NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|736425800|ref|WP_034447960|]
View 

RNA polymerase sigma factor RpoD [Bartonella henselae]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 20-667 0e+00

RNA polymerase sigma factor RpoD; Validated


:

Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 1028.20  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  20 DSPLLDFSDDAIKKMVKIAKKNGYVTMDELNAVLPPDEVTSEQIEDTLAMFSEMGINVVD--DEGEAENYEEEVRVEGGD 97
Cdd:PRK05658   2 DSPMLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEeaPDADDLLLAENEADAQTD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  98 LVEATSNALVTTAKRELTDRTDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWREELKE 177
Cdd:PRK05658  82 EDAEEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLEN 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 178 QRILLREIIDLEmtyAGPEAKQAPVIERSEVQKVKEEksssamrDMENIARDigveeddeeddDVNLSLAAMENELCPQV 257
Cdd:PRK05658 162 GERRLRELIDGF---VDPNAEEDPAHVGSELEELDDD-------EDEEEEED-----------ENDDSLAADESELPEKV 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 258 METLDFIAETYVKLRKLQDQHVESSLAerkegalspsQRKKCIQLKSELVQAVKSLSLNQNRIESLVEQLYDINKRLIHN 337
Cdd:PRK05658 221 LEKFKALAKQYKKLRKAQEKKVEGRLA----------QHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQ 290

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 338 EGKLKRIANNYGVGHEEFLKEYQGRELDADWINYIAtLSGRGWKEFSKREAKEIKTLRSEIQNLAQETAISIGEFRRIVT 417
Cdd:PRK05658 291 ERELLRLVERLKMPRKDFLKLFQGNELDITWLEKEI-ASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINR 369

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 418 QVQKGERESTIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 497
Cdd:PRK05658 370 QISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 449

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 498 ADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLGDFI 577
Cdd:PRK05658 450 ADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFI 529

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 578 EDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 657
Cdd:PRK05658 530 EDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 609

                        650
                 ....*....|
gi 736425800 658 SRKLRSFLDS 667
Cdd:PRK05658 610 SRKLRSFLDN 619
 
Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 20-667 0e+00

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 1028.20  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  20 DSPLLDFSDDAIKKMVKIAKKNGYVTMDELNAVLPPDEVTSEQIEDTLAMFSEMGINVVD--DEGEAENYEEEVRVEGGD 97
Cdd:PRK05658   2 DSPMLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEeaPDADDLLLAENEADAQTD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  98 LVEATSNALVTTAKRELTDRTDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWREELKE 177
Cdd:PRK05658  82 EDAEEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLEN 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 178 QRILLREIIDLEmtyAGPEAKQAPVIERSEVQKVKEEksssamrDMENIARDigveeddeeddDVNLSLAAMENELCPQV 257
Cdd:PRK05658 162 GERRLRELIDGF---VDPNAEEDPAHVGSELEELDDD-------EDEEEEED-----------ENDDSLAADESELPEKV 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 258 METLDFIAETYVKLRKLQDQHVESSLAerkegalspsQRKKCIQLKSELVQAVKSLSLNQNRIESLVEQLYDINKRLIHN 337
Cdd:PRK05658 221 LEKFKALAKQYKKLRKAQEKKVEGRLA----------QHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQ 290

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 338 EGKLKRIANNYGVGHEEFLKEYQGRELDADWINYIAtLSGRGWKEFSKREAKEIKTLRSEIQNLAQETAISIGEFRRIVT 417
Cdd:PRK05658 291 ERELLRLVERLKMPRKDFLKLFQGNELDITWLEKEI-ASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINR 369

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 418 QVQKGERESTIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 497
Cdd:PRK05658 370 QISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 449

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 498 ADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLGDFI 577
Cdd:PRK05658 450 ADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFI 529

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 578 EDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 657
Cdd:PRK05658 530 EDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 609

                        650
                 ....*....|
gi 736425800 658 SRKLRSFLDS 667
Cdd:PRK05658 610 SRKLRSFLDN 619
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 429-666 2.37e-152

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: 439.81  E-value: 2.37e-152
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 508
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  509 HMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLGDFIEDRNALLPIDA 588
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 736425800  589 AIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 666
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 407-666 9.16e-150

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: 434.48  E-value: 9.16e-150
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 407 ISIGEFRRIVTQVQKGEREstiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 486
Cdd:COG0568   12 LTAEEEVELARRIQAGDEE---AKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYAT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 487 WWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVG 566
Cdd:COG0568   89 WWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVG 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 567 DEDDSHLGDFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 646
Cdd:COG0568  169 DDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEA 248

                        250       260
                 ....*....|....*....|
gi 736425800 647 KALRKLKHPSRSRKLRSFLD 666
Cdd:COG0568  249 KALRKLRHPLRSRKLRDYLD 268
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 512-589 1.25e-26

