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Conserved domains on  [gi|647321318|ref|WP_025758549|]
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MULTISPECIES: RNA polymerase sigma factor RpoD [Enterobacter]

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: 1040.91  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318   1 MEQNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE--TSNNTDEDA 78
Cdd:PRK05658   5 MLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAEneADAQTDEDA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  79 EEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEA 158
Cdd:PRK05658  85 EEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGER 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 159 RLSDLITGFVDPNAEEDMAPTATHVGSElsqeeMDDDEDEDEEESDDDTADDDNSIDPELAREKFAELRTQYEVTRDTIK 238
Cdd:PRK05658 165 RLRELIDGFVDPNAEEDPAHVGSELEEL-----DDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQE 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 239 AKG----RSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKlCVEQCKMPKKNFITLFTGNETS 314
Cdd:PRK05658 240 KKVegrlAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLR-LVERLKMPRKDFLKLFQGNELD 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 315 ETWFNAAIAMNKPWSEKLHDVKEDVYRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 394
Cdd:PRK05658 319 ITWLEKEIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAK 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 395 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 474
Cdd:PRK05658 399 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 478

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 475 EMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLT 554
Cdd:PRK05658 479 EIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLT 558

                        570       580       590       600       610       620
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 647321318 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: 1040.91  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318   1 MEQNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE--TSNNTDEDA 78
Cdd:PRK05658   5 MLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAEneADAQTDEDA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  79 EEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEA 158
Cdd:PRK05658  85 EEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGER 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 159 RLSDLITGFVDPNAEEDMAPTATHVGSElsqeeMDDDEDEDEEESDDDTADDDNSIDPELAREKFAELRTQYEVTRDTIK 238
Cdd:PRK05658 165 RLRELIDGFVDPNAEEDPAHVGSELEEL-----DDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQE 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 239 AKG----RSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKlCVEQCKMPKKNFITLFTGNETS 314
Cdd:PRK05658 240 KKVegrlAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLR-LVERLKMPRKDFLKLFQGNELD 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 315 ETWFNAAIAMNKPWSEKLHDVKEDVYRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 394
Cdd:PRK05658 319 ITWLEKEIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAK 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 395 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 474
Cdd:PRK05658 399 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 478

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 475 EMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLT 554
Cdd:PRK05658 479 EIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLT 558

                        570       580       590       600       610       620
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 647321318 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 3.26e-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: 3.26e-160
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 456
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  457 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDS 536
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 647321318  537 ATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 344-614 2.22e-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: 454.51  E-value: 2.22e-158
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 344 QKLQQIEEETGLTIEQVKDINRRMSIGeakARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 423
Cdd:COG0568    1 AYLREIGRVPLLTAEEEVELARRIQAG---DEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 424 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIA 503
Cdd:COG0568   78 ERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 504 KEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFD 583
Cdd:COG0568  158 REPVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFG 237

                        250       260       270
                 ....*....|....*....|....*....|.
gi 647321318 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 3.41e-63

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: 205.87  E-value: 3.41e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  140 PEAITYLLEQYDRVEAEEarlsdlitgfvDPNAEEDMAPTAthvgselsqeemdddededeeesdddtaddDNSIDPELA 219
Cdd:pfam04546   1 PLTIAEILEWYDRVEAGD-----------DDDDDDSESLAA------------------------------DEGPDPEEA 39

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  220 REKFAELRTQYEVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKM 299
Cdd:pfam04546  40 LERFEELREQYEKLRKAIEKHGRSSKKYLKLREELSEEFMQFRLVPKQFDRLVDQLREMVDRVRAQEREIMRLCVERAKM 119

