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Conserved domains on  [gi|1193660533|gb|OTV73017|]
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RNA polymerase sigma factor RpoD [Salmonella enterica subsp. enterica serovar Typhimurium]

Protein Classification

sigma-70 family RNA polymerase sigma factor( domain architecture ID 11481401)

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
SCOP:  4003741

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 1-615 0e+00

RNA polymerase sigma factor RpoD; Validated


:

Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 1045.92  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533   1 MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTS--TDEDA 78
Cdd:PRK05658    5 MLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADaqTDEDA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533  79 EEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEA 158
Cdd:PRK05658   85 EEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGER 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 159 RLSDLITGFVDPNAEEEMAPTATHVGSElsqedLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIK 238
Cdd:PRK05658  165 RLRELIDGFVDPNAEEDPAHVGSELEEL-----DDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQE 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 239 AKG----RSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKlCVEQCKMPKKNFITLFTGNETS 314
Cdd:PRK05658  240 KKVegrlAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLR-LVERLKMPRKDFLKLFQGNELD 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 315 ETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 394
Cdd:PRK05658  319 ITWLEKEIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAK 398

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 395 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 474
Cdd:PRK05658  399 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 478

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 475 EMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLT 554
Cdd:PRK05658  479 EIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLT 558

                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1193660533 555 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD 615
Cdd:PRK05658  559 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLDN 619
 
Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 1-615 0e+00

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 1045.92  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533   1 MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTS--TDEDA 78
Cdd:PRK05658    5 MLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADaqTDEDA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533  79 EEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEA 158
Cdd:PRK05658   85 EEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGER 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 159 RLSDLITGFVDPNAEEEMAPTATHVGSElsqedLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIK 238
Cdd:PRK05658  165 RLRELIDGFVDPNAEEDPAHVGSELEEL-----DDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQE 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 239 AKG----RSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKlCVEQCKMPKKNFITLFTGNETS 314
Cdd:PRK05658  240 KKVegrlAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLR-LVERLKMPRKDFLKLFQGNELD 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 315 ETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 394
Cdd:PRK05658  319 ITWLEKEIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAK 398

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 395 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 474
Cdd:PRK05658  399 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 478

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 475 EMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLT 554
Cdd:PRK05658  479 EIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLT 558

                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1193660533 555 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD 615
Cdd:PRK05658  559 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLDN 619
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 377-614 2.68e-160

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: 458.30  E-value: 2.68e-160
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 456
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 457 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDS 536
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1193660533 537 ATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 344-614 3.58e-158

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: 454.13  E-value: 3.58e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 344 QKLRQIEEETGLTIEQVKDINRRMSIGeakARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 423
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQAG---DEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 424 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIA 503
Cdd:COG0568    78 ERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 504 KEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFD 583
Cdd:COG0568   158 REPVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFG 237

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1193660533 584 VTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614
Cdd:COG0568   238 VSRERVRQIEAKALRKLRHPLRSRKLRDYLD 268
Sigma70_ner pfam04546
Sigma-70, non-essential region; The domain is found in the primary vegetative sigma factor. ...
 140-349 8.94e-64

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: 207.41  E-value: 8.94e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 140 PEAITYLLEQYDRVEAEEarlsdlitgfvDPNAEEEMAPTAthvgselsqedldddededeedgdddaaddDNSIDPELA 219
Cdd:pfam04546   1 PLTIAEILEWYDRVEAGD-----------DDDDDDSESLAA------------------------------DEGPDPEEA 39

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 220 REKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKM 299
Cdd:pfam04546  40 LERFEELREQYEKLRKAIEKHGRSSKKYLKLREELSEEFMQFRLVPKQFDRLVDQLREMVDRVRAQEREIMRLCVERAKM 119

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1193660533 300 PKKNFITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQI 349
Cdd:pfam04546 120 PRKDFIKSFPGNETNLEWLDKEIAAGKPWSEKLERVAEDIRRAQQKLADI 169
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 543-601 2.50e-11