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: 103.45  E-value: 1.25e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 736425800  512 ETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLGDFIEDRNALLPIDAA 589
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 595-653 6.58e-10

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: 55.19  E-value: 6.58e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 736425800 595 RDTTTRVLASLTPREERVLRMRFGIGMntdhTLEEVGQQFSVTRERIRQIEAKALRKLK 653
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGL----SYEEIAEILGISRSTVRQRLHRALKKLR 55
 
Name Accession Description Interval E-value
PRK05658 PRK05658
RNA polymerase sigma factor RpoD; Validated
 20-667 0e+00

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 235549 [Multi-domain]  Cd Length: 619  Bit Score: 1028.20  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  20 DSPLLDFSDDAIKKMVKIAKKNGYVTMDELNAVLPPDEVTSEQIEDTLAMFSEMGINVVD--DEGEAENYEEEVRVEGGD 97
Cdd:PRK05658   2 DSPMLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEeaPDADDLLLAENEADAQTD 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  98 LVEATSNALVTTAKRELTDRTDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRETMIAGLCESPLTFQALIIWREELKE 177
Cdd:PRK05658  82 EDAEEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAILEWYDRLEN 161

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 178 QRILLREIIDLEmtyAGPEAKQAPVIERSEVQKVKEEksssamrDMENIARDigveeddeeddDVNLSLAAMENELCPQV 257
Cdd:PRK05658 162 GERRLRELIDGF---VDPNAEEDPAHVGSELEELDDD-------EDEEEEED-----------ENDDSLAADESELPEKV 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 258 METLDFIAETYVKLRKLQDQHVESSLAerkegalspsQRKKCIQLKSELVQAVKSLSLNQNRIESLVEQLYDINKRLIHN 337
Cdd:PRK05658 221 LEKFKALAKQYKKLRKAQEKKVEGRLA----------QHKKYAKLREKLKEELKSLRLTSKQIDELVEQLRDINKRVRGQ 290

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 338 EGKLKRIANNYGVGHEEFLKEYQGRELDADWINYIAtLSGRGWKEFSKREAKEIKTLRSEIQNLAQETAISIGEFRRIVT 417
Cdd:PRK05658 291 ERELLRLVERLKMPRKDFLKLFQGNELDITWLEKEI-ASGKPWSEFLVRVYDEIKKLQQELEAIEEETGLTIEELKEINR 369

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 418 QVQKGERESTIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 497
Cdd:PRK05658 370 QISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 449

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 498 ADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLGDFI 577
Cdd:PRK05658 450 ADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFI 529

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 578 EDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 657
Cdd:PRK05658 530 EDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSR 609

                        650
                 ....*....|
gi 736425800 658 SRKLRSFLDS 667
Cdd:PRK05658 610 SRKLRSFLDN 619
RpoD_Cterm TIGR02393
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ...
 429-666 2.37e-152

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: 439.81  E-value: 2.37e-152
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 508
Cdd:TIGR02393   1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  509 HMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLGDFIEDRNALLPIDA 588
Cdd:TIGR02393  81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 736425800  589 AIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 666
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 407-666 9.16e-150

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: 434.48  E-value: 9.16e-150
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 407 ISIGEFRRIVTQVQKGEREstiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 486
Cdd:COG0568   12 LTAEEEVELARRIQAGDEE---AKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYAT 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 487 WWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVG 566
Cdd:COG0568   89 WWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVG 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 567 DEDDSHLGDFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 646
Cdd:COG0568  169 DDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEA 248

                        250       260
                 ....*....|....*....|
gi 736425800 647 KALRKLKHPSRSRKLRSFLD 666
Cdd:COG0568  249 KALRKLRHPLRSRKLRDYLD 268
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 419-666 6.92e-144

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 423.24  E-value: 6.92e-144
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 419 VQKGEREstiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 498
Cdd:PRK09210 123 IEEGDEE---AKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIA 199

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 499 DQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLGDFIE 578
Cdd:PRK09210 200 DQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIE 279

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 579 DRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 658
Cdd:PRK09210 280 DQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 359


                 ....*...
gi 736425800 659 RKLRSFLD 666
Cdd:PRK09210 360 KQLKDFLE 367
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 388-666 8.73e-142

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 423.25  E-value: 8.73e-142
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 388 AKEIKTLRSEIQNLAQETAISIGEFRRIVTQVQKGERestiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 467
Cdd:PRK05901 235 AKRIEAGLYAEELLAEGEKLDPELRRDLQWIGRDGKR----AKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLI 310

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 468 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEK 547
Cdd:PRK05901 311 KAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEK 390

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 548 VRKVLKIAKEPISLETPVGDEDDSHLGDFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTL 627
Cdd:PRK05901 391 VREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTL 470