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 647321318  300 PKKNFITLFTGNETSETWFNAAIAMNKPWSEKLHDVKEDVYRGLQKLQQI 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 2.00e-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: 59.43  E-value: 2.00e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 647321318 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: 1040.91  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318   1 MEQNPQSQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAE--TSNNTDEDA 78
Cdd:PRK05658   5 MLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAEneADAQTDEDA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  79 EEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEA 158
Cdd:PRK05658  85 EEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGER 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 159 RLSDLITGFVDPNAEEDMAPTATHVGSElsqeeMDDDEDEDEEESDDDTADDDNSIDPELAREKFAELRTQYEVTRDTIK 238
Cdd:PRK05658 165 RLRELIDGFVDPNAEEDPAHVGSELEEL-----DDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQE 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 239 AKG----RSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKlCVEQCKMPKKNFITLFTGNETS 314
Cdd:PRK05658 240 KKVegrlAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLR-LVERLKMPRKDFLKLFQGNELD 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 315 ETWFNAAIAMNKPWSEKLHDVKEDVYRGLQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 394
Cdd:PRK05658 319 ITWLEKEIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAK 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 395 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 474
Cdd:PRK05658 399 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 478

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 475 EMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLT 554
Cdd:PRK05658 479 EIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLT 558

                        570       580       590       600       610       620
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 647321318 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 3.26e-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: 3.26e-160
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 456
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  457 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDS 536
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 647321318  537 ATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 344-614 2.22e-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: 454.51  E-value: 2.22e-158
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 344 QKLQQIEEETGLTIEQVKDINRRMSIGeakARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 423
Cdd:COG0568    1 AYLREIGRVPLLTAEEEVELARRIQAG---DEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDP 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 424 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIA 503
Cdd:COG0568   78 ERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLA 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 504 KEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFD 583
Cdd:COG0568  158 REPVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFG 237

                        250       260       270
                 ....*....|....*....|....*....|.
gi 647321318 584 VTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614
Cdd:COG0568  238 VSRERVRQIEAKALRKLRHPLRSRKLRDYLD 268
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 342-614 1.94e-148

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 438.66  E-value: 1.94e-148
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 342 GLQKLQQIEEETGLTIEQVKDINRRMSIGeakaRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 421
Cdd:PRK05901 241 GLYAEELLAEGEKLDPELRRDLQWIGRDG----KRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKF 316

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 422 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLK 501
Cdd:PRK05901 317 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQK 396

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 502 IAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQ 581
Cdd:PRK05901 397 YNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQV 476

                        250       260       270
                 ....*....|....*....|....*....|...
gi 647321318 582 FDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 614
Cdd:PRK05901 477 YGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 355-614 5.35e-147

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 429.41  E-value: 5.35e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 355 LTIEQVKDINRRMsigEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 434
Cdd:PRK09210 111 LTAEEEIELAKRI---EEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYAT 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 435 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIG 514
Cdd:PRK09210 188 WWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIG 267

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 515 DDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 594
Cdd:PRK09210 268 EEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEA 347

                        250       260
                 ....*....|....*....|
gi 647321318 595 KALRKLRHPSRSEVLRSFLD 614
Cdd:PRK09210 348 KALRKLRHPSRSKQLKDFLE 367
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 351-613 1.58e-113

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 344.07  E-value: 1.58e-113
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 351 EETGLTIEQVKdinRRMSIGeakaRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 430
Cdd:PRK07406 118 ELVDMPLPKFR---RRLMLG----RRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFS 190

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 431 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISME 510
Cdd:PRK07406 191 TYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLE 270

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 511 TPIGDDEDSHLGDFIEdTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 590
Cdd:PRK07406 271 TPIGKEEDSRLGDFIE-ADGETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 349

                        250       260
                 ....*....|....*....|...
gi 647321318 591 QIEAKALRKLRHPSRSEVLRSFL 613
Cdd:PRK07406 350 QIEAKALRKLRHPNRNSVLKEYI 372
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 343-601 4.01e-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: 332.29  E-value: 4.01e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  343 LQKLQQIEEET---GLTIEQ--------VKDINRRMSIGeakaRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 411
Cdd:TIGR02997  34 LEELREELEEQlgrEPSKEEwaaaaglsEAELRQRLRQG----QRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGS 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  412 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 491
Cdd:TIGR02997 110 LGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALEL 189

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  492 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTlELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNT 571
Cdd:TIGR02997 190 EPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDG-ESPEEQVERESLRQDLESLLAELTPRERQVLRLRFGLDGGE 268

                         250       260       270
                  ....*....|....*....|....*....|
gi 647321318  572 DHTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:TIGR02997 269 PLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 352-612 2.70e-105