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: 59.04  E-value: 2.50e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1193660533 543 RAATHDVLAGLTAREAKVLRMRFGidmnTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 1-615 0e+00

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 1045.92  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533   1 MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTS--TDEDA 78
Cdd:PRK05658    5 MLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADaqTDEDA 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533  79 EEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEA 158
Cdd:PRK05658   85 EEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGER 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 159 RLSDLITGFVDPNAEEEMAPTATHVGSElsqedLDDDEDEDEEDGDDDAADDDNSIDPELAREKFAELRAQYVVTRDTIK 238
Cdd:PRK05658  165 RLRELIDGFVDPNAEEDPAHVGSELEEL-----DDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQE 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 239 AKG----RSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKlCVEQCKMPKKNFITLFTGNETS 314
Cdd:PRK05658  240 KKVegrlAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLR-LVERLKMPRKDFLKLFQGNELD 318

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 315 ETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 394
Cdd:PRK05658  319 ITWLEKEIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAK 398

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 395 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 474
Cdd:PRK05658  399 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 478

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 475 EMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLT 554
Cdd:PRK05658  479 EIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLT 558

                         570       580       590       600       610       620
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1193660533 555 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD 615
Cdd:PRK05658  559 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLDN 619
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 377-614 2.68e-160

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: 458.30  E-value: 2.68e-160
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 456
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 457 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDS 536
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1193660533 537 ATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 344-614 3.58e-158

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: 454.13  E-value: 3.58e-158
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 344 QKLRQIEEETGLTIEQVKDINRRMSIGeakARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 423
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQAG---DEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 424 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIA 503
Cdd:COG0568    78 ERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLA 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 504 KEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFD 583
Cdd:COG0568   158 REPVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFG 237

                         250       260       270
                  ....*....|....*....|....*....|.
gi 1193660533 584 VTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614
Cdd:COG0568   238 VSRERVRQIEAKALRKLRHPLRSRKLRDYLD 268
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 348-614 1.07e-147

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 436.73  E-value: 1.07e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 348 QIEEETGLTIEQVKDINRRMSIGeakaRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 427
Cdd:PRK05901  247 LLAEGEKLDPELRRDLQWIGRDG----KRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGY 322

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 428 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPI 507
Cdd:PRK05901  323 KFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPI 402

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 508 SMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRE 587
Cdd:PRK05901  403 SLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRE 482

                         250       260
                  ....*....|....*....|....*..
gi 1193660533 588 RIRQIEAKALRKLRHPSRSEVLRSFLD 614
Cdd:PRK05901  483 RIRQIESKTLRKLRHPSRSQVLRDFLD 509
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 355-614 5.13e-147

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 429.41  E-value: 5.13e-147
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 355 LTIEQVKDINRRMsigEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 434
Cdd:PRK09210  111 LTAEEEIELAKRI---EEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYAT 187

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 435 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIG 514
Cdd:PRK09210  188 WWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIG 267

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 515 DDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 594
Cdd:PRK09210  268 EEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEA 347

                         250       260
                  ....*....|....*....|
gi 1193660533 595 KALRKLRHPSRSEVLRSFLD 614
Cdd:PRK09210  348 KALRKLRHPSRSKQLKDFLE 367
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 331-613 1.08e-113

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 344.46  E-value: 1.08e-113
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 331 KLHDVAEEVQRCLQKLRQIEEETGLTIEQVKDINRRMSIGeakaRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 410
Cdd:PRK07406   95 ELEELREQFESELGREPSDKEWAELVDMPLPKFRRRLMLG----RRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEG 170

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 411 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERML 490
Cdd:PRK07406  171 SLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESME 250

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 491 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEdTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMN 570
Cdd:PRK07406  251 MTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDG 329

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 1193660533 571 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 613
Cdd:PRK07406  330 RMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEYI 372
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 336-601 3.41e-110