                        250       260       270
                 ....*....|....*....|....*....|....*....
gi 736425800 628 EEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 666
Cdd:PRK05901 471 DEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDFLD 509
Sig70-cyanoRpoD TIGR02997
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ...
 385-653 6.28e-109

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: 331.13  E-value: 6.28e-109
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  385 KREAKEIKTLRSEIQNLAQETAISIGEFRRIVTQvqkGERestiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 464
Cdd:TIGR02997  38 REELEEQLGREPSKEEWAAAAGLSEAELRQRLRQ---GQR----AKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSL 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  465 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMP 544
Cdd:TIGR02997 111 GLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELE 190

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  545 LEKVRKVLKIAKEPISLETPVGDEDDSHLGDFIEDrNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTD 624
Cdd:TIGR02997 191 PEQVRELLQRARQPVSLDAPVGDEEDTELGDLLED-DGESPEEQVERESLRQDLESLLAELTPRERQVLRLRFGLDGGEP 269

                         250       260
                  ....*....|....*....|....*....
gi 736425800  625 HTLEEVGQQFSVTRERIRQIEAKALRKLK 653
Cdd:TIGR02997 270 LTLAEIGRRLNLSRERVRQIEAKALRKLR 298
PRK07406 PRK07406
RNA polymerase sigma factor RpoD; Validated
 402-665 3.43e-107

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236012 [Multi-domain]  Cd Length: 373  Bit Score: 329.44  E-value: 3.43e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 402 AQETAISIGEFRRIVtqvQKGERestiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 481
Cdd:PRK07406 117 AELVDMPLPKFRRRL---MLGRR----AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKF 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 482 STYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISL 561
Cdd:PRK07406 190 STYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISL 269

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 562 ETPVGDEDDSHLGDFIE-DRNAllPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 640
Cdd:PRK07406 270 ETPIGKEEDSRLGDFIEaDGET--PEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRER 347

                        250       260
                 ....*....|....*....|....*
gi 736425800 641 IRQIEAKALRKLKHPSRSRKLRSFL 665
Cdd:PRK07406 348 IRQIEAKALRKLRHPNRNSVLKEYI 372
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 424-664 2.59e-102

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 315.13  E-value: 2.59e-102
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 424 RESTIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 503
Cdd:PRK07921  82 RDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRT 161

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 504 IRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLGDFIEDRNAL 583
Cdd:PRK07921 162 IRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEAT 241

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 584 LPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRS 663
Cdd:PRK07921 242 SAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRS 321


                 .
gi 736425800 664 F 664
Cdd:PRK07921 322 Y 322
rpoS_proteo TIGR02394
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ...
 385-662 7.72e-85

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


Pssm-ID: 131447 [Multi-domain]  Cd Length: 285  Bit Score: 268.13  E-value: 7.72e-85
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  385 KREAKEIKTLRSEIQNLAQETAISIGEFRRIVTQVQKGEREstiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNI 464
Cdd:TIGR02394   6 ETETRVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDFE---ARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNL 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  465 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMP 544
Cdd:TIGR02394  83 GLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKP 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  545 LEKVRKVLKIAKEPISLETPVGDEDDSHLGDFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTD 624
Cdd:TIGR02394 163 VEDVSRVLALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEP 242

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 736425800  625 HTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLR 662
Cdd:TIGR02394 243 ATLEEVAAEVGLTRERVRQIQVEALKKLRRILERDGVD 280
PRK07598 PRK07598
RNA polymerase sigma factor SigC; Validated
 416-667 1.63e-81

RNA polymerase sigma factor SigC; Validated


Pssm-ID: 236067 [Multi-domain]  Cd Length: 415  Bit Score: 264.04  E-value: 1.63e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 416 VTQVQKGERESTIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 495
Cdd:PRK07598 163 VEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITR 242

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 496 SIADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLGD 575
Cdd:PRK07598 243 AIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGD 322

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 576 FIEdRNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHP 655
Cdd:PRK07598 323 LLE-TDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQP 401

                        250
                 ....*....|..
gi 736425800 656 SRSRKLRSFLDS 667
Cdd:PRK07598 402 KRRNRIRDYLEL 413
PRK05949 PRK05949
RNA polymerase sigma factor; Validated
 402-667 2.52e-76

RNA polymerase sigma factor; Validated


Pssm-ID: 180321 [Multi-domain]  Cd Length: 327  Bit Score: 247.45  E-value: 2.52e-76
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 402 AQETAISIGEFRRIVTQvqkGERestiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 481
Cdd:PRK05949  72 AEAVNLSETELKQTLKQ---GKR----AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKF 144

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 482 STYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISL 561
Cdd:PRK05949 145 STYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISL 224

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 562 ETPVGDEDDSHLGDFIEDrNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 641
Cdd:PRK05949 225 DVRVGDNQDTELSELLED-EGPSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERV 303