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 320.91  E-value: 2.70e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 352 ETGLTIEQVKDINRRMSIGEAK--------ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 423
Cdd:PRK07921  54 EAGLYAEHLLETRKRLSEARKRdlaavvrdGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 424 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIA 503
Cdd:PRK07921 134 TKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHS 213

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 504 KEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFD 583
Cdd:PRK07921 214 RDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFG 293

                        250       260
                 ....*....|....*....|....*....
gi 647321318 584 VTRERIRQIEAKALRKLRHPSRSEVLRSF 612
Cdd:PRK07921 294 LSRERVRQIEREVMSKLRNGERADRLRSY 322
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 355-602 4.32e-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: 267.36  E-value: 4.32e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  355 LTIEQVKDINRRMSIGEAKARRAkkeMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 434
Cdd:TIGR02394  28 LTAEEEIAYARRALAGDFEARKV---MIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYAT 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  435 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIG 514
Cdd:TIGR02394 105 WWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLD 184

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  515 DDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 594
Cdd:TIGR02394 185 DDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQV 264


                  ....*...
gi 647321318  595 KALRKLRH 602
Cdd:TIGR02394 265 EALKKLRR 272
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 351-614 1.98e-84

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 270.20  E-value: 1.98e-84
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 351 EETGLTIEQVKDInrrmsigEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 430
Cdd:PRK07598 157 EIAKLTVEELEQI-------QKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFS 229

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 431 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISME 510
Cdd:PRK07598 230 TYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLE 309

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 511 TPIGDDEDSHLGDFIEDTTLElPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 590
Cdd:PRK07598 310 TKVGKDKDTELGDLLETDDIS-PEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVR 388

                        250       260
                 ....*....|....*....|....
gi 647321318 591 QIEAKALRKLRHPSRSEVLRSFLD 614
Cdd:PRK07598 389 QIESKALQKLRQPKRRNRIRDYLE 412
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 332-601 8.22e-78

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 250.14  E-value: 8.22e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 332 LHDVKEDVYRGLQKLQQIEEETGLTIEQVKDINRRMSIGEakarRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 411
Cdd:PRK05949  51 LLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGK----RAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGT 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 412 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 491
Cdd:PRK05949 127 LGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELEL 206

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 492 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLElPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNT 571
Cdd:PRK05949 207 EPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGPS-PDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGK 285

                        250       260       270
                 ....*....|....*....|....*....|
gi 647321318 572 DHTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:PRK05949 286 ELSLAKVGERLNLSRERVRQLEHQALAHLR 315
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 355-611 2.45e-72

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 235.62  E-value: 2.45e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 355 LTIEQVKDINRRMSIGEAKARrakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 434
Cdd:PRK05657  68 LTAEEEVYFARRALRGDFAAR---QRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYAT 144

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 435 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIG 514
Cdd:PRK05657 145 WWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLG 224

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 515 DDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 594
Cdd:PRK05657 225 GDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQV 304

                        250
                 ....*....|....*..
gi 647321318 595 KALRKLRHPSRSEVLRS 611
Cdd:PRK05657 305 EALRRLREILQTQGLSI 321
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 331-601 1.49e-71

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 233.11  E-value: 1.49e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 331 KLHDVKEDVYRGLQKLQQIEEETGLTIEQVKDINRRMSIGEakarRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 410
Cdd:PRK07405  40 ALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGE----AAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEG 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 411 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERML 490
Cdd:PRK07405 116 TIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELE 195

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 491 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTlELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMN 570
Cdd:PRK07405 196 LTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDG 274

                        250       260       270
                 ....*....|....*....|....*....|.
gi 647321318 571 TDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:PRK07405 275 QPLTLAKIGERLNISRERVRQIEREALSKLR 305
Sigma70_ner pfam04546
Sigma-70, non-essential region; The domain is found in the primary vegetative sigma factor. ...
 140-349 3.41e-63

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: 205.87  E-value: 3.41e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  140 PEAITYLLEQYDRVEAEEarlsdlitgfvDPNAEEDMAPTAthvgselsqeemdddededeeesdddtaddDNSIDPELA 219
Cdd:pfam04546   1 PLTIAEILEWYDRVEAGD-----------DDDDDDSESLAA------------------------------DEGPDPEEA 39

