPVRLYLREMGTVPLLTHDEEIAYAQRIERGRAASVAVLCGDPDALDALASIRREIAEGRAAASAYL-MFVD 184
Cdd:PRK05658   96 ESEIgRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGERRLRELIdGFVD 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 185 EGRHADAAAAVDPHGDAQHDDMRPGDPHVCDAALVR---------LSSLDALAR---DMRAAL----ASGGTASPAYRAA 248
Cdd:PRK05658  176 PNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAAdeselpekvLEKFKALAKqykKLRKAQekkvEGRLAQHKKYAKL 255

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 249 VHDAAALLRPLRLSARAVERIGAPLRGRARRHREQRARMTRVLHHAGIPSQTTWRCHDAHDDDhARWLAAGIAAHPECER 328
Cdd:PRK05658  256 REKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLRLVERLKMPRKDFLKLFQGNELD-ITWLEKEIASGKPWSE 334

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 329 ALIRSAPVLFDAREAIAADARASVLPPRTVALLDARLDAIERATHAAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEG 408
Cdd:PRK05658  335 FLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 414

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 409 NIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAGAAATPDELAAQMG 488
Cdd:PRK05658  415 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLG 494

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 489 EPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPEDAADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAG 568
Cdd:PRK05658  495 MPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMN 574

                         570       580       590
                  ....*....|....*....|....*....|.
gi 1061915492 569 EGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:PRK05658  575 TDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 367-612 3.87e-100

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: 305.44  E-value: 3.87e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 367 AIERATHAAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADL 446
Cdd:COG0568    23 RIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQ 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 447 GRTIRVPTHTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVPDA 526
Cdd:COG0568   103 WRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDE 182

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 527 STPSPEDAADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRASDALAV 606
Cdd:COG0568   183 EAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRK 262


                  ....*.
gi 1061915492 607 LRPFVG 612
Cdd:COG0568   263 LRDYLD 268
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 375-610 7.99e-98

RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc. [Transcription, Transcription factors]


Pssm-ID: 274108 [Multi-domain]  Cd Length: 238  Bit Score: 298.44  E-value: 7.99e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 375 AKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVPT 454
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 455 HTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPEDA 534
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1061915492 535 ADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRASDALAVLRPF 610
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDF 236
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 458-532 1.48e-18

Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.


Pssm-ID: 427997 [Multi-domain]  Cd Length: 78  Bit Score: 80.34  E-value: 1.48e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1061915492 458 DAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPE 532
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPE 75
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 551-599 4.94e-09

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


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 52.49  E-value: 4.94e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1061915492 551 LPPREALIVRLRYGlhagEGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:cd06171    11 LPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 27-599 9.33e-123

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 376.06  E-value: 9.33e-123
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492  27 LIALGLSRGFVTRGDVIDALPDDDAHDAGIDAATAVLAELGIAVSDDAHAETDWSLDRHFRPPPLSRAAAESNSAFAAFD 106
Cdd:PRK05658   16 LIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADAQTDEDAEEEAAAALSSV 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 107 LLAP-RTTDPVRLYLREMGTVPLLTHDEEIAYAQRIERGRAASVAVLCGDPDALDALASIRREIAEGRAAASAYL-MFVD 184
Cdd:PRK05658   96 ESEIgRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGERRLRELIdGFVD 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 185 EGRHADAAAAVDPHGDAQHDDMRPGDPHVCDAALVR---------LSSLDALAR---DMRAAL----ASGGTASPAYRAA 248
Cdd:PRK05658  176 PNAEEDPAHVGSELEELDDDEDEEEEEDENDDSLAAdeselpekvLEKFKALAKqykKLRKAQekkvEGRLAQHKKYAKL 255

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 249 VHDAAALLRPLRLSARAVERIGAPLRGRARRHREQRARMTRVLHHAGIPSQTTWRCHDAHDDDhARWLAAGIAAHPECER 328
Cdd:PRK05658  256 REKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLRLVERLKMPRKDFLKLFQGNELD-ITWLEKEIASGKPWSE 334

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 329 ALIRSAPVLFDAREAIAADARASVLPPRTVALLDARLDAIERATHAAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEG 408
Cdd:PRK05658  335 FLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 414

