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Conserved domains on  [gi|15833204|ref|NP_311977|]
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RNA polymerase sigma 70 factor RpoD [Escherichia coli O157:H7 str. Sakai]

Protein Classification

RNA polymerase sigma factor RpoD( domain architecture ID 11481401)

RNA polymerase sigma factor RpoD 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 Symbol:  rpoD
Gene Ontology:  GO:0016987|GO:0006352|GO:0003700|GO:0003677
PubMed:  25002089|18375176
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
 1-613 0e+00

RNA polymerase sigma factor RpoD; Validated


:

Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 1032.05  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204    1 MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAENTADEDA---- 76
Cdd:PRK05658   5 MLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADAQTdeda 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   77 AEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEA 156
Cdd:PRK05658  85 EEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGER 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  157 RLSDLITGFVDPNAEEDLAPTATHVGSElsqedLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIK 236
Cdd:PRK05658 165 RLRELIDGFVDPNAEEDPAHVGSELEEL-----DDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQE 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  237 AKG----RSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKlCVEQCKMPKKNFITLFTGNETS 312
Cdd:PRK05658 240 KKVegrlAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLR-LVERLKMPRKDFLKLFQGNELD 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  313 DTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 392
Cdd:PRK05658 319 ITWLEKEIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAK 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  393 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 472
Cdd:PRK05658 399 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 478

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  473 EMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLT 552
Cdd:PRK05658 479 EIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLT 558

                        570       580       590       600       610       620
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15833204  553 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD 613
Cdd:PRK05658 559 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLDN 619
 
Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 1-613 0e+00

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 1032.05  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204    1 MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAENTADEDA---- 76
Cdd:PRK05658   5 MLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADAQTdeda 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   77 AEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEA 156
Cdd:PRK05658  85 EEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGER 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  157 RLSDLITGFVDPNAEEDLAPTATHVGSElsqedLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIK 236
Cdd:PRK05658 165 RLRELIDGFVDPNAEEDPAHVGSELEEL-----DDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQE 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  237 AKG----RSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKlCVEQCKMPKKNFITLFTGNETS 312
Cdd:PRK05658 240 KKVegrlAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLR-LVERLKMPRKDFLKLFQGNELD 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  313 DTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 392
Cdd:PRK05658 319 ITWLEKEIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAK 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  393 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 472
Cdd:PRK05658 399 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 478

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  473 EMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLT 552
Cdd:PRK05658 479 EIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLT 558

                        570       580       590       600       610       620
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15833204  553 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD 613
Cdd:PRK05658 559 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLDN 619
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 375-612 1.32e-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: 459.07  E-value: 1.32e-160
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 454
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   455 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDS 534
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15833204   535 ATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 342-612 1.55e-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: 454.90  E-value: 1.55e-158
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204 342 QKLQQIEEETGLTIEQVKDINRRMSIGeakARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 421
Cdd:COG0568   1 AYLREIGRVPLLTAEEEVELARRIQAG---DEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDP 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204 422 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIA 501
Cdd:COG0568  78 ERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLA 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204 502 KEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFD 581
Cdd:COG0568 158 REPVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFG 237

                       250       260       270
                ....*....|....*....|....*....|.
gi 15833204 582 VTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612
Cdd:COG0568 238 VSRERVRQIEAKALRKLRHPLRSRKLRDYLD 268
Sigma70_ner pfam04546
Sigma-70, non-essential region; The domain is found in the primary vegetative sigma factor. ...
 138-347 9.87e-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: 9.87e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   138 PEAITYLLEQYDRVEAEEArlsdlitgfVDPNAEEDLAptathvgselsqedldddededeedgdddsadDDNSIDPELA 217
Cdd:pfam04546   1 PLTIAEILEWYDRVEAGDD---------DDDDDSESLA--------------------------------ADEGPDPEEA 39

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   218 REKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKM 297
Cdd:pfam04546  40 LERFEELREQYEKLRKAIEKHGRSSKKYLKLREELSEEFMQFRLVPKQFDRLVDQLREMVDRVRAQEREIMRLCVERAKM 119