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  220 REKFAELRTQYEVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERIIMKLCVEQCKM 299
Cdd:pfam04546  40 LERFEELREQYEKLRKAIEKHGRSSKKYLKLREELSEEFMQFRLVPKQFDRLVDQLREMVDRVRAQEREIMRLCVERAKM 119

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 647321318  300 PKKNFITLFTGNETSETWFNAAIAMNKPWSEKLHDVKEDVYRGLQKLQQI 349
Cdd:pfam04546 120 PRKDFIKSFPGNETNLEWLDKEIAAGKPWSEKLERVAEDIRRAQQKLADI 169
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 375-601 4.24e-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: 149.20  E-value: 4.24e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 375 RRAKKEMVEANLRLVISIAKKYTNRGLQFL-DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQArtiR 453
Cdd:COG1191   14 EEAREELIEEYLPLVKKIASRLAGRLPAELdDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLRDED---W 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 454 IPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK--EPISMETPIGDDEDshLGDFIEDTTle 531
Cdd:COG1191   91 VPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANayQLLSLDEPLEDGDD--LLDLLESGD-- 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 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 2.78e-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: 2.78e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  355 LTIEQVKDINRRMSigEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 434
Cdd:TIGR02392  16 LTPEEEYQLAKRLR--EHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAV 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  435 WWIRQAITRSIadqARTIRIpVHMIETIN--KLNRISRQMLQEMGREPTPEE---LAERMLMPEDKIRKV-LKIAKEPIS 508
Cdd:TIGR02392  94 HWIKAEIHEYI---LRNWRL-VKVATTKAqrKLFFNLRKMKKRLQGWLNPEEveaIAEELGVSEREVREMeSRLSGQDMS 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  509 METPIGDDEDS------HLGDFIEDTTLELpLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTdhTLEEVGKQF 582
Cdd:TIGR02392 170 LNASIDDDEDDggapiaYLVDKRSDPEDTL-EEEQWEELQRQALANALGSLDARSRRIIEARWLDDDKL--TLQELAAEY 246

                         250
                  ....*....|....*....
gi 647321318  583 DVTRERIRQIEAKALRKLR 601
Cdd:TIGR02392 247 GVSAERIRQIEKNAMKKLK 265
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 355-601 6.40e-32

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 124.90  E-value: 6.40e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 355 LTIEQVKDINRRMSigEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 434
Cdd:PRK06596  29 LTAEEEYMLAKRLR--EHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAV 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 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 647321318 509 MET-----------PIGDDEDSH--LGDFIEDTT--LELPLDSATTESLR-AATHDVLAGLTAREAKVLRMRFGIDMNTd 572
Cdd:PRK06596 171 MESrlsgqdasldaPIDDDDEESgaPQDYLEDKSsdPADVLEEDNWEDQRrALLADALEGLDERSRDIIEARWLDDDKS- 249

                        250       260
                 ....*....|....*....|....*....
gi 647321318 573 hTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:PRK06596 250 -TLQELAAEYGVSAERVRQIEKNAMKKLK 277
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 371-613 6.72e-29

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 116.67  E-value: 6.72e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 371 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIadqAR 450
Cdd:PRK07500  35 DHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYI---LR 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 451 TIRIPVHMIETINK-----LNRISRQMLQ---EMGREPTPEELAERMLMPEDKIRKV-LKIAKEPISMETPIGDDEDSHL 521
Cdd:PRK07500 112 NWSIVRGGTSSAQKalffnLRRLRARLAQadeELTKQEIHREIATALGVSLSDVEMMdARLSGPDASLNAPQSEEDEGRS 191

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 522 G--DFIEDTTL---ELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDmnTDHTLEEVGKQFDVTRERIRQIEAKA 596
Cdd:PRK07500 192 ErmDFLVDDSPlpdEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLRE--DGATLEALGEELGISKERVRQIEARA 269

                        250
                 ....*....|....*....
gi 647321318 597 LRKLRHP--SRSEVLRSFL 613
Cdd:PRK07500 270 LEKLRRAllSQSPEVAYFA 288
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 2.04e-28