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: 332.67  E-value: 3.41e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 336 AEEVQR--CLQKLRQIEEET---GLTIEQ--------VKDINRRMSIGeakaRRAKKEMVEANLRLVISIAKKYTNRGLQ 402
Cdd:TIGR02997  25 ARQVQQmmVLEELREELEEQlgrEPSKEEwaaaaglsEAELRQRLRQG----QRAKEKMIKANLRLVVSVAKKYQNRGLE 100

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 403 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482
Cdd:TIGR02997 101 LLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSE 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 483 EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTlELPLDSATTESLRAATHDVLAGLTAREAKVLR 562
Cdd:TIGR02997 181 AEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDG-ESPEEQVERESLRQDLESLLAELTPRERQVLR 259

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1193660533 563 MRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:TIGR02997 260 LRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 352-612 3.45e-105

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 320.91  E-value: 3.45e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 352 ETGLTIEQVKDINRRMSIGEAK--------ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 423
Cdd:PRK07921   54 EAGLYAEHLLETRKRLSEARKRdlaavvrdGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 424 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIA 503
Cdd:PRK07921  134 TKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHS 213

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 504 KEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFD 583
Cdd:PRK07921  214 RDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFG 293

                         250       260
                  ....*....|....*....|....*....
gi 1193660533 584 VTRERIRQIEAKALRKLRHPSRSEVLRSF 612
Cdd:PRK07921  294 LSRERVRQIEREVMSKLRNGERADRLRSY 322
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 334-614 8.25e-86

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 274.05  E-value: 8.25e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 334 DVAEEVQRCLQKLRQIEEETGLTIEQVKDInrrmsigEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 413
Cdd:PRK07598  140 SLADLKPTLAEGKRRWAEIAKLTVEELEQI-------QKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLG 212

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 414 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPE 493
Cdd:PRK07598  213 LERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTP 292

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 494 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLElPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDH 573
Cdd:PRK07598  293 TQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDDIS-PEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTY 371

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 1193660533 574 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614
Cdd:PRK07598  372 SLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE 412
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 346-602 1.58e-85

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: 268.52  E-value: 1.58e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 346 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAkkeMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 425
Cdd:TIGR02394  19 LREIGFKPLLTAEEEIAYARRALAGDFEARKV---MIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPER 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 426 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKE 505
Cdd:TIGR02394  96 GFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNER 175

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 506 PISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 585
Cdd:TIGR02394 176 ITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLT 255

                         250
                  ....*....|....*..
gi 1193660533 586 RERIRQIEAKALRKLRH 602
Cdd:TIGR02394 256 RERVRQIQVEALKKLRR 272
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 360-601 2.61e-77

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 248.60  E-value: 2.61e-77
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 360 VKDINRRMSIGEakarRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 439
Cdd:PRK05949   79 ETELKQTLKQGK----RAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQ 154

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 440 AITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 519
Cdd:PRK05949  155 AITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDT 234

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 520 HLGDFIEDTTLElPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 599
Cdd:PRK05949  235 ELSELLEDEGPS-PDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAH 313


                  ..
gi 1193660533 600 LR 601
Cdd:PRK05949  314 LR 315
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 355-611 2.81e-72

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 235.23  E-value: 2.81e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 355 LTIEQVKDINRRMSIGEAKARrakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 434
Cdd:PRK05657   68 LTAEEEVYFARRALRGDFAAR---QRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYAT 144

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 435 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIG 514
Cdd:PRK05657  145 WWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLG 224

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 515 DDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 594
Cdd:PRK05657  225 GDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQV 304

                         250
                  ....*....|....*..
gi 1193660533 595 KALRKLRHPSRSEVLRS 611
Cdd:PRK05657  305 EALRRLREILQTQGLSI 321
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 336-601 2.27e-71

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 232.73  E-value: 2.27e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 336 AEEVQRC--LQKLRQ-IEEETGL--TIEQ--------VKDINRRMSIGEakarRAKKEMVEANLRLVISIAKKYTNRGLQ 402
Cdd:PRK07405   32 GKQVQRLvaLQEIREeLAEELGRepTDAEwakaaklsEEELRSAIAEGE----AAKRKMVEANLRLVVSVAKKYLKRNVD 107