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 15833204   298 PKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQI 347
Cdd:pfam04546 120 PRKDFIKSFPGNETNLEWLDKEIAAGKPWSEKLERVAEDIRRAQQKLADI 169
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 541-599 2.13e-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: 2.13e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15833204 541 RAATHDVLAGLTAREAKVLRMRFGidmnTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 1-613 0e+00

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 1032.05  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204    1 MEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAENTADEDA---- 76
Cdd:PRK05658   5 MLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADDLLLAENEADAQTdeda 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   77 AEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEA 156
Cdd:PRK05658  85 EEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLENGER 164

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  157 RLSDLITGFVDPNAEEDLAPTATHVGSElsqedLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIK 236
Cdd:PRK05658 165 RLRELIDGFVDPNAEEDPAHVGSELEEL-----DDDEDEEEEEDENDDSLAADESELPEKVLEKFKALAKQYKKLRKAQE 239

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  237 AKG----RSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKlCVEQCKMPKKNFITLFTGNETS 312
Cdd:PRK05658 240 KKVegrlAQHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQERELLR-LVERLKMPRKDFLKLFQGNELD 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  313 DTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAK 392
Cdd:PRK05658 319 ITWLEKEIASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAK 398

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  393 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 472
Cdd:PRK05658 399 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 478

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  473 EMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLT 552
Cdd:PRK05658 479 EIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLT 558

                        570       580       590       600       610       620
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15833204  553 AREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD 613
Cdd:PRK05658 559 PREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSFLDN 619
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 375-612 1.32e-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: 459.07  E-value: 1.32e-160
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 454
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   455 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDS 534
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15833204   535 ATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 342-612 1.55e-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: 454.90  E-value: 1.55e-158
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204 342 QKLQQIEEETGLTIEQVKDINRRMSIGeakARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 421
Cdd:COG0568   1 AYLREIGRVPLLTAEEEVELARRIQAG---DEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDP 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204 422 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIA 501
Cdd:COG0568  78 ERGFRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLA 157

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204 502 KEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFD 581
Cdd:COG0568 158 REPVSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFG 237

                       250       260       270
                ....*....|....*....|....*....|.
gi 15833204 582 VTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612
Cdd:COG0568 238 VSRERVRQIEAKALRKLRHPLRSRKLRDYLD 268
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 345-612 7.16e-149

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 439.43  E-value: 7.16e-149
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  345 QQIEEETGLTIEQVKDINRRMSIGeakaRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 424
Cdd:PRK05901 246 ELLAEGEKLDPELRRDLQWIGRDG----KRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKG 321

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  425 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEP 504
Cdd:PRK05901 322 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREP 401

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  505 ISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 584
Cdd:PRK05901 402 ISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTR 481

                        250       260
                 ....*....|....*....|....*...
gi 15833204  585 ERIRQIEAKALRKLRHPSRSEVLRSFLD 612
Cdd:PRK05901 482 ERIRQIESKTLRKLRHPSRSQVLRDFLD 509
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 353-612 1.01e-147

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 431.33  E-value: 1.01e-147
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  353 LTIEQVKDINRRMsigEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 432
Cdd:PRK09210 111 LTAEEEIELAKRI---EEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYAT 187

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  433 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIG 512
Cdd:PRK09210 188 WWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIG 267

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  513 DDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 592
Cdd:PRK09210 268 EEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEA 347

                        250       260
                 ....*....|....*....|
gi 15833204  593 KALRKLRHPSRSEVLRSFLD 612
Cdd:PRK09210 348 KALRKLRHPSRSKQLKDFLE 367
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 349-611 5.76e-114

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 345.23  E-value: 5.76e-114
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  349 EETGLTIEQVKdinRRMSIGeakaRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 428
Cdd:PRK07406 118 ELVDMPLPKFR---RRLMLG----RRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFS 190

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  429 TYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISME 508
Cdd:PRK07406 191 TYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLE 270

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  509 TPIGDDEDSHLGDFIEdTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 588
Cdd:PRK07406 271 TPIGKEEDSRLGDFIE-ADGETPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 349