                        250       260
                 ....*....|....*....|....*.
gi 736425800 642 RQIEAKALRKLKHpsRSRKLRSFLDS 667
Cdd:PRK05949 304 RQLEHQALAHLRR--RRANVKEYLAS 327
PRK05657 PRK05657
RNA polymerase sigma factor RpoS; Validated
 417-663 2.21e-73

RNA polymerase sigma factor RpoS; Validated


Pssm-ID: 235548 [Multi-domain]  Cd Length: 325  Bit Score: 239.47  E-value: 2.21e-73
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 417 TQVQKGEREstiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRS 496
Cdd:PRK05657  78 RRALRGDFA---ARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERA 154

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 497 IADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLGDF 576
Cdd:PRK05657 155 IMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDI 234

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 577 IEDRNALLPiDAAIQanLRDTTTRV---LASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 653
Cdd:PRK05657 235 LADEQENGP-EDTTQ--DDDMKQSIvkwLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311

                        250
                 ....*....|
gi 736425800 654 HPSRSRKLRS 663
Cdd:PRK05657 312 EILQTQGLSI 321
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 402-653 3.39e-72

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 236.19  E-value: 3.39e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 402 AQETAISIGEFRRIVtqvqkgeRESTIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 481
Cdd:PRK07405  62 AKAAKLSEEELRSAI-------AEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRF 134

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 482 STYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISL 561
Cdd:PRK07405 135 STYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSL 214

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 562 ETPVGDEDDSHLGDFIEDrNALLPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 641
Cdd:PRK07405 215 DLRVGDNQDTELGELLED-TGASPEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERV 293

                        250
                 ....*....|..
gi 736425800 642 RQIEAKALRKLK 653
Cdd:PRK07405 294 RQIEREALSKLR 305
FliA COG1191
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ...
 419-653 1.97e-40

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: 147.66  E-value: 1.97e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 419 VQKGERESTIAKKEMVEANLRLVISIAKKYTNRGLQFL-DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 497
Cdd:COG1191    6 LRRYQEGDEEAREELIEEYLPLVKKIASRLAGRLPAELdDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGAILDYL 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 498 ADQArtiRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAK--EPISLETPVGDEDDshLGD 575
Cdd:COG1191   86 RDED---WVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANayQLLSLDEPLEDGDD--LLD 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 736425800 576 FIEDRNallPIDAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMntdhTLEEVGQQFSVTRERIRQIEAKALRKLK 653
Cdd:COG1191  161 LLESGD---PEEELEHEELREALAEAIEQLPERERLVLSLYYFEEL----TLKEIAEVLGVSESRVSRLHKKALARLR 231
rpoH_proteo TIGR02392
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ...
 429-653 2.55e-31

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: 123.16  E-value: 2.55e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIadqARTIRIpV 508
Cdd:TIGR02392  36 AAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYI---LRNWRL-V 111

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  509 HMIETIN--KIVRTSRQILHEIGREPTPEE---LSSKLSMPLEKVRKV-LKIAKEPISLETPVGDEDDS------HLGDF 576
Cdd:TIGR02392 112 KVATTKAqrKLFFNLRKMKKRLQGWLNPEEveaIAEELGVSEREVREMeSRLSGQDMSLNASIDDDEDDggapiaYLVDK 191

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 736425800  577 IEDRNALLpIDAAIQANLRDTTTRVLASLTPREERVLRMRFgigMNTDH-TLEEVGQQFSVTRERIRQIEAKALRKLK 653
Cdd:TIGR02392 192 RSDPEDTL-EEEQWEELQRQALANALGSLDARSRRIIEARW---LDDDKlTLQELAAEYGVSAERIRQIEKNAMKKLK 265
PRK06596 PRK06596
RNA polymerase factor sigma-32; Reviewed
 429-653 5.00e-31

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 235838 [Multi-domain]  Cd Length: 284  Bit Score: 122.59  E-value: 5.00e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIadqARTIRIpV 508
Cdd:PRK06596  49 AAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYI---LRNWRI-V 124

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 509 HMIETIN--KI---VRTSRQILHEIgrepTPEELSS---KLSMPLEKVRKV-LKIAKEPISLETPVGDEDDSH--LGDFI 577
Cdd:PRK06596 125 KVATTKAqrKLffnLRKAKKRLGWL----NPEEVEMvaeELGVSEEEVREMeSRLSGQDASLDAPIDDDDEESgaPQDYL 200

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 578 EDRNALLPIDAAIQANLRDTTTRV---LASLTPREERVLRMRFgigMNTDH-TLEEVGQQFSVTRERIRQIEAKALRKLK 653
Cdd:PRK06596 201 EDKSSDPADVLEEDNWEDQRRALLadaLEGLDERSRDIIEARW---LDDDKsTLQELAAEYGVSAERVRQIEKNAMKKLK 277
rpoH2 PRK07500
RNA polymerase factor sigma-32; Reviewed
 429-665 2.77e-29