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 403 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTP 482
Cdd:PRK07405  108 LLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATI 187

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 483 EELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTlELPLDSATTESLRAATHDVLAGLTAREAKVLR 562
Cdd:PRK07405  188 GELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQSSLQLDLERLMEDLTPQQKEVIA 266

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1193660533 563 MRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:PRK07405  267 LRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305
Sigma70_ner pfam04546
Sigma-70, non-essential region; The domain is found in the primary vegetative sigma factor. ...
 140-349 8.94e-64

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: 207.41  E-value: 8.94e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 140 PEAITYLLEQYDRVEAEEarlsdlitgfvDPNAEEEMAPTAthvgselsqedldddededeedgdddaaddDNSIDPELA 219
Cdd:pfam04546   1 PLTIAEILEWYDRVEAGD-----------DDDDDDSESLAA------------------------------DEGPDPEEA 39

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 220 REKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKM 299
Cdd:pfam04546  40 LERFEELREQYEKLRKAIEKHGRSSKKYLKLREELSEEFMQFRLVPKQFDRLVDQLREMVDRVRAQEREIMRLCVERAKM 119

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1193660533 300 PKKNFITLFTGNETSETWFNAAIAMNKPWSEKLHDVAEEVQRCLQKLRQI 349
Cdd:pfam04546 120 PRKDFIKSFPGNETNLEWLDKEIAAGKPWSEKLERVAEDIRRAQQKLADI 169
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 375-601 5.57e-41

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: 148.82  E-value: 5.57e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 375 RRAKKEMVEANLRLVISIAKKYTNRGLQFL-DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQArtiR 453
Cdd:COG1191    14 EEAREELIEEYLPLVKKIASRLAGRLPAELdDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLRDED---W 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 454 IPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK--EPISMETPIGDDEDshLGDFIEDTTle 531
Cdd:COG1191    91 VPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANayQLLSLDEPLEDGDD--LLDLLESGD-- 166

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 532 lPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMntdhTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:COG1191   167 -PEEELEHEELREALAEAIEQLPERERLVLSLYYFEEL----TLKEIAEVLGVSESRVSRLHKKALARLR 231
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 355-601 2.95e-35

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: 133.95  E-value: 2.95e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 355 LTIEQVKDINRRMSigEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 434
Cdd:TIGR02392  16 LTPEEEYQLAKRLR--EHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAV 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 435 WWIRQAITRSIadqARTIRIpVHMIETIN--KLNRISRQMLQEMGREPTPEE---LAERMLMPEDKIRKV-LKIAKEPIS 508
Cdd:TIGR02392  94 HWIKAEIHEYI---LRNWRL-VKVATTKAqrKLFFNLRKMKKRLQGWLNPEEveaIAEELGVSEREVREMeSRLSGQDMS 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 509 METPIGDDEDS------HLGDFIEDTTLELpLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTdhTLEEVGKQF 582
Cdd:TIGR02392 170 LNASIDDDEDDggapiaYLVDKRSDPEDTL-EEEQWEELQRQALANALGSLDARSRRIIEARWLDDDKL--TLQELAAEY 246

                         250
                  ....*....|....*....
gi 1193660533 583 DVTRERIRQIEAKALRKLR 601
Cdd:TIGR02392 247 GVSAERIRQIEKNAMKKLK 265
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 355-601 6.72e-32

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 124.90  E-value: 6.72e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 355 LTIEQVKDINRRMSigEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 434
Cdd:PRK06596   29 LTAEEEYMLAKRLR--EHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAV 106

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 435 WWIRQAITRSIadqARTIRIpVHMIETIN--KL--N-RISRQMLQEMgrepTPEELaermlmpeDKIRKVLKIA-KEPIS 508
Cdd:PRK06596  107 HWIKAEIHEYI---LRNWRI-VKVATTKAqrKLffNlRKAKKRLGWL----NPEEV--------EMVAEELGVSeEEVRE 170