                        250       260
                 ....*....|....*....|...
gi 15833204  589 QIEAKALRKLRHPSRSEVLRSFL 611
Cdd:PRK07406 350 QIEAKALRKLRHPNRNSVLKEYI 372
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 340-599 1.63e-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: 333.44  E-value: 1.63e-110
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   340 ALQKLQQIEEET---GLTIEQ--------VKDINRRMSIGeakaRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 408
Cdd:TIGR02997  33 VLEELREELEEQlgrEPSKEEwaaaaglsEAELRQRLRQG----QRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEG 108

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   409 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERML 488
Cdd:TIGR02997 109 SLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALE 188

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   489 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTlELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMN 568
Cdd:TIGR02997 189 LEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDG-ESPEEQVERESLRQDLESLLAELTPRERQVLRLRFGLDGG 267

                         250       260       270
                  ....*....|....*....|....*....|.
gi 15833204   569 TDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599
Cdd:TIGR02997 268 EPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 350-610 1.36e-105

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 321.68  E-value: 1.36e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  350 ETGLTIEQVKDINRRMSIGEAK--------ARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 421
Cdd:PRK07921  54 EAGLYAEHLLETRKRLSEARKRdlaavvrdGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 133

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  422 RRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIA 501
Cdd:PRK07921 134 TKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHS 213

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  502 KEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFD 581
Cdd:PRK07921 214 RDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFG 293

                        250       260
                 ....*....|....*....|....*....
gi 15833204  582 VTRERIRQIEAKALRKLRHPSRSEVLRSF 610
Cdd:PRK07921 294 LSRERVRQIEREVMSKLRNGERADRLRSY 322
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 353-600 2.95e-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: 267.75  E-value: 2.95e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   353 LTIEQVKDINRRMSIGEAKARRAkkeMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 432
Cdd:TIGR02394  28 LTAEEEIAYARRALAGDFEARKV---MIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYAT 104

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   433 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIG 512
Cdd:TIGR02394 105 WWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLD 184

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   513 DDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 592
Cdd:TIGR02394 185 DDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQV 264


                  ....*...
gi 15833204   593 KALRKLRH 600
Cdd:TIGR02394 265 EALKKLRR 272
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 332-612 8.49e-85

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 271.36  E-value: 8.49e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  332 DVSEEVHRALQKLQQIEEETGLTIEQVKDInrrmsigEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 411
Cdd:PRK07598 140 SLADLKPTLAEGKRRWAEIAKLTVEELEQI-------QKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLG 212

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  412 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPE 491
Cdd:PRK07598 213 LERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTP 292

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  492 DKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLElPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDH 571
Cdd:PRK07598 293 TQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDDIS-PEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTY 371

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|.
gi 15833204  572 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLD 612
Cdd:PRK07598 372 SLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLE 412
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 330-599 4.87e-78

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 250.53  E-value: 4.87e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  330 LHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEakarRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 409
Cdd:PRK05949  51 LLEAKEALAKKLGREPSLPEWAEAVNLSETELKQTLKQGK----RAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGT 126

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  410 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLM 489
Cdd:PRK05949 127 LGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELEL 206

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  490 PEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLElPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNT 569
Cdd:PRK05949 207 EPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEGPS-PDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGK 285

                        250       260       270
                 ....*....|....*....|....*....|
gi 15833204  570 DHTLEEVGKQFDVTRERIRQIEAKALRKLR 599
Cdd:PRK05949 286 ELSLAKVGERLNLSRERVRQLEHQALAHLR 315
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 353-609 1.71e-72

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 236.01  E-value: 1.71e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  353 LTIEQVKDINRRMSIGEAKARrakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 432
Cdd:PRK05657  68 LTAEEEVYFARRALRGDFAAR---QRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYAT 144

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  433 WWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIG 512
Cdd:PRK05657 145 WWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLG 224

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  513 DDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 592
Cdd:PRK05657 225 GDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQV 304