RNA polymerase factor sigma-32; Reviewed


Pssm-ID: 236033 [Multi-domain]  Cd Length: 289  Bit Score: 117.83  E-value: 2.77e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR--- 505
Cdd:PRK07500  41 ALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRggt 120

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 506 ------IPVHMIETINKIVRTSRQI-LHEIGReptpeELSSKLSMPLEKVRKV-LKIAKEPISLETPVGDEDDSHLG--D 575
Cdd:PRK07500 121 ssaqkaLFFNLRRLRARLAQADEELtKQEIHR-----EIATALGVSLSDVEMMdARLSGPDASLNAPQSEEDEGRSErmD 195

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 576 FIEDrNALLP---IDAAIQ-ANLRDTTTRVLASLTPREERVLRMRfgiGMNTD-HTLEEVGQQFSVTRERIRQIEAKALR 650
Cdd:PRK07500 196 FLVD-DSPLPdeqVESSIDgERRRRWLTQALQTLNERELRIIRER---RLREDgATLEALGEELGISKERVRQIEARALE 271

                        250
                 ....*....|....*..
gi 736425800 651 KLKHP--SRSRKLRSFL 665
Cdd:PRK07500 272 KLRRAllSQSPEVAYFA 288
Sigma70_r3 pfam04539
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ...
 512-589 1.25e-26

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: 103.45  E-value: 1.25e-26
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 736425800  512 ETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPVGDEDDSHLGDFIEDRNALLPIDAA 589
Cdd:pfam04539   1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
PRK08215 PRK08215
RNA polymerase sporulation sigma factor SigG;
411-653 3.68e-26

RNA polymerase sporulation sigma factor SigG;


Pssm-ID: 181296 [Multi-domain]  Cd Length: 258  Bit Score: 108.11  E-value: 3.68e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 411 EFRRIVTQVQKGEREstiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIR 490
Cdd:PRK08215  23 EMRELFERMQNGDKE---AREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAVPMII 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 491 QAITRSIADQaRTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPV----- 565
Cdd:PRK08215 100 GEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIyhdgg 178

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 566 ---------GDEDDshlgdfiEDRNALLPIdaaiqaNLRDTttrvLASLTPREERVLRMRFGIGmntdHTLEEVGQQFSV 636
Cdd:PRK08215 179 dpiyvmdqiSDEKN-------KDENWLEEI------ALKEA----MKKLNDREKLILNLRFFQG----KTQMEVAEEIGI 237

                        250
                 ....*....|....*..
gi 736425800 637 TRERIRQIEAKALRKLK 653
Cdd:PRK08215 238 SQAQVSRLEKAALKHMR 254
FliA_WhiG TIGR02479
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ...
 457-653 4.61e-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: 106.59  E-value: 4.61e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  457 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI---TRSIADQARTIRIPVHMIEtinkivRTSRQILHEIGREPT 533
Cdd:TIGR02479  28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLRQKARKLE------RAIRELEARLGREPT 101

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  534 PEELSSKLSMPLEKVRKVLK--IAKEPISLETPVGDEDDS-HLGDFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREE 610
Cdd:TIGR02479 102 EEEIAEELGMDLKEYRQALNeiNALSLVSLDELLESGDDGgSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQ 181

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 736425800  611 RVLRMRFGIGMNtdhtLEEVGQQFSVTRERIRQIEAKALRKLK 653
Cdd:TIGR02479 182 LVLSLYYYEELN----LKEIGEVLGLTESRVSQIHSQALKKLR 220
spore_sigF TIGR02885
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ...
 415-653 8.04e-25

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: 103.26  E-value: 8.04e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  415 IVTQVQKGEREstiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 494
Cdd:TIGR02885   1 LIKLAQNGDKE---ARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIK 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  495 RSIADQArTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEPISLETPV--GDEDDSH 572
Cdd:TIGR02885  78 RFLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVhqDDGDPIY 156

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  573 LGDFIEDRNALlpiDAAIQANLrdTTTRVLASLTPREERVLRMRFgigmNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 652
Cdd:TIGR02885 157 LLDQIADKGSE---DSDWLEKI--ALKEAISKLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKM 227


                  .
gi 736425800  653 K 653
Cdd:TIGR02885 228 K 228
PRK05572 PRK05572
RNA polymerase sporulation sigma factor, SigF/SigG family;
394-653 6.70e-24

RNA polymerase sporulation sigma factor, SigF/SigG family;