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 409 NIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAGAAATPDELAAQMG 488
Cdd:PRK05658  415 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLG 494

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 489 EPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPEDAADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAG 568
Cdd:PRK05658  495 MPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMN 574

                         570       580       590
                  ....*....|....*....|....*....|.
gi 1061915492 569 EGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:PRK05658  575 TDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 367-612 3.87e-100

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: 305.44  E-value: 3.87e-100
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 367 AIERATHAAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADL 446
Cdd:COG0568    23 RIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYATWWIRQAITRAIADQ 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 447 GRTIRVPTHTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVPDA 526
Cdd:COG0568   103 WRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVGDDEDSELGDLLEDE 182

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 527 STPSPEDAADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRASDALAV 606
Cdd:COG0568   183 EAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEAKALRKLRHPLRSRK 262


                  ....*.
gi 1061915492 607 LRPFVG 612
Cdd:COG0568   263 LRDYLD 268
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 375-610 7.99e-98

RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc. [Transcription, Transcription factors]


Pssm-ID: 274108 [Multi-domain]  Cd Length: 238  Bit Score: 298.44  E-value: 7.99e-98
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 375 AKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVPT 454
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 455 HTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPEDA 534
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1061915492 535 ADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRASDALAVLRPF 610
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDF 236
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 367-599 6.21e-83

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 264.54  E-value: 6.21e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 367 AIERATHAAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADL 446
Cdd:PRK09210  122 RIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 201

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 447 GRTIRVPTHTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVPDA 526
Cdd:PRK09210  202 ARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQ 281

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1061915492 527 STPSPEDAADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:PRK09210  282 DATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 354
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 375-599 4.14e-81

RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).


Pssm-ID: 274382 [Multi-domain]  Cd Length: 298  Bit Score: 257.56  E-value: 4.14e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 375 AKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVPT 454
Cdd:TIGR02997  75 AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPI 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 455 HTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVPDaSTPSPEDA 534
Cdd:TIGR02997 155 HITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLED-DGESPEEQ 233

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1061915492 535 ADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:TIGR02997 234 VERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 365-610 1.28e-78

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 258.00  E-value: 1.28e-78
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 365 LDAIERATHAAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALA 444
Cdd:PRK05901  262 LQWIGRDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMA 341

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 445 DLGRTIRVPTHTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVP 524
Cdd:PRK05901  342 DQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIE 421

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 525 DASTPSPEDAADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRASDAL 604
Cdd:PRK05901  422 DSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRS 501


                  ....*.
gi 1061915492 605 AVLRPF 610
Cdd:PRK05901  502 QVLRDF 507
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 365-610 4.94e-77

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 247.72  E-value: 4.94e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 365 LDAIERATHAAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALA 444
Cdd:PRK07921   77 LAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMA 156

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 445 DLGRTIRVPTHTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVP 524
Cdd:PRK07921  157 DQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIE 236

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 525 DASTPSPEDAADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRASDAL 604
Cdd:PRK07921  237 DSEATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERA 316


                  ....*.
gi 1061915492 605 AVLRPF 610
Cdd:PRK07921  317 DRLRSY 322
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 374-599 4.48e-70

RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393). [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 131447 [Multi-domain]  Cd Length: 285  Bit Score: 228.07  E-value: 4.48e-70
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 374 AAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVP 453
Cdd:TIGR02394  46 EARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLP 125

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 454 THTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPED 533
Cdd:TIGR02394 126 VHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPES 205

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1061915492 534 AADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:TIGR02394 206 LVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLR 271
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 337-599 1.71e-61

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 207.00  E-value: 1.71e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 337 LFDAREAIAAD-ARASVLP--PRTVALLDARLDAIERATHAAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLL 413
Cdd:PRK05949   51 LLEAKEALAKKlGREPSLPewAEAVNLSETELKQTLKQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLE 130

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 414 KAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDK 493
Cdd:PRK05949  131 RGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQ 210

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 494 VRELMAIVKEPVSADLPIAPDGDMTFVDVVPDaSTPSPEDAADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSL 573
Cdd:PRK05949  211 IREYLSMARQPISLDVRVGDNQDTELSELLED-EGPSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSL 289