                        250
                 ....*....|....*..
gi 15833204  593 KALRKLRHPSRSEVLRS 609
Cdd:PRK05657 305 EALRRLREILQTQGLSI 321
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 329-599 1.18e-71

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 233.50  E-value: 1.18e-71
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  329 KLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEakarRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEG 408
Cdd:PRK07405  40 ALQEIREELAEELGREPTDAEWAKAAKLSEEELRSAIAEGE----AAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEG 115

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  409 NIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERML 488
Cdd:PRK07405 116 TIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELE 195

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  489 MPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTlELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMN 568
Cdd:PRK07405 196 LTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDG 274

                        250       260       270
                 ....*....|....*....|....*....|.
gi 15833204  569 TDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599
Cdd:PRK07405 275 QPLTLAKIGERLNISRERVRQIEREALSKLR 305
Sigma70_ner pfam04546
Sigma-70, non-essential region; The domain is found in the primary vegetative sigma factor. ...
 138-347 9.87e-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: 9.87e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   138 PEAITYLLEQYDRVEAEEArlsdlitgfVDPNAEEDLAptathvgselsqedldddededeedgdddsadDDNSIDPELA 217
Cdd:pfam04546   1 PLTIAEILEWYDRVEAGDD---------DDDDDSESLA--------------------------------ADEGPDPEEA 39

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   218 REKFAELRAQYVVTRDTIKAKGRSHAAAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKM 297
Cdd:pfam04546  40 LERFEELREQYEKLRKAIEKHGRSSKKYLKLREELSEEFMQFRLVPKQFDRLVDQLREMVDRVRAQEREIMRLCVERAKM 119

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 15833204   298 PKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQI 347
Cdd:pfam04546 120 PRKDFIKSFPGNETNLEWLDKEIAAGKPWSEKLERVAEDIRRAQQKLADI 169
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 373-599 3.39e-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: 3.39e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204 373 RRAKKEMVEANLRLVISIAKKYTNRGLQFL-DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQArtiR 451
Cdd:COG1191  14 EEAREELIEEYLPLVKKIASRLAGRLPAELdDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYLRDED---W 90

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204 452 IPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK--EPISMETPIGDDEDshLGDFIEDTTle 529
Cdd:COG1191  91 VPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANayQLLSLDEPLEDGDD--LLDLLESGD-- 166

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204 530 lPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMntdhTLEEVGKQFDVTRERIRQIEAKALRKLR 599
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 ...
 353-599 2.16e-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: 134.33  E-value: 2.16e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   353 LTIEQVKDINRRMSigEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 432
Cdd:TIGR02392  16 LTPEEEYQLAKRLR--EHGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAV 93

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   433 WWIRQAITRSIadqARTIRIpVHMIETIN--KLNRISRQMLQEMGREPTPEE---LAERMLMPEDKIRKV-LKIAKEPIS 506
Cdd:TIGR02392  94 HWIKAEIHEYI---LRNWRL-VKVATTKAqrKLFFNLRKMKKRLQGWLNPEEveaIAEELGVSEREVREMeSRLSGQDMS 169

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   507 METPIGDDEDS------HLGDFIEDTTLELpLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTdhTLEEVGKQF 580
Cdd:TIGR02392 170 LNASIDDDEDDggapiaYLVDKRSDPEDTL-EEEQWEELQRQALANALGSLDARSRRIIEARWLDDDKL--TLQELAAEY 246

                         250
                  ....*....|....*....
gi 15833204   581 DVTRERIRQIEAKALRKLR 599
Cdd:TIGR02392 247 GVSAERIRQIEKNAMKKLK 265
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 353-599 4.95e-32