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 509 MET-----------PIGDDEDSH--LGDFIEDTT--LELPLDSATTESLR-AATHDVLAGLTAREAKVLRMRFGIDMNTd 572
Cdd:PRK06596  171 MESrlsgqdasldaPIDDDDEESgaPQDYLEDKSsdPADVLEEDNWEDQRrALLADALEGLDERSRDIIEARWLDDDKS- 249

                         250       260
                  ....*....|....*....|....*....
gi 1193660533 573 hTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:PRK06596  250 -TLQELAAEYGVSAERVRQIEKNAMKKLK 277
Sigma70_r1_1 pfam03979
Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is ...
 7-75 6.67e-29

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: 109.20  E-value: 6.67e-29
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1193660533   7 SQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTD 75
Cdd:pfam03979   1 AQLKELIKKGKKKGYLTYDEINDALPDDILDSEQIEDIIEMLNDMGIDVVEEAPDADELLLSDEADDAE 69
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 371-613 9.42e-29

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 116.29  E-value: 9.42e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 371 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIadqAR 450
Cdd:PRK07500   35 DHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYI---LR 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 451 TIRIPVHMIETINK-----LNRISRQMLQ---EMGREPTPEELAERMLMPEDKIRKV-LKIAKEPISMETPIGDDEDSHL 521
Cdd:PRK07500  112 NWSIVRGGTSSAQKalffnLRRLRARLAQadeELTKQEIHREIATALGVSLSDVEMMdARLSGPDASLNAPQSEEDEGRS 191

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 522 G--DFIEDTTL---ELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDmnTDHTLEEVGKQFDVTRERIRQIEAKA 596
Cdd:PRK07500  192 ErmDFLVDDSPlpdEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLRE--DGATLEALGEELGISKERVRQIEARA 269

                         250
                  ....*....|....*....
gi 1193660533 597 LRKLRHP--SRSEVLRSFL 613
Cdd:PRK07500  270 LEKLRRAllSQSPEVAYFA 288
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 460-537 2.73e-28

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: 108.08  E-value: 2.73e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1193660533 460 ETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 537
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
351-601 7.01e-27

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 109.68  E-value: 7.01e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 351 EETGLTIEQVKDINRRMSIGEAKARrakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 430
Cdd:PRK05572   10 KKPQLKDEENKELIKKSQDGDQEAR---DTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFS 86

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 431 TYATWWIRQAITRSIADQArTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISM- 509
Cdd:PRK05572   87 TYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIh 165

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 510 ETPIGDDEDS-HLGDFIEDTTLELPLDsatteslRAATHDVLAGLTAREAKVLRMRFgidmNTDHTLEEVGKQFDVTRER 588
Cdd:PRK05572  166 ETVHENDGDPiTLLDQIADQSEEDWFD-------KIALKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQ 234

                         250
                  ....*....|...
gi 1193660533 589 IRQIEAKALRKLR 601
Cdd:PRK05572  235 VSRLEKKILKQMK 247
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 405-601 2.18e-26

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: 107.36  E-value: 2.18e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 405 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI---TRSIADQARTIRipvhmiETINKLNRISRQMLQEMGREPT 481
Cdd:TIGR02479  28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLR------QKARKLERAIRELEARLGREPT 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 482 PEELAERMLMPEDKIRKVLK--IAKEPISMETPIGDDEDS-HLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 558
Cdd:TIGR02479 102 EEEIAEELGMDLKEYRQALNeiNALSLVSLDELLESGDDGgSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQ 181

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 1193660533 559 KVLRMRFGIDMNtdhtLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:TIGR02479 182 LVLSLYYYEELN----LKEIGEVLGLTESRVSQIHSQALKKLR 220
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 377-601 5.10e-26

RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore. [Transcription, Transcription factors, Cellular processes, Sporulation and germination]