                         250       260
                  ....*....|....*....|....*.
gi 1061915492 574 RDIGRRLNLSAERVRQIEASALARLR 599
Cdd:PRK05949  290 AKVGERLNLSRERVRQLEHQALAHLR 315
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 375-611 2.13e-60

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 205.40  E-value: 2.13e-60
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 375 AKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVPT 454
Cdd:PRK07406  137 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 216

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 455 HTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVpDASTPSPEDA 534
Cdd:PRK07406  217 HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFI-EADGETPEDD 295

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1061915492 535 ADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRASDALAVLRPFV 611
Cdd:PRK07406  296 VAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 374-599 1.35e-59

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 201.72  E-value: 1.35e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 374 AAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVP 453
Cdd:PRK05657   86 AARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLP 165

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 454 THTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPED 533
Cdd:PRK05657  166 VHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPED 245

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1061915492 534 AADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:PRK05657  246 TTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 316-599 1.66e-57

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 198.94  E-value: 1.66e-57
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 316 LAAGIAAHPECERALIRSAPVLFDAREAIAADARASvlpPRTVALLDARLDAIERATHAAKTALFDANLRLVVSIAKRYP 395
Cdd:PRK07598  120 LTSELGHRPSLERWAKTADISLADLKPTLAEGKRRW---AEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQ 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 396 DRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAG 475
Cdd:PRK07598  197 NRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKG 276

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 476 AAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVpDASTPSPEDAADAAQRRAAIAAAIDRLPPRE 555
Cdd:PRK07598  277 RTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLL-ETDDISPEEMLMRESLQRDLQHLLADLTSRE 355

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 1061915492 556 ALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:PRK07598  356 RDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLR 399
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 363-603 1.81e-55

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 190.74  E-value: 1.81e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 363 ARLDAIERATHAAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHA 442
Cdd:PRK07405   70 EELRSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRA 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 443 LADLGRTIRVPTHTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDV 522
Cdd:PRK07405  150 IAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGEL 229

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 523 VPDAStPSPEDAADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRASD 602
Cdd:PRK07405  230 LEDTG-ASPEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKRK 308


                  .
gi 1061915492 603 A 603
Cdd:PRK07405  309 A 309
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 361-600 2.49e-38

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: 141.50  E-value: 2.49e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 361 LDARLDAIERATHAAKTALFDANLRLVVSIAKRYPDRGLP-FADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSI 439
Cdd:COG1191     2 LEELLRRYQEGDEEAREELIEEYLPLVKKIASRLAGRLPAeLDDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAI 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 440 THALADLGrtiRVPTHTVDAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVK--EPVSADLPIAPDGDm 517
Cdd:COG1191    82 LDYLRDED---WVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANayQLLSLDEPLEDGDD- 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 518 tFVDVVpdaSTPSPEDAADAAQRRAAIAAAIDRLPPREALIVRLRYglhaGEGCSLRDIGRRLNLSAERVRQIEASALAR 597
Cdd:COG1191   158 -LLDLL---ESGDPEEELEHEELREALAEAIEQLPERERLVLSLYY----FEELTLKEIAEVLGVSESRVSRLHKKALAR 229


                  ...
gi 1061915492 598 LRA 600
Cdd:COG1191   230 LRE 232
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 374-600 5.28e-30

alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors. [Cellular processes, Adaptations to atypical conditions, Transcription, Transcription factors]


Pssm-ID: 274107 [Multi-domain]  Cd Length: 270  Bit Score: 119.31  E-value: 5.28e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 374 AAKtALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVP 453
Cdd:TIGR02392  36 AAK-KLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVA 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 454 thTVDAINKLARLAREHRQRAGAAATPDE---LAAQMGEPVDKVRELMAIVKEP-VSADLPIAPDGD--MTFVDVVPDaS 527
Cdd:TIGR02392 115 --TTKAQRKLFFNLRKMKKRLQGWLNPEEveaIAEELGVSEREVREMESRLSGQdMSLNASIDDDEDdgGAPIAYLVD-K 191