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 125.29  E-value: 4.95e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  353 LTIEQVKDINRRMSigEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 432
Cdd:PRK06596  29 LTAEEEYMLAKRLR--EHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAV 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  433 WWIRQAITRSIadqARTIRIpVHMIETIN--KL--N-RISRQMLQEMgrepTPEELaermlmpeDKIRKVLKIA-KEPIS 506
Cdd:PRK06596 107 HWIKAEIHEYI---LRNWRI-VKVATTKAqrKLffNlRKAKKRLGWL----NPEEV--------EMVAEELGVSeEEVRE 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  507 MET-----------PIGDDEDSH--LGDFIEDTT--LELPLDSATTESLR-AATHDVLAGLTAREAKVLRMRFGIDMNTd 570
Cdd:PRK06596 171 MESrlsgqdasldaPIDDDDEESgaPQDYLEDKSsdPADVLEEDNWEDQRrALLADALEGLDERSRDIIEARWLDDDKS- 249

                        250       260
                 ....*....|....*....|....*....
gi 15833204  571 hTLEEVGKQFDVTRERIRQIEAKALRKLR 599
Cdd:PRK06596 250 -TLQELAAEYGVSAERVRQIEKNAMKKLK 277
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 369-611 5.33e-29

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 116.67  E-value: 5.33e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  369 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIadqAR 448
Cdd:PRK07500  35 DHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYI---LR 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  449 TIRIPVHMIETINK-----LNRISRQMLQ---EMGREPTPEELAERMLMPEDKIRKV-LKIAKEPISMETPIGDDEDSHL 519
Cdd:PRK07500 112 NWSIVRGGTSSAQKalffnLRRLRARLAQadeELTKQEIHREIATALGVSLSDVEMMdARLSGPDASLNAPQSEEDEGRS 191

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  520 G--DFIEDTTL---ELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDmnTDHTLEEVGKQFDVTRERIRQIEAKA 594
Cdd:PRK07500 192 ErmDFLVDDSPlpdEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLRE--DGATLEALGEELGISKERVRQIEARA 269

                        250
                 ....*....|....*....
gi 15833204  595 LRKLRHP--SRSEVLRSFL 611
Cdd:PRK07500 270 LEKLRRAllSQSPEVAYFA 288
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 458-535 1.35e-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: 108.85  E-value: 1.35e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15833204   458 ETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSA 535
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
Sigma70_r1_1 pfam03979
Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is ...
 7-71 1.93e-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: 1.93e-28
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15833204     7 SQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAENT 71
Cdd:pfam03979   1 AQLKELIKKGKKKGYLTYDEINDALPDDILDSEQIEDIIEMLNDMGIDVVEEAPDADELLLSDEA 65
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
349-599 7.16e-27

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 109.68  E-value: 7.16e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  349 EETGLTIEQVKDINRRMSIGEAKARrakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 428
Cdd:PRK05572  10 KKPQLKDEENKELIKKSQDGDQEAR---DTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFS 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  429 TYATWWIRQAITRSIADQArTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISM- 507
Cdd:PRK05572  87 TYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIh 165

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  508 ETPIGDDEDS-HLGDFIEDTTLELPLDsatteslRAATHDVLAGLTAREAKVLRMRFgidmNTDHTLEEVGKQFDVTRER 586
Cdd:PRK05572 166 ETVHENDGDPiTLLDQIADQSEEDWFD-------KIALKEAIRELDERERLIVYLRY----FKDKTQSEVAKRLGISQVQ 234

                        250
                 ....*....|...
gi 15833204  587 IRQIEAKALRKLR 599
Cdd:PRK05572 235 VSRLEKKILKQMK 247
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 403-599 1.74e-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: 1.74e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   403 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI---TRSIADQARTIRipvhmiETINKLNRISRQMLQEMGREPT 479
Cdd:TIGR02479  28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLR------QKARKLERAIRELEARLGREPT 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   480 PEELAERMLMPEDKIRKVLK--IAKEPISMETPIGDDEDS-HLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREA 556
Cdd:TIGR02479 102 EEEIAEELGMDLKEYRQALNeiNALSLVSLDELLESGDDGgSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQ 181

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 15833204   557 KVLRMRFGIDMNtdhtLEEVGKQFDVTRERIRQIEAKALRKLR 599
Cdd:TIGR02479 182 LVLSLYYYEELN----LKEIGEVLGLTESRVSQIHSQALKKLR 220
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 375-599 4.92e-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: 4.92e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQArTIRIPV 454
Cdd:TIGR02885  12 ARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRDDG-IIKVSR 90