Pssm-ID: 180137 [Multi-domain]  Cd Length: 252  Bit Score: 101.20  E-value: 6.70e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 394 LRSEIQNLAQETAISIGEFRRIVTQVQKGEREstiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKF 473
Cdd:PRK05572   1 MDIEVKNKKKKPQLKDEENKELIKKSQDGDQE---ARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKF 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 474 EYRRGYKFSTYATWWIRQAITRSIADQArTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLK 553
Cdd:PRK05572  78 DLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQE 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 554 IAKEPISLETPV--GDEDDSHLGDFIEDRNALLPIDaaiQANLRDtttrVLASLTPREERVLRMRFgigmNTDHTLEEVG 631
Cdd:PRK05572 157 ASRSPQSIHETVheNDGDPITLLDQIADQSEEDWFD---KIALKE----AIRELDERERLIVYLRY----FKDKTQSEVA 225

                        250       260
                 ....*....|....*....|..
gi 736425800 632 QQFSVTRERIRQIEAKALRKLK 653
Cdd:PRK05572 226 KRLGISQVQVSRLEKKILKQMK 247
Sigma70_r2 pfam04542
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ...
 433-503 7.72e-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: 92.27  E-value: 7.72e-23
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 736425800  433 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 503
Cdd:pfam04542   1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
Sigma70_ner pfam04546
Sigma-70, non-essential region; The domain is found in the primary vegetative sigma factor. ...
 238-401 1.52e-22

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: 94.93  E-value: 1.52e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  238 EDDDVNLSLAAMENELCPQVMETLDFIAETYVKLRKLQDQHvesslaerkegalsPSQRKKCIQLKSELVQAVKSLSLNQ 317
Cdd:pfam04546  20 DDDDDSESLAADEGPDPEEALERFEELREQYEKLRKAIEKH--------------GRSSKKYLKLREELSEEFMQFRLVP 85

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  318 NRIESLVEQLYDINKRLIHNEGKLKRI-ANNYGVGHEEFLKEYQGRELDADWINYIATlSGRGWKEFSKREAKEIKTLRS 396
Cdd:pfam04546  86 KQFDRLVDQLREMVDRVRAQEREIMRLcVERAKMPRKDFIKSFPGNETNLEWLDKEIA-AGKPWSEKLERVAEDIRRAQQ 164


                  ....*
gi 736425800  397 EIQNL 401
Cdd:pfam04546 165 KLADI 169
PRK06288 PRK06288
RNA polymerase sigma factor WhiG; Reviewed
 454-653 2.00e-21

RNA polymerase sigma factor WhiG; Reviewed


Pssm-ID: 235770 [Multi-domain]  Cd Length: 268  Bit Score: 94.37  E-value: 2.00e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 454 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI----------TRSIADQARTIRIPVHMIEtinkivrtsrq 523
Cdd:PRK06288  60 EFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIfdelrsidwiPRSVRQKARQIERAIAMLE----------- 128

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 524 ilHEIGREPTPEELSSKLSMPLEKVRKVLK--IAKEPISLET--PVGDEDDS-HLGDFIEDRNALLPIDAAIQANLRDTT 598
Cdd:PRK06288 129 --ARLGRTPSDEEIADELGISLEEYNSLLSklSGTSVVSLNDlwFGGDEGDEvSLMDTLESPAALNPDEIAEREEIKRVI 206

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 736425800 599 TRVLASLTPREERVLRMRFGIGMntdhTLEEVGQQFSVTRERIRQIEAKALRKLK 653
Cdd:PRK06288 207 VEAIKTLPEREKKVLILYYYEDL----TLKEIGKVLGVTESRISQLHTKAVLQLR 257
PRK07122 PRK07122
RNA polymerase sigma factor SigF; Reviewed
 430-653 2.22e-21

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 168831 [Multi-domain]  Cd Length: 264  Bit Score: 94.46  E-value: 2.22e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 430 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 509
Cdd:PRK07122  42 RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRR 121

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 510 MIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKI--AKEPISLETPVGDEDDSH------LGDF----- 576
Cdd:PRK07122 122 LKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAgsAYNTLSIDSGGGSGDDDAraiadtLGDVdagld 201

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 736425800 577 -IEDRNALLPIdaaiqanlrdtttrvLASLTPREERVLRMRFGIGMNTDHTLEEVG-QQFSVTRerirqIEAKALRKLK 653
Cdd:PRK07122 202 qIENREALRPL---------------LAALPERERTVLVLRFFESMTQTQIAERVGiSQMHVSR-----LLAKTLARLR 260
PRK09210 PRK09210
RNA polymerase sigma factor RpoD; Validated
 28-152 8.85e-20

RNA polymerase sigma factor RpoD; Validated


Pssm-ID: 236413 [Multi-domain]  Cd Length: 367  Bit Score: 91.59  E-value: 8.85e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  28 DDAIKKMVKIAKKNGYVTMDELNAVLPPDEVTSEQIEDTLAMFSEMGINVVDDEGEAENYEEEVRVEGGDLVEATSnaLV 107
Cdd:PRK09210  12 EQVVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEEEEEELDNDLS--VP 89