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1061915492 528 TPSPEDAAD----AAQRRAAIAAAIDRLPPREALIVRLRYglHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRA 600
Cdd:TIGR02392 192 RSDPEDTLEeeqwEELQRQALANALGSLDARSRRIIEARW--LDDDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 401-600 4.28e-27

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


Pssm-ID: 274153 [Multi-domain]  Cd Length: 224  Bit Score: 109.67  E-value: 4.28e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 401 FADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSIthaLADLGRTIRVPTHTVDAINKLARLAREHRQRAGAAATP 480
Cdd:TIGR02479  26 LDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAM---LDELRRLDWVPRSLRQKARKLERAIRELEARLGREPTE 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 481 DELAAQMGEPVDKVRELM--AIVKEPVSADLPIAPDGD-MTFVDVVPDASTPSPEDAADAAQRRAAIAAAIDRLPPREAL 557
Cdd:TIGR02479 103 EEIAEELGMDLKEYRQALneINALSLVSLDELLESGDDgGSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQL 182

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1061915492 558 IVRLRYglhaGEGCSLRDIGRRLNLSAERVRQIEASALARLRA 600
Cdd:TIGR02479 183 VLSLYY----YEELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 374-601 2.83e-25

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 106.03  E-value: 2.83e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 374 AAKTaLFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSItH--ALadlgRTIR 451
Cdd:PRK06596   49 AAKQ-LVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEI-HeyIL----RNWR 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 452 -VPTHTVDAINKLARLAREHRQRAGaAATPDE---LAAQMGEPVDKVREL---MAivKEPVSADLPIAPDGDMTF--VDV 522
Cdd:PRK06596  123 iVKVATTKAQRKLFFNLRKAKKRLG-WLNPEEvemVAEELGVSEEEVREMesrLS--GQDASLDAPIDDDDEESGapQDY 199

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 523 VPDaSTPSPEDAADAAQRRAAIAAAIDR----LPPREALIVRLRYgLHAgEGCSLRDIGRRLNLSAERVRQIEASALARL 598
Cdd:PRK06596  200 LED-KSSDPADVLEEDNWEDQRRALLADalegLDERSRDIIEARW-LDD-DKSTLQELAAEYGVSAERVRQIEKNAMKKL 276


                  ...
gi 1061915492 599 RAS 601
Cdd:PRK06596  277 KAA 279
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 369-601 1.47e-24

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 103.96  E-value: 1.47e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 369 ERATHAaktaLFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALadLGR 448
Cdd:PRK07500   39 EDALHR----IISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYI--LRN 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 449 TIRVPTHTVDAINKL--------ARLAREHRQRAGAAATpDELAAQMGEPVDKVrELM--------AIVKEPVSADlpia 512
Cdd:PRK07500  113 WSIVRGGTSSAQKALffnlrrlrARLAQADEELTKQEIH-REIATALGVSLSDV-EMMdarlsgpdASLNAPQSEE---- 186

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 513 PDGDMTFVDVVPDAStPSPEDAADAAQRRAAIAA----AIDRLPPREALIVRLRYglHAGEGCSLRDIGRRLNLSAERVR 588
Cdd:PRK07500  187 DEGRSERMDFLVDDS-PLPDEQVESSIDGERRRRwltqALQTLNERELRIIRERR--LREDGATLEALGEELGISKERVR 263

                         250
                  ....*....|...
gi 1061915492 589 QIEASALARLRAS 601
Cdd:PRK07500  264 QIEARALEKLRRA 276
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 398-601 3.09e-21

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 93.60  E-value: 3.09e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 398 GLP----FADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLG---RTIRVPTHTVDAInkLARL-ARE 469
Cdd:PRK06288   54 GMPqnveFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDELRSIDwipRSVRQKARQIERA--IAMLeARL 131

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 470 HRQragaaATPDELAAQMGEPVDKVRELMAIVKE--PVSAD--LPIAPDGD-MTFVDVVPDASTPSPEDAADAAQRRAAI 544
Cdd:PRK06288  132 GRT-----PSDEEIADELGISLEEYNSLLSKLSGtsVVSLNdlWFGGDEGDeVSLMDTLESPAALNPDEIAEREEIKRVI 206