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   455 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISM-ETPIGDDEDS-HLGDFIEDTTLElpl 532
Cdd:TIGR02885  91 SLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLyDTVHQDDGDPiYLLDQIADKGSE--- 167

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15833204   533 DSATTESLraATHDVLAGLTAREAKVLRMRFGIDMntdhTLEEVGKQFDVTRERIRQIEAKALRKLR 599
Cdd:TIGR02885 168 DSDWLEKI--ALKEAISKLDERERQIIMLRYFKDK----TQTEVANMLGISQVQVSRLEKKVLKKMK 228
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
353-599 7.71e-26

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 106.96  E-value: 7.71e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  353 LTIEQVKDINRRMSIGEAKARrakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 432
Cdd:PRK08215  19 LKNEEMRELFERMQNGDKEAR---EKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAV 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  433 WWIRQAITRSIADQaRTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPI- 511
Cdd:PRK08215  96 PMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIy 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  512 ---GD---------DEDSHLGDFIEDTTLElpldsatteslraathDVLAGLTAREAKVLRMRF--GidmntdHTLEEVG 577
Cdd:PRK08215 175 hdgGDpiyvmdqisDEKNKDENWLEEIALK----------------EAMKKLNDREKLILNLRFfqG------KTQMEVA 232

                        250       260
                 ....*....|....*....|..
gi 15833204  578 KQFDVTRERIRQIEAKALRKLR 599
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. ...
 379-449 4.66e-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: 92.65  E-value: 4.66e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15833204   379 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 449
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 363-599 6.20e-23

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 98.69  E-value: 6.20e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  363 RRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 442
Cdd:PRK07122  29 AGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRH 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  443 IADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKI--AKEPISMETPIG--DDEDSH 518
Cdd:PRK07122 109 FRDNSWSVKVPRRLKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAgsAYNTLSIDSGGGsgDDDARA 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  519 LGDFIEDttLELPLDSATT-ESLRAathdVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG-KQFDVTRerirqIEAKALR 596
Cdd:PRK07122 189 IADTLGD--VDAGLDQIENrEALRP----LLAALPERERTVLVLRFFESMTQTQIAERVGiSQMHVSR-----LLAKTLA 257


                 ...
gi 15833204  597 KLR 599
Cdd:PRK07122 258 RLR 260
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 400-599 2.90e-21

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 93.98  E-value: 2.90e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  400 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI----------TRSIADQARTIRIPVHMIETinklnrisrq 469
Cdd:PRK06288  60 EFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIfdelrsidwiPRSVRQKARQIERAIAMLEA---------- 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  470 mlqEMGREPTPEELAERMLMPEDKIRKVLK--IAKEPISMET--PIGDDEDS-HLGDFIEDTTLELPLDSATTESLRAAT 544
Cdd:PRK06288 130 ---RLGRTPSDEEIADELGISLEEYNSLLSklSGTSVVSLNDlwFGGDEGDEvSLMDTLESPAALNPDEIAEREEIKRVI 206

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 15833204  545 HDVLAGLTAREAKVLRMRFGIDMntdhTLEEVGKQFDVTRERIRQIEAKALRKLR 599
Cdd:PRK06288 207 VEAIKTLPEREKKVLILYYYEDL----TLKEIGKVLGVTESRISQLHTKAVLQLR 257
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 8-126 9.58e-21

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 94.28  E-value: 9.58e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204    8 QLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAENTADEDAAEAaaqvLSSV 87
Cdd:PRK09210  14 VVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEEEEEELDND----LSVP 89

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 15833204   88 ESEigRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDG 126
Cdd:PRK09210  90 PGV--KINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEG 126
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 378-563 2.00e-19

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 88.05  E-value: 2.00e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  378 EMVEANLRLVISIAKKYTNRGLQ-FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 456
Cdd:PRK07408  29 QLVELNLGLVRKEAHRWSNQCSEpYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRW 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  457 IETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVlKIA---KEPISMETPIGDDEDSH--LGDFIEDttlelp 531
Cdd:PRK07408 109 QELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI-KLAlqnRTPLSLDAPVNQDEDGStsLGDLLPD------ 181