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: 108.04  E-value: 2.04e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 647321318    7 SQLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAETSNNTD 75
Cdd:pfam03979   1 AQLKELIKKGKKKGYLTYDEINDALPDDILDSEQIEDIIEMLNDMGIDVVEEAPDADELLLSDEADDAE 69
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 460-537 2.50e-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: 2.50e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 647321318  460 ETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 537
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
351-601 8.75e-27

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 109.29  E-value: 8.75e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 351 EETGLTIEQVKDINRRMSIGEAKARrakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 430
Cdd:PRK05572  10 KKPQLKDEENKELIKKSQDGDQEAR---DTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFS 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 431 TYATWWIRQAITRSIADQArTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISM- 509
Cdd:PRK05572  87 TYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIh 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 510 ETPIGDDEDS-HLGDFIEDTTLELPLDsatteslRAATHDVLAGLTAREAKVLRMRFgidmNTDHTLEEVGKQFDVTRER 588
Cdd:PRK05572 166 ETVHENDGDPiTLLDQIADQSEEDWFD-------KIALKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQ 234

                        250
                 ....*....|...
gi 647321318 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 2.00e-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: 107.74  E-value: 2.00e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  405 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI---TRSIADQARTIRipvhmiETINKLNRISRQMLQEMGREPT 481
Cdd:TIGR02479  28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLR------QKARKLERAIRELEARLGREPT 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  482 PEELAERMLMPEDKIRKVLK--IAKEPISMETPIGDDEDS-HLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 558
Cdd:TIGR02479 102 EEEIAEELGMDLKEYRQALNeiNALSLVSLDELLESGDDGgSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQ 181

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 647321318  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 6.42e-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: 106.34  E-value: 6.42e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQArTIRIPV 456
Cdd:TIGR02885  12 ARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-IIKVSR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  457 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISM-ETPIGDDEDS-HLGDFIEDTTLElpl 534
Cdd:TIGR02885  91 SLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLyDTVHQDDGDPiYLLDQIADKGSE--- 167

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 647321318  535 DSATTESLraATHDVLAGLTAREAKVLRMRFGIDMntdhTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:TIGR02885 168 DSDWLEKI--ALKEAISKLDERERQIIMLRYFKDK----TQTEVANMLGISQVQVSRLEKKVLKKMK 228
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
355-601 9.59e-26

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 106.57  E-value: 9.59e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 355 LTIEQVKDINRRMSIGEAKARrakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 434
Cdd:PRK08215  19 LKNEEMRELFERMQNGDKEAR---EKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAV 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 435 WWIRQAITRSIADQaRTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPI- 513
Cdd:PRK08215  96 PMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIy 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 514 ---GD---------DEDSHLGDFIEDTTLElpldsatteslraathDVLAGLTAREAKVLRMRF--GidmntdHTLEEVG 579
Cdd:PRK08215 175 hdgGDpiyvmdqisDEKNKDENWLEEIALK----------------EAMKKLNDREKLILNLRFfqG------KTQMEVA 232

                        250       260
                 ....*....|....*....|..
gi 647321318 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 3.78e-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: 3.78e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 647321318  381 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 451
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 365-601 6.23e-23

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 98.69  E-value: 6.23e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 365 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 444
Cdd:PRK07122  29 AGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRH 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 445 IADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKI--AKEPISMETPIG--DDEDSH 520
Cdd:PRK07122 109 FRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAgsAYNTLSIDSGGGsgDDDARA 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 521 LGDFIEDttLELPLDSATT-ESLRAathdVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG-KQFDVTRerirqIEAKALR 598
Cdd:PRK07122 189 IADTLGD--VDAGLDQIENrEALRP----LLAALPERERTVLVLRFFESMTQTQIAERVGiSQMHVSR-----LLAKTLA 257


                 ...
gi 647321318 599 KLR 601
Cdd:PRK07122 258 RLR 260
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 8-128 5.51e-22

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 98.13  E-value: 5.51e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318   8 QLKLLVQRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLLLAEtsnntdEDAEEAAAQVLS 87
Cdd:PRK09210  14 VVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVE------EEEEEELDNDLS 87