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1061915492 545 AAAIDRLPPREALIVRLRYglhaGEGCSLRDIGRRLNLSAERVRQIEASALARLRAS 601
Cdd:PRK06288  207 VEAIKTLPEREKKVLILYY----YEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 400-530 1.21e-19

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 88.82  E-value: 1.21e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 400 PFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAGAAAT 479
Cdd:PRK07408   52 PYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRWQELQRQAKKVRQELRQELGRQPT 131

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1061915492 480 PDELAAQMGEPVDKVRE--LMAIVKEPVSADLPIAPDGD--MTFVDVVPDASTPS 530
Cdd:PRK07408  132 DQEIAQALDISLEEWQEikLALQNRTPLSLDAPVNQDEDgsTSLGDLLPDPRYRS 186
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 458-532 1.48e-18

Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.


Pssm-ID: 427997 [Multi-domain]  Cd Length: 78  Bit Score: 80.34  E-value: 1.48e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1061915492 458 DAINKLARLAREHRQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPE 532
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPE 75
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 379-449 2.06e-18

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: 79.55  E-value: 2.06e-18
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1061915492 379 LFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRT 449
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
374-599 1.30e-17

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 83.07  E-value: 1.30e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 374 AAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADlGRTIRVP 453
Cdd:PRK08215   37 EAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRD-NNPIRVS 115

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 454 THTVDAINKlARLAREH-RQRAGAAATPDELAAQMGEPVDKVRELMAIVKEPVSADLPIAPD-GDMTFV-DVVPDAstps 530
Cdd:PRK08215  116 RSLRDIAYK-ALQVREKlINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIYHDgGDPIYVmDQISDE---- 190

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1061915492 531 pEDAADAAQRRAAIAAAIDRLPPREALIVRLRYglhaGEGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:PRK08215  191 -KNKDENWLEEIALKEAMKKLNDREKLILNLRF----FQGKTQMEVAEEIGISQAQVSRLEKAALKHMR 254
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
403-599 3.09e-17

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 81.63  E-value: 3.09e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 403 DLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALAD---LGRTIRVPTHTVDA-INKLarlarehRQRAGAAA 478
Cdd:PRK07670   54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKedwLPRSMREKTKKVEAaIEKL-------EQRYMRNV 126

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 479 TPDELAAQMGEPVDKVRELMA---------IVKEPVSADlpiapDGDMTFVdVVPDASTPSPEDAADAAQRRAAIAAAID 549
Cdd:PRK07670  127 TPKEVAAELGMTEEEVEATMNegffanllsIDEKTHDQD-----DGENVSV-TIRDDKTPTPEEKLLKEELIEELAEKIK 200

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1061915492 550 RLPPREALIVRLRYglhaGEGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:PRK07670  201 QLSEKEQLVISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLK 246
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
375-599 2.39e-15

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 76.16  E-value: 2.39e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 375 AKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGrTIRVPT 454
Cdd:PRK05572   33 ARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSR 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 455 HTVDAINKLARLAREHRQRAGAAATPDELAAQMGepVDKVRELMAI--VKEPVSA-DLPIAPDGD-MTFVDVVPDASTps 530
Cdd:PRK05572  112 SLKETANKIRKDKDELSKELGREPTIEELAEYLG--VTPEEVVLAQeaSRSPQSIhETVHENDGDpITLLDQIADQSE-- 187

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1061915492 531 pedaaDAAQRRAAIAAAIDRLPPREALIVRLRYglhagegcsLRD-----IGRRLNLSAERVRQIEASALARLR 599
Cdd:PRK05572  188 -----EDWFDKIALKEAIRELDERERLIVYLRY---------FKDktqseVAKRLGISQVQVSRLEKKILKQMK 247
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 403-601 2.98e-15

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 75.65  E-value: 2.98e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 403 DLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHAL--AD-LGRTIRVPTHTV-DAInklarlaREHRQRAGAAA 478
Cdd:PRK06986   40 DLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELrsLDwVPRSVRRNAREVaQAI-------RQLEQELGREP 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 479 TPDELAAQMGEPVDKVRE-LMAIVkepVSADLPI----APDGDmtFVDVVPDASTPSPEDAADAAQRRAAIAAAIDRLPP 553
Cdd:PRK06986  113 TDTEVAEKLGLSLEEYREmLLDTN---ISQLFSIdelrGEHGD--SILVTEDHQDEDPLQQLEDEELREALVEAIESLPE 187