                        170       180       190
                 ....*....|....*....|....*....|....*...
gi 15833204  532 ldsATTESLRAATHD------VLAGLTAREAKVLRMRF 563
Cdd:PRK07408 182 ---PRYRSFQLAQEDrirlqqALAQLEERTREVLEFVF 216
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
364-600 2.34e-19

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 87.31  E-value: 2.34e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  364 RMSIGEAKARRAkkeMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAtwwirqaitrsi 443
Cdd:PRK05803  42 LMKEGDEEARNI---LIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA------------ 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  444 adqARTIRipvhmietinklNRIsrqmlqemgreptpeelaermLMpedKIRKVLKIAKEpISMETPIGDDEDSH---LG 520
Cdd:PRK05803 107 ---ARCIE------------NEI---------------------LM---HLRNLKKTKKE-VSLQDPIGVDKEGNeisLI 146

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  521 DFI---EDTTLELPLDSATTESLRAAthdvLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 597
Cdd:PRK05803 147 DILgseEDDVIEQVELKMEVEKLYKK----IDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKK 222


                 ...
gi 15833204  598 LRH 600
Cdd:PRK05803 223 LFK 225
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
403-600 8.59e-19

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 86.25  E-value: 8.59e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  403 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITrsiaDQARTI-RIPVHMIETINKLNRISRQMLQEMGREPTPE 481
Cdd:PRK07670  54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAII----DGLRKEdWLPRSMREKTKKVEAAIEKLEQRYMRNVTPK 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  482 ELAERMLMPEDKIRKVLK--IAKEPISM-ETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKV 558
Cdd:PRK07670 130 EVAAELGMTEEEVEATMNegFFANLLSIdEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLV 209

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 15833204  559 LRMRFgidmNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 600
Cdd:PRK07670 210 ISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 399-599 1.08e-17

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 82.59  E-value: 1.08e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  399 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI----------TRSIADQARTIRIPVhmietinklnrisR 468
Cdd:PRK06986  36 VDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMldelrsldwvPRSVRRNAREVAQAI-------------R 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  469 QMLQEMGREPTPEELAERMLMPEDKIRKVLkiakepisMETPIG-----DDEDSHLGDFIEDTTL---ELPLDSATTESL 540
Cdd:PRK06986 103 QLEQELGREPTDTEVAEKLGLSLEEYREML--------LDTNISqlfsiDELRGEHGDSILVTEDhqdEDPLQQLEDEEL 174

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 15833204  541 RAATHDVLAGLTAREAKVLRMRFGIDMNtdhtLEEVGKQFDVTRERIRQIEAKALRKLR 599
Cdd:PRK06986 175 REALVEAIESLPEREQLVLSLYYQEELN----LKEIGAVLGVSESRVSQIHSQAIKRLR 229
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 374-599 1.19e-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: 1.19e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   374 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRrgYKFSTYATWWIRQAITRSIADQARtirip 453
Cdd:TIGR02937   1 EAFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR----- 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   454 vhmietinkLNRISRQMLQEMGREPTPEELAERmlmpedkirkvlkiakepismetpigddedshlgdfiedttlelpld 533
Cdd:TIGR02937  74 ---------LRRELDLLEELLDSDPSPEEELEQ----------------------------------------------- 97

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15833204   534 sattESLRAATHDVLAGLTAREAKVLRMRFGIDMntdhTLEEVGKQFDVTRERIRQIEAKALRKLR 599
Cdd:TIGR02937  98 ----EEEREALREALEKLPEREREVLVLRYLEGL----SYKEIAEILGISVGTVKRRLKRARKKLR 155
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 379-599 3.64e-14