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 736425800 108 TTAKreltdrTDDPVRMYLREMGAVELLSREGEIAIAKRIEAGRE 152
Cdd:PRK09210  90 PGVK------INDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDE 128
PRK07408 PRK07408
RNA polymerase sigma factor SigF; Reviewed
 432-581 1.92e-19

RNA polymerase sigma factor SigF; Reviewed


Pssm-ID: 180965 [Multi-domain]  Cd Length: 256  Bit Score: 88.44  E-value: 1.92e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 432 EMVEANLRLVISIAKKYTNRGLQ-FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 510
Cdd:PRK07408  29 QLVELNLGLVRKEAHRWSNQCSEpYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRW 108

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 736425800 511 IETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVlKIA---KEPISLETPVGDEDDSH--LGDFIEDRN 581
Cdd:PRK07408 109 QELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI-KLAlqnRTPLSLDAPVNQDEDGStsLGDLLPDPR 183
PRK07670 PRK07670
FliA/WhiG family RNA polymerase sigma factor;
457-654 2.93e-19

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 181075 [Multi-domain]  Cd Length: 251  Bit Score: 87.79  E-value: 2.93e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 457 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITrsiaDQARTI-RIPVHMIETINKIVRTSRQILHEIGREPTPE 535
Cdd:PRK07670  54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAII----DGLRKEdWLPRSMREKTKKVEAAIEKLEQRYMRNVTPK 129

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 536 ELSSKLSMPLEKVRKVLK--IAKEPISL-ETPVGDEDDSHLGDFIEDRNALLPIDAAIQANLRDTTTRVLASLTPREERV 612
Cdd:PRK07670 130 EVAAELGMTEEEVEATMNegFFANLLSIdEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLV 209

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 736425800 613 LRMRFgigmNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKH 654
Cdd:PRK07670 210 ISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247
PRK05803 PRK05803
RNA polymerase sporulation sigma factor SigK;
389-654 8.80e-19

RNA polymerase sporulation sigma factor SigK;


Pssm-ID: 180266 [Multi-domain]  Cd Length: 233  Bit Score: 85.77  E-value: 8.80e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 389 KEIKTLRSEIQNLAQETAISIGEFRRIVTQVQKGEREstiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 468
Cdd:PRK05803  13 KEILFLVSYVKNNSFPQPLSEEEERKYLELMKEGDEE---ARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIK 89

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 469 AVDKFEYRRGYKFSTYAtwwirqaitrsiadqARTIRipvhmietiNKIVrtsrqilheigreptpeelssklsMPLEKV 548
Cdd:PRK05803  90 AIESFDAGKGTKLATYA---------------ARCIE---------NEIL------------------------MHLRNL 121

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 549 RKVlkiaKEPISLETPVG-DEDDSH--LGDFIEDRNAllPIDAAIQANLRDTTTRV-LASLTPREERVLRMRFGIGMNTD 624
Cdd:PRK05803 122 KKT----KKEVSLQDPIGvDKEGNEisLIDILGSEED--DVIEQVELKMEVEKLYKkIDILDEREKEVIEMRYGLGNGKE 195

                        250       260       270
                 ....*....|....*....|....*....|
gi 736425800 625 HTLEEVGQQFSVTRERIRQIEAKALRKLKH 654
Cdd:PRK05803 196 KTQREIAKALGISRSYVSRIEKRALKKLFK 225
Sigma70_r1_1 pfam03979
Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is ...
 29-80 6.05e-17

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: 75.30  E-value: 6.05e-17
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 736425800   29 DAIKKMVKIAKKNGYVTMDELNAVLPPDEVTSEQIEDTLAMFSEMGINVVDD 80
Cdd:pfam03979   1 AQLKELIKKGKKKGYLTYDEINDALPDDILDSEQIEDIIEMLNDMGIDVVEE 52
sigma70-ECF TIGR02937
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ...
 429-653 1.24e-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: 1.24e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRrgYKFSTYATWWIRQAITRSIADQARtiripv 508
Cdd:TIGR02937   2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR------ 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800  509 hmietinkIVRTSRQILHEIGREPTPEELSsklsmplekvrkvlkiakepisletpvgdeddshlgDFIEDRNALLpida 588
Cdd:TIGR02937  74 --------LRRELDLLEELLDSDPSPEEEL------------------------------------EQEEEREALR---- 105