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 1061915492 554 REALIVRLRYglhaGEGCSLRDIGRRLNLSAERVRQIEASALARLRAS 601
Cdd:PRK06986  188 REQLVLSLYY----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
375-598 8.54e-15

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 74.21  E-value: 8.54e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 375 AKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSIthaladlgrtirvpt 454
Cdd:PRK05803   50 ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCIENEI--------------- 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 455 htvdainklarlarehrqragaaatpdelaaqmgepvdkvreLMAI-----VKEPVSADLPIAPDGD---MTFVDVVPDA 526
Cdd:PRK05803  115 ------------------------------------------LMHLrnlkkTKKEVSLQDPIGVDKEgneISLIDILGSE 152

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1061915492 527 STPSPEdAADAAQRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARL 598
Cdd:PRK05803  153 EDDVIE-QVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKL 223
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 25-144 1.49e-14

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 75.41  E-value: 1.49e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492  25 AGLIALGLSRGFVTRGDVIDALPDDDAHDAGIDAATAVLAELGIAVSDDAHAetdwsldrhfrPPPLSRAAAESNSAFAA 104
Cdd:PRK09210   16 KELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGN-----------PSSAQVVEEEEEEELDN 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1061915492 105 fDLLAP---RTTDPVRLYLREMGTVPLLTHDEEIAYAQRIERG 144
Cdd:PRK09210   85 -DLSVPpgvKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEG 126
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 374-599 8.17e-13

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: 66.60  E-value: 8.17e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 374 AAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRgfRFSTYATWWIRQSITHALadlgrtirvp 453
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYL---------- 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 454 thtvdainklarlarehRQRAGAAATPDELAAQmgepvdkvrelmaivkepvsadlpiapdgdmtfvdvvpDASTPSPED 533
Cdd:TIGR02937  69 -----------------RRKRRLRRELDLLEEL--------------------------------------LDSDPSPEE 93

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1061915492 534 AADAAQRRAAIAAAIDRLPPREALIVRLRYglhaGEGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:TIGR02937  94 ELEQEEEREALREALEKLPEREREVLVLRY----LEGLSYKEIAEILGISVGTVKRRLKRARKKLR 155
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
114-147 2.72e-12

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 61.17  E-value: 2.72e-12
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1061915492 114 DPVRLYLREMGTVPLLTHDEEIAYAQRIERGRAA 147
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAGDEA 34
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 384-599 6.30e-11

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 63.26  E-value: 6.30e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 384 LRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVPTHTVDAINKL 463
Cdd:PRK07122   50 LPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLKELHLRL 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 464 ARLAREHRQRAGAAATPDELAAQMGEPVDKVRE--LMAIVKEPVSADLPIAP--DGDMTFVDVVPDAstpspEDAADAAQ 539
Cdd:PRK07122  130 GRATAELSQRLGRAPTASELAAELGMDREEVVEglVAGSAYNTLSIDSGGGSgdDDARAIADTLGDV-----DAGLDQIE 204

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 540 RRAAIAAAIDRLPPREALIVRLRYglhaGEGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:PRK07122  205 NREALRPLLAALPERERTVLVLRF----FESMTQTQIAERVGISQMHVSRLLAKTLARLR 260
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 551-600 7.42e-11

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: 57.44  E-value: 7.42e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1061915492 551 LPPREALIVRLRYGlhagEGCSLRDIGRRLNLSAERVRQIEASALARLRA 600
Cdd:pfam04545   5 LPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 376-601 4.74e-10