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 72.73  E-value: 3.64e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  379 MVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAItrsIADQARTIRIPVH 455
Cdd:PRK05911  28 LIEFYLPLVKNVAHRLISgmpSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI---IDDLRKQDWVPRS 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  456 MIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISM----ETPIGDDEDSHLG--DFIEDTTLE 529
Cdd:PRK05911 105 VHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALILslneEFPCQSDDEAGLAleERIADERAE 184

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  530 LPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMntdhTLEEVGKQFDVTRERIRQIEAKALRKLR 599
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 ...
 547-600 1.50e-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: 1.50e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 15833204   547 VLAGLTAREAKVLRMRFGidmnTDHTLEEVGKQFDVTRERIRQIEAKALRKLRH 600
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 ...
 541-599 2.13e-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: 2.13e-11
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 15833204 541 RAATHDVLAGLTAREAKVLRMRFGidmnTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 599
Cdd:cd06171   1 RERLEEALDKLPEREREVILLRFG----EGLSYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 375-605 1.48e-10

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 62.02  E-value: 1.48e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 454
Cdd:PRK08583  30 AQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPR 109

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  455 HMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK--EPISMETPIGDDEDShlgdfiedTTLELpL 532
Cdd:PRK08583 110 RIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKsyQALSVDHSIEADSDG--------STVTL-L 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  533 DSATTE-------SLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG-KQFDVTRerirqIEAKALRKLRHPSRS 604
Cdd:PRK08583 181 DIVGQQedgyeltEQRMILEKILPVLSDREKSIIQCTFIENLSQKETGERLGiSQMHVSR-----LQRQAIKKLREAAFL 255


                 .
gi 15833204  605 E 605
Cdd:PRK08583 256 D 256
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
353-431 4.37e-10

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 60.25  E-value: 4.37e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 15833204  353 LTIEQVKDINRRMSIGEAKARrakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 431
Cdd:PRK08301  34 LSKEEEEYLLNKLPKGDEAVR---SLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA 109
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
96-126 3.09e-09

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 52.31  E-value: 3.09e-09
                          10        20        30
                  ....*....|....*....|....*....|.
gi 15833204    96 DPVRMYMREMGTVELLTREGEIDIAKRIEDG 126
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAG 31
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 26-131 5.13e-08

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 55.77  E-value: 5.13e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204   26 EVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAENTADEDAAEAAAQVlssveSEIGRTTDPVRMYMREM 105
Cdd:PRK05901 146 DIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQARKD-----AKLTATADPVKAYLKQI 220

                         90       100
                 ....*....|....*....|....*.
gi 15833204  106 GTVELLTREGEIDIAKRIEDGINQVQ 131
Cdd:PRK05901 221 GKVKLLNAEEEVELAKRIEAGLYAEE 246
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
403-599 5.80e-05

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 44.85  E-value: 5.80e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  403 DLIQEGNIGLMKAVDKFEYRRGyKFSTYATWWIRQAIT---RSIADQARTIRIPVHmietinKLNRISRQMLQEMGREPT 479
Cdd:PRK12427  47 DMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILdelRELDWRPRRLRQKTH------KTNDAIREIAKRLGHEPN 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15833204  480 PEELA-ERMLMPEDKIR-KVLKIAKEPISMETPIGDDEDshlGDFIEDTTLELPLdsATTESLRAAthdvLAGLTAREAK 557
Cdd:PRK12427 120 FEEISaELNLTAEEYQEyLLLENAGTLESLDELLALEAH---NDILQSRDLEENI--IIEDNLKQA----LSQLDEREQL 190

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 15833204  558 VLRMRFGIDMNtdhtLEEVGKQFDVTRERIRQIEAKALRKLR 599
Cdd:PRK12427 191 ILHLYYQHEMS----LKEIALVLDLTEARICQLNKKIAQKIK 228
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
386-440 2.69e-04

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 42.59  E-value: 2.69e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 15833204  386 LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI-RQAIT 440
Cdd:PRK08295  36 FVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCItRQIIT 91
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 100-126 6.06e-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: 6.06e-03
                        10        20
                ....*....|....*....|....*..
gi 15833204 100 MYMREMGTVELLTREGEIDIAKRIEDG 126
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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