Pssm-ID: 131931 [Multi-domain]  Cd Length: 231  Bit Score: 106.72  E-value: 5.10e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQArTIRIPV 456
Cdd:TIGR02885  12 ARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-IIKVSR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 457 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISM-ETPIGDDEDS-HLGDFIEDTTLElpl 534
Cdd:TIGR02885  91 SLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLyDTVHQDDGDPiYLLDQIADKGSE--- 167

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1193660533 535 DSATTESLraATHDVLAGLTAREAKVLRMRFGIDMntdhTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:TIGR02885 168 DSDWLEKI--ALKEAISKLDERERQIIMLRYFKDK----TQTEVANMLGISQVQVSRLEKKVLKKMK 228
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
355-601 7.76e-26

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 106.96  E-value: 7.76e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 355 LTIEQVKDINRRMSIGEAKARrakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 434
Cdd:PRK08215   19 LKNEEMRELFERMQNGDKEAR---EKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAV 95

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 435 WWIRQAITRSIADQaRTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPI- 513
Cdd:PRK08215   96 PMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIy 174

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 514 ---GD---------DEDSHLGDFIEDTTLElpldsatteslraathDVLAGLTAREAKVLRMRF--GidmntdHTLEEVG 579
Cdd:PRK08215  175 hdgGDpiyvmdqisDEKNKDENWLEEIALK----------------EAMKKLNDREKLILNLRFfqG------KTQMEVA 232

                         250       260
                  ....*....|....*....|..
gi 1193660533 580 KQFDVTRERIRQIEAKALRKLR 601
Cdd:PRK08215  233 EEIGISQAQVSRLEKAALKHMR 254
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 381-451 4.50e-23

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: 93.04  E-value: 4.50e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1193660533 381 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 451
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 365-601 7.54e-23

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 98.31  E-value: 7.54e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 365 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 444
Cdd:PRK07122   29 AGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRH 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 445 IADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKI--AKEPISMETPIG--DDEDSH 520
Cdd:PRK07122  109 FRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAgsAYNTLSIDSGGGsgDDDARA 188

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 521 LGDFIEDttLELPLDSATT-ESLRAathdVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG-KQFDVTRerirqIEAKALR 598
Cdd:PRK07122  189 IADTLGD--VDAGLDQIENrEALRP----LLAALPERERTVLVLRFFESMTQTQIAERVGiSQMHVSR-----LLAKTLA 257


                  ...
gi 1193660533 599 KLR 601
Cdd:PRK07122  258 RLR 260
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 8-128 5.26e-22

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 98.13  E-value: 5.26e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533   8 QLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAENTTSTDEDAEeaaaqvLS 87
Cdd:PRK09210   14 VVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEEEEEELDND------LS 87

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1193660533  88 SVESEigRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 128
Cdd:PRK09210   88 VPPGV--KINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEG 126
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 402-601 3.63e-21

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 93.60  E-value: 3.63e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 402 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI----------TRSIADQARTIRIPVHMIETinklnrisrq 471
Cdd:PRK06288   60 EFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIfdelrsidwiPRSVRQKARQIERAIAMLEA---------- 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 472 mlqEMGREPTPEELAERMLMPEDKIRKVLK--IAKEPISMET--PIGDDEDS-HLGDFIEDTTLELPLDSATTESLRAAT 546
Cdd:PRK06288  130 ---RLGRTPSDEEIADELGISLEEYNSLLSklSGTSVVSLNDlwFGGDEGDEvSLMDTLESPAALNPDEIAEREEIKRVI 206

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1193660533 547 HDVLAGLTAREAKVLRMRFGIDMntdhTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:PRK06288  207 VEAIKTLPEREKKVLILYYYEDL----TLKEIGKVLGVTESRISQLHTKAVLQLR 257
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 380-565 2.12e-19