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 60.40  E-value: 4.74e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 376 KTALFDANLRLVVSIAKRYPDrGLP----FADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSIthaLADLGRTIR 451
Cdd:PRK05911   25 RDVLIEFYLPLVKNVAHRLIS-GMPshvkTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI---IDDLRKQDW 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 452 VPTHTVDAINKLARLAREHRQRAGAAATPDELAaqmgepvdkvrELMAIVKEPVSA---------------DLPIAPDGD 516
Cdd:PRK05911  101 VPRSVHQKANKLADAMDSLRQSLGKEPTDGELC-----------EYLNISQQELSGwfssarpalilslneEFPCQSDDE 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 517 --MTFVDVVPDASTPSPEDAADAAQRRAAIAAAIDRLPPREALIVRLRYglhaGEGCSLRDIGRRLNLSAERVRQIEASA 594
Cdd:PRK05911  170 agLALEERIADERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKA 245


                  ....*..
gi 1061915492 595 LARLRAS 601
Cdd:PRK05911  246 LLKLRAT 252
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 551-599 4.94e-09

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


Pssm-ID: 100119 [Multi-domain]  Cd Length: 55  Bit Score: 52.49  E-value: 4.94e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1061915492 551 LPPREALIVRLRYGlhagEGCSLRDIGRRLNLSAERVRQIEASALARLR 599
Cdd:cd06171    11 LPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
365-431 5.20e-09

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 57.17  E-value: 5.20e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1061915492 365 LDAIERATHAAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYA 431
Cdd:PRK08301   43 LNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA 109
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 375-606 1.76e-08

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 55.86  E-value: 1.76e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 375 AKTALFDANLRLVVSIAKRYpDRGLPF-ADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQSITHALADLGRTIRVP 453
Cdd:PRK08583   30 AQEKLVKHYKNLVESLAYKY-SKGQSHhEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVP 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 454 THTVDAINKLARLARE---HRQRagaAATPDELAAQMGEPVDKVRELMAIVK--EPVSADLPIAPDGD---MTFVDVVpd 525
Cdd:PRK08583  109 RRIKELGPKIKKAVDElttELQR---SPKISEIADRLGVSEEEVLEAMEMGKsyQALSVDHSIEADSDgstVTLLDIV-- 183

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 526 astPSPEDAADAAQRRAAIAAAIDRLPPREALIVRLRYglhaGEGCSLRDIGRRLNLSAERVRQIEASALARLRasDALA 605
Cdd:PRK08583  184 ---GQQEDGYELTEQRMILEKILPVLSDREKSIIQCTF----IENLSQKETGERLGISQMHVSRLQRQAIKKLR--EAAF 254


                  .
gi 1061915492 606 V 606
Cdd:PRK08583  255 L 255
Sigma70_r1_1 pfam03979
Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is ...
 27-74 6.47e-06

Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase. Region 1.1 is also involved in promoter binding


Pssm-ID: 461117 [Multi-domain]  Cd Length: 69  Bit Score: 44.10  E-value: 6.47e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1061915492  27 LIALGLSRGFVTRGDVIDALPDDDAHDAGIDAATAVLAELGIAVSDDA 74
Cdd:pfam03979   6 LIKKGKKKGYLTYDEINDALPDDILDSEQIEDIIEMLNDMGIDVVEEA 53
Sigma70_ner pfam04546
Sigma-70, non-essential region; The domain is found in the primary vegetative sigma factor. ...
 217-297 6.79e-06

Sigma-70, non-essential region; The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function.


Pssm-ID: 461348  Cd Length: 169  Bit Score: 46.78  E-value: 6.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 217 ALVRLSSLDALARDMRAALASGGTASPAYRAAVHDAAALLRPLRLSARAVERIGAPLRGRARRHREQ-RARMTRVLHHAG 295
Cdd:pfam04546  39 ALERFEELREQYEKLRKAIEKHGRSSKKYLKLREELSEEFMQFRLVPKQFDRLVDQLREMVDRVRAQeREIMRLCVERAK 118


                  ..
gi 1061915492 296 IP 297
Cdd:pfam04546 119 MP 120
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
386-440 1.47e-05

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 46.44  E-value: 1.47e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1061915492 386 LVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWI-RQSIT 440
Cdd:PRK08295   36 FVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCItRQIIT 91
COG3903 COG3903
Predicted ATPase [General function prediction only];
3-386 3.64e-05

Predicted ATPase [General function prediction only];