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 647321318  88 SVESEigRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 128
Cdd:PRK09210  88 VPPGV--KINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEG 126
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 402-601 3.73e-21

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 93.60  E-value: 3.73e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 402 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI----------TRSIADQARTIRIPVHMIETinklnrisrq 471
Cdd:PRK06288  60 EFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIfdelrsidwiPRSVRQKARQIERAIAMLEA---------- 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 472 mlqEMGREPTPEELAERMLMPEDKIRKVLK--IAKEPISMET--PIGDDEDS-HLGDFIEDTTLELPLDSATTESLRAAT 546
Cdd:PRK06288 130 ---RLGRTPSDEEIADELGISLEEYNSLLSklSGTSVVSLNDlwFGGDEGDEvSLMDTLESPAALNPDEIAEREEIKRVI 206

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 647321318 547 HDVLAGLTAREAKVLRMRFGIDMntdhTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:PRK06288 207 VEAIKTLPEREKKVLILYYYEDL----TLKEIGKVLGVTESRISQLHTKAVLQLR 257
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 380-565 1.91e-19

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 88.44  E-value: 1.91e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 380 EMVEANLRLVISIAKKYTNRGLQ-FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 458
Cdd:PRK07408  29 QLVELNLGLVRKEAHRWSNQCSEpYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRW 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 459 IETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVlKIA---KEPISMETPIGDDEDSH--LGDFIEDttlelp 533
Cdd:PRK07408 109 QELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI-KLAlqnRTPLSLDAPVNQDEDGStsLGDLLPD------ 181

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 647321318 534 ldsATTESLRAATHD------VLAGLTAREAKVLRMRF 565
Cdd:PRK07408 182 ---PRYRSFQLAQEDrirlqqALAQLEERTREVLEFVF 216
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
366-602 2.93e-19

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 87.31  E-value: 2.93e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 366 RMSIGEAKARRAkkeMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAtwwirqaitrsi 445
Cdd:PRK05803  42 LMKEGDEEARNI---LIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA------------ 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 446 adqARTIRipvhmietinklNRIsrqmlqemgreptpeelaermLMpedKIRKVLKIAKEpISMETPIGDDEDSH---LG 522
Cdd:PRK05803 107 ---ARCIE------------NEI---------------------LM---HLRNLKKTKKE-VSLQDPIGVDKEGNeisLI 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 523 DFI---EDTTLELPLDSATTESLRAAthdvLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 599
Cdd:PRK05803 147 DILgseEDDVIEQVELKMEVEKLYKK----IDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKK 222


                 ...
gi 647321318 600 LRH 602
Cdd:PRK05803 223 LFK 225
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
405-602 1.14e-18

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 85.87  E-value: 1.14e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 405 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITrsiaDQARTI-RIPVHMIETINKLNRISRQMLQEMGREPTPE 483
Cdd:PRK07670  54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAII----DGLRKEdWLPRSMREKTKKVEAAIEKLEQRYMRNVTPK 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 484 ELAERMLMPEDKIRKVLK--IAKEPISM-ETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKV 560
Cdd:PRK07670 130 EVAAELGMTEEEVEATMNegFFANLLSIdEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLV 209

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 647321318 561 LRMRFgidmNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 602
Cdd:PRK07670 210 ISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 401-601 1.31e-17

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 82.59  E-value: 1.31e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 401 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI----------TRSIADQARTIRIPVhmietinklnrisR 470
Cdd:PRK06986  36 VDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMldelrsldwvPRSVRRNAREVAQAI-------------R 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 471 QMLQEMGREPTPEELAERMLMPEDKIRKVLkiakepisMETPIG-----DDEDSHLGDFIEDTTL---ELPLDSATTESL 542
Cdd:PRK06986 103 QLEQELGREPTDTEVAEKLGLSLEEYREML--------LDTNISqlfsiDELRGEHGDSILVTEDhqdEDPLQQLEDEEL 174

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 647321318 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 1.28e-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: 74.69  E-value: 1.28e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  376 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRrgYKFSTYATWWIRQAITRSIADQARtirip 455
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR----- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318  456 vhmietinkLNRISRQMLQEMGREPTPEELAERmlmpedkirkvlkiakepismetpigddedshlgdfiedttlelpld 535
Cdd:TIGR02937  74 ---------LRRELDLLEELLDSDPSPEEELEQ----------------------------------------------- 97