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 88.05  E-value: 2.12e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 380 EMVEANLRLVISIAKKYTNRGLQ-FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 458
Cdd:PRK07408   29 QLVELNLGLVRKEAHRWSNQCSEpYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRW 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 459 IETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVlKIA---KEPISMETPIGDDEDSH--LGDFIEDttlelp 533
Cdd:PRK07408  109 QELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI-KLAlqnRTPLSLDAPVNQDEDGStsLGDLLPD------ 181

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1193660533 534 ldsATTESLRAATHD------VLAGLTAREAKVLRMRF 565
Cdd:PRK07408  182 ---PRYRSFQLAQEDrirlqqALAQLEERTREVLEFVF 216
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
336-602 2.24e-19

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 87.31  E-value: 2.24e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 336 AEEVQRCLQKLRQIEEEtgltieqvkdinrrmsigeakarrAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 415
Cdd:PRK05803   33 EEEERKYLELMKEGDEE------------------------ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLI 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 416 KAVDKFEYRRGYKFSTYAtwwirqaitrsiadqARTIRipvhmietinklNRIsrqmlqemgreptpeelaermLMpedK 495
Cdd:PRK05803   89 KAIESFDAGKGTKLATYA---------------ARCIE------------NEI---------------------LM---H 117

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 496 IRKVLKIAKEpISMETPIGDDEDSH---LGDFI---EDTTLELPLDSATTESLRAAthdvLAGLTAREAKVLRMRFGIDM 569
Cdd:PRK05803  118 LRNLKKTKKE-VSLQDPIGVDKEGNeisLIDILgseEDDVIEQVELKMEVEKLYKK----IDILDEREKEVIEMRYGLGN 192

                         250       260       270
                  ....*....|....*....|....*....|...
gi 1193660533 570 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602
Cdd:PRK05803  193 GKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
405-602 1.07e-18

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 85.87  E-value: 1.07e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 405 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITrsiaDQARTI-RIPVHMIETINKLNRISRQMLQEMGREPTPE 483
Cdd:PRK07670   54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAII----DGLRKEdWLPRSMREKTKKVEAAIEKLEQRYMRNVTPK 129

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 484 ELAERMLMPEDKIRKVLK--IAKEPISM-ETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKV 560
Cdd:PRK07670  130 EVAAELGMTEEEVEATMNegFFANLLSIdEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLV 209

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1193660533 561 LRMRFgidmNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602
Cdd:PRK07670  210 ISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 401-601 1.27e-17

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 82.59  E-value: 1.27e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 401 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI----------TRSIADQARTIRIPVhmietinklnrisR 470
Cdd:PRK06986   36 VDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMldelrsldwvPRSVRRNAREVAQAI-------------R 102

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 471 QMLQEMGREPTPEELAERMLMPEDKIRKVLkiakepisMETPIG-----DDEDSHLGDFIEDTTL---ELPLDSATTESL 542
Cdd:PRK06986  103 QLEQELGREPTDTEVAEKLGLSLEEYREML--------LDTNISqlfsiDELRGEHGDSILVTEDhqdEDPLQQLEDEEL 174

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1193660533 543 RAATHDVLAGLTAREAKVLRMRFGIDMNtdhtLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:PRK06986  175 REALVEAIESLPEREQLVLSLYYQEELN----LKEIGAVLGVSESRVSQIHSQAIKRLR 229
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 376-601 1.64e-15

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: 74.31  E-value: 1.64e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 376 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRrgYKFSTYATWWIRQAITRSIADQARtirip 455
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR----- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 456 vhmietinkLNRISRQMLQEMGREPTPEELAERmlmpedkirkvlkiakepismetpigddedshlgdfiedttlelpld 535
Cdd:TIGR02937  74 ---------LRRELDLLEELLDSDPSPEEELEQ----------------------------------------------- 97

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1193660533 536 sattESLRAATHDVLAGLTAREAKVLRMRFGIDMntdhTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:TIGR02937  98 ----EEEREALREALEKLPEREREVLVLRYLEGL----SYKEIAEILGISVGTVKRRLKRARKKLR 155
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 381-601 4.17e-14