Pssm-ID: 443109 [Multi-domain]  Cd Length: 933  Bit Score: 46.93  E-value: 3.64e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492   3 NARQPAPAAGHDDALASASAPFAGLIALGLSRGFVTRGDVIDALPDDDAHDAGIDAATAVLAELGIAVSDDAHAETDWSL 82
Cdd:COG3903   527 NLRAALRWALAHGDAELALRLAAALAPFWFLRGLLREGRRWLERALAAAGEAAAALAAAAALAAAAAAARAAAAAAAAAA 606

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492  83 DRHFRPPPLSRAAAESNSAFAAFDLLAPRTTDPVRLYLREMGTVPLLTHDEEIAYAQRIERGRAASVAVLCGDPDALDAL 162
Cdd:COG3903   607 AAAAAAAAAAAAAAAALLLLAALAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAALAAAAAAAAAAAAAAAAAAAA 686

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 163 ASIRREIAEGRAAASAYLMFVDEGRHADAAAAVDPHGDAQHDDMRPGDPHVCDAALVRLSSLDALARDMRAALASGGTAS 242
Cdd:COG3903   687 LAAAAAALAAAAAAAALAAAAAAALAAAAAAAAAAAAAAALLAAAAAAALAAAAAAAALALAAAAAAAAAAAAAAALAAA 766

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 243 PAYRAAVHDAAALLRPLRLSARAVERIGAPLRGRARRHREQRARMTRVLHHAGIPSQTTWRCHDAHDDDHARWLAAGIAA 322
Cdd:COG3903   767 AAAAALAALLLALAAAAAALAAAAAAAAAAAAAAAAAAAAAAAAAAAAALAAAAAAAAAAAAALAAALAAAAAAAAAAAA 846

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1061915492 323 HPECERALIRSAPVLFDAREAIAADARASVLPPRTVALLDARLDAIERATHAAKTALFDANLRL 386
Cdd:COG3903   847 AAAAAAALAAALAAAAAAAAAAALAAAAAAAAAAAAALLAAAAAAAAAAAAAAAAAAALAAAAA 910
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 118-147 7.82e-05

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: 44.66  E-value: 7.82e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1061915492 118 LYLREMGTVPLLTHDEEIAYAQRIERG--RAA 147
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQAGdeEAK 32
COG3903 COG3903
Predicted ATPase [General function prediction only];
32-375 3.91e-03

Predicted ATPase [General function prediction only];


Pssm-ID: 443109 [Multi-domain]  Cd Length: 933  Bit Score: 40.39  E-value: 3.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492  32 LSRGFVTRGDVIDALPDDDAHDAGIDAATAVLAELGIAVSDDAHAETDWSLDRHFRPPPLSRAAAESNSAFAAFDLLAPR 111
Cdd:COG3903   518 LARLDAEHDNLRAALRWALAHGDAELALRLAAALAPFWFLRGLLREGRRWLERALAAAGEAAAALAAAAALAAAAAAARA 597

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 112 TTDPVRLYLREMGTVPLLTHDEEIAYAQRIERGRAASVAVLCGDPDALDALASIRREIAEGRAAASAYLMFVDEGRHADA 191
Cdd:COG3903   598 AAAAAAAAAAAAAAAAAAAAAAAAALLLLAALAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAALAAAAAAAAAAA 677

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 192 AAAVDPHGDAQHDDMRPGDPHVCDAALVRLSSLDALARDMRAALASGGTASPAYRAAVHDAAALLRPLRLSARAVERIGA 271
Cdd:COG3903   678 AAAAAAAAALAAAAAALAAAAAAAALAAAAAAALAAAAAAAAAAAAAAALLAAAAAAALAAAAAAAALALAAAAAAAAAA 757

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061915492 272 PLRGRARRHREQRARMTRVLHHAGIPSQTTWRCHDAHDDDHARWLAAGIAAHPECERALIRSAPVLFDAREAIAADARAS 351
Cdd:COG3903   758 AAAAALAAAAAAAALAALLLALAAAAAALAAAAAAAAAAAAAAAAAAAAAAAAAAAAALAAAAAAAAAAAAALAAALAAA 837

                         330       340
                  ....*....|....*....|....
gi 1061915492 352 VLPPRTVALLDARLDAIERATHAA 375
Cdd:COG3903   838 AAAAAAAAAAAAAAAALAAALAAA 861
 
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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