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 647321318  536 sattESLRAATHDVLAGLTAREAKVLRMRFGIDMntdhTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:TIGR02937  98 ----EEEREALREALEKLPEREREVLVLRYLEGL----SYKEIAEILGISVGTVKRRLKRARKKLR 155
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 381-601 4.25e-14

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 72.73  E-value: 4.25e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 381 MVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAItrsIADQARTIRIPVH 457
Cdd:PRK05911  28 LIEFYLPLVKNVAHRLISgmpSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI---IDDLRKQDWVPRS 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 458 MIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISM----ETPIGDDEDSHLG--DFIEDTTLE 531
Cdd:PRK05911 105 VHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILslneEFPCQSDDEAGLAleERIADERAE 184

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 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 1.33e-13

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif. 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: 65.14  E-value: 1.33e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 647321318  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 2.00e-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: 59.43  E-value: 2.00e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 647321318 543 RAATHDVLAGLTAREAKVLRMRFGidmnTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 336-607 1.14e-10

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 62.40  E-value: 1.14e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 336 KEDVYRGLQKLQQIEEEtgltieqvkdinrrmsigeakarRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 415
Cdd:PRK08583  12 KEEVNKWIAEYQENQDE-----------------------EAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLL 68

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 416 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDK 495
Cdd:PRK08583  69 GAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEE 148

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 496 IRKVLKIAK--EPISMETPIGDDEDShlgdfiedTTLELpLDSATTE-------SLRAATHDVLAGLTAREAKVLRMRFG 566
Cdd:PRK08583 149 VLEAMEMGKsyQALSVDHSIEADSDG--------STVTL-LDIVGQQedgyeltEQRMILEKILPVLSDREKSIIQCTFI 219

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|..
gi 647321318 567 IDMNTDHTLEEVG-KQFDVTRerirqIEAKALRKLRHPSRSE 607
Cdd:PRK08583 220 ENLSQKETGERLGiSQMHVSR-----LQRQAIKKLREAAFLD 256
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 57-133 3.12e-10

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 62.70  E-value: 3.12e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 647321318  57 EEAPDADDLLLAETSNNTDEDAEEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQ 133
Cdd:PRK05901 170 EEKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAKLTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYAEE 246
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
355-433 4.68e-10

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 60.25  E-value: 4.68e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 647321318 355 LTIEQVKDINRRMSIGEAKARrakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 433
Cdd:PRK08301  34 LSKEEEEYLLNKLPKGDEAVR---SLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA 109
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
98-128 3.77e-09

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 52.31  E-value: 3.77e-09
                          10        20        30
                  ....*....|....*....|....*....|.
gi 647321318   98 DPVRMYMREMGTVELLTREGEIDIAKRIEDG 128
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAG 31
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
405-601 6.38e-05

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 44.85  E-value: 6.38e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 405 DLIQEGNIGLMKAVDKFEYRRGyKFSTYATWWIRQAIT---RSIADQARTIRIPVHmietinKLNRISRQMLQEMGREPT 481
Cdd:PRK12427  47 DMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILdelRELDWRPRRLRQKTH------KTNDAIREIAKRLGHEPN 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 647321318 482 PEELA-ERMLMPEDKIR-KVLKIAKEPISMETPIGDDEDshlGDFIEDTTLELPLdsATTESLRAAthdvLAGLTAREAK 559
Cdd:PRK12427 120 FEEISaELNLTAEEYQEyLLLENAGTLESLDELLALEAH---NDILQSRDLEENI--IIEDNLKQA----LSQLDEREQL 190

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 647321318 560 VLRMRFGIDMNtdhtLEEVGKQFDVTRERIRQIEAKALRKLR 601
Cdd:PRK12427 191 ILHLYYQHEMS----LKEIALVLDLTEARICQLNKKIAQKIK 228
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
388-442 3.22e-04

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 42.20  E-value: 3.22e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 647321318 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 6.20e-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: 6.20e-03
                         10        20
                 ....*....|....*....|....*..
gi 647321318 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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