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 72.73  E-value: 4.17e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 381 MVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAItrsIADQARTIRIPVH 457
Cdd:PRK05911   28 LIEFYLPLVKNVAHRLISgmpSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI---IDDLRKQDWVPRS 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 458 MIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISM----ETPIGDDEDSHLG--DFIEDTTLE 531
Cdd:PRK05911  105 VHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILslneEFPCQSDDEAGLAleERIADERAE 184

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 532 LPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMntdhTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:PRK05911  185 TGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEEL----VLKEIGKILGVSESRVSQIHSKALLKLR 250
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 549-602 1.78e-13

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. 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: 64.76  E-value: 1.78e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1193660533 549 VLAGLTAREAKVLRMRFGidmnTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602
Cdd:pfam04545   1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 543-601 2.50e-11

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: 59.04  E-value: 2.50e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1193660533 543 RAATHDVLAGLTAREAKVLRMRFGidmnTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:cd06171     1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 377-607 1.52e-10

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 62.02  E-value: 1.52e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 456
Cdd:PRK08583   30 AQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPR 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 457 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK--EPISMETPIGDDEDShlgdfiedTTLELpL 534
Cdd:PRK08583  110 RIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKsyQALSVDHSIEADSDG--------STVTL-L 180

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 535 DSATTE-------SLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG-KQFDVTRerirqIEAKALRKLRHPSRS 606
Cdd:PRK08583  181 DIVGQQedgyeltEQRMILEKILPVLSDREKSIIQCTFIENLSQKETGERLGiSQMHVSR-----LQRQAIKKLREAAFL 255


                  .
gi 1193660533 607 E 607
Cdd:PRK08583  256 D 256
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 57-133 2.58e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 63.09  E-value: 2.58e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1193660533  57 EEAPDADDLLLAENTTSTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQ 133
Cdd:PRK05901  170 EEKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAKLTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEE 246
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
355-433 4.38e-10

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 60.25  E-value: 4.38e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1193660533 355 LTIEQVKDINRRMSIGEAKARrakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 433
Cdd:PRK08301   34 LSKEEEEYLLNKLPKGDEAVR---SLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA 109
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
98-128 3.85e-09

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 52.31  E-value: 3.85e-09
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1193660533  98 DPVRMYMREMGTVELLTREGEIDIAKRIEDG 128
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAG 31
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
405-601 6.32e-05

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 44.85  E-value: 6.32e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 405 DLIQEGNIGLMKAVDKFEYRRGyKFSTYATWWIRQAIT---RSIADQARTIRIPVHmietinKLNRISRQMLQEMGREPT 481
Cdd:PRK12427   47 DMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILdelRELDWRPRRLRQKTH------KTNDAIREIAKRLGHEPN 119

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1193660533 482 PEELA-ERMLMPEDKIR-KVLKIAKEPISMETPIGDDEDshlGDFIEDTTLELPLdsATTESLRAAthdvLAGLTAREAK 559
Cdd:PRK12427  120 FEEISaELNLTAEEYQEyLLLENAGTLESLDELLALEAH---NDILQSRDLEENI--IIEDNLKQA----LSQLDEREQL 190

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 1193660533 560 VLRMRFGIDMNtdhtLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:PRK12427  191 ILHLYYQHEMS----LKEIALVLDLTEARICQLNKKIAQKIK 228
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
388-442 2.70e-04

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 42.59  E-value: 2.70e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1193660533 388 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI-RQAIT 442
Cdd:PRK08295   36 FVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCItRQIIT 91
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 102-128 6.48e-03

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


Pssm-ID: 440334 [Multi-domain]  Cd Length: 268  Bit Score: 38.88  E-value: 6.48e-03
                          10        20
                  ....*....|....*....|....*..
gi 1193660533 102 MYMREMGTVELLTREGEIDIAKRIEDG 128
Cdd:COG0568     1 AYLREIGRVPLLTAEEEVELARRIQAG 27
 
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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