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 736425800  589 aiqanlrdtttRVLASLTPREERVLRMRFGIGMntdhTLEEVGQQFSVTRERIRQIEAKALRKLK 653
Cdd:TIGR02937 106 -----------EALEKLPEREREVLVLRYLEGL----SYKEIAEILGISVGTVKRRLKRARKKLR 155
fliA PRK06986
flagellar biosynthesis sigma factor; Validated
 453-653 2.55e-14

flagellar biosynthesis sigma factor; Validated


Pssm-ID: 235901 [Multi-domain]  Cd Length: 236  Bit Score: 72.96  E-value: 2.55e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 453 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI----------TRSIADQARTIRIPVhmietinkivrtsR 522
Cdd:PRK06986  36 VDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMldelrsldwvPRSVRRNAREVAQAI-------------R 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 523 QILHEIGREPTPEELSSKLSMPLEKVRKVL------KIakepISLETPVGDEDDSHLGdfIEDRNALLPIDAAIQANLRD 596
Cdd:PRK06986 103 QLEQELGREPTDTEVAEKLGLSLEEYREMLldtnisQL----FSIDELRGEHGDSILV--TEDHQDEDPLQQLEDEELRE 176

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 736425800 597 TTTRVLASLTPREERVLRMRFGIGMNtdhtLEEVGQQFSVTRERIRQIEAKALRKLK 653
Cdd:PRK06986 177 ALVEAIESLPEREQLVLSLYYQEELN----LKEIGAVLGVSESRVSQIHSQAIKRLR 229
Sigma70_r4 pfam04545
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 601-654 6.74e-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: 63.22  E-value: 6.74e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 736425800  601 VLASLTPREERVLRMRFGigmnTDHTLEEVGQQFSVTRERIRQIEAKALRKLKH 654
Cdd:pfam04545   1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
PRK08583 PRK08583
RNA polymerase sigma factor SigB; Validated
 403-653 1.08e-10

RNA polymerase sigma factor SigB; Validated


Pssm-ID: 236306 [Multi-domain]  Cd Length: 257  Bit Score: 62.40  E-value: 1.08e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 403 QETAISIGEFRRIVTQVQKGEREStiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 482
Cdd:PRK08583   6 QPTKLTKEEVNKWIAEYQENQDEE--AQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFE 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 483 TYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAK--EPIS 560
Cdd:PRK08583  84 AFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKsyQALS 163

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 561 LETPV-GDEDDSHLgdfiedrnALLPI-----DAAIQANLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-QQ 633
Cdd:PRK08583 164 VDHSIeADSDGSTV--------TLLDIvgqqeDGYELTEQRMILEKILPVLSDREKSIIQCTFIENLSQKETGERLGiSQ 235

                        250       260
                 ....*....|....*....|
gi 736425800 634 FSVTRerirqIEAKALRKLK 653
Cdd:PRK08583 236 MHVSR-----LQRQAIKKLR 250
PRK05911 PRK05911
RNA polymerase sigma factor sigma-28; Reviewed
 433-653 1.80e-10

RNA polymerase sigma factor sigma-28; Reviewed


Pssm-ID: 235644 [Multi-domain]  Cd Length: 257  Bit Score: 61.94  E-value: 1.80e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 433 MVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAItrsIADQARTIRIPVH 509
Cdd:PRK05911  28 LIEFYLPLVKNVAHRLISgmpSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI---IDDLRKQDWVPRS 104

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 510 MIETINKIVRTSRQILHEIGREPTPEELSSKLSMPLEKVRKVLKIAKEP--ISL--ETPVGDEDDS--HLGDFIEDRNAL 583
Cdd:PRK05911 105 VHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPAliLSLneEFPCQSDDEAglALEERIADERAE 184

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 584 LPIDAAIQANLRDTTTRVLASLTPREERVLRMRFgigmNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 653
Cdd:PRK05911 185 TGYDVVDKKEFSSILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALLKLR 250
Sigma70_r1_2 pfam00140
Sigma-70 factor, region 1.2;
120-152 3.80e-10

Sigma-70 factor, region 1.2;


Pssm-ID: 425482 [Multi-domain]  Cd Length: 34  Bit Score: 55.01  E-value: 3.80e-10
                          10        20        30
                  ....*....|....*....|....*....|...
gi 736425800  120 DPVRMYLREMGAVELLSREGEIAIAKRIEAGRE 152
Cdd:pfam00140   1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAGDE 33
Sigma70_r4 cd06171
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ...
 595-653 6.58e-10

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: 55.19  E-value: 6.58e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 736425800 595 RDTTTRVLASLTPREERVLRMRFGIGMntdhTLEEVGQQFSVTRERIRQIEAKALRKLK 653
Cdd:cd06171    1 RERLEEALDKLPEREREVILLRFGEGL----SYEEIAEILGISRSTVRQRLHRALKKLR 55
PRK08301 PRK08301
RNA polymerase sporulation sigma factor SigE;
429-485 4.48e-09

RNA polymerase sporulation sigma factor SigE;


Pssm-ID: 236228 [Multi-domain]  Cd Length: 234  Bit Score: 57.17  E-value: 4.48e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 736425800 429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 485
Cdd:PRK08301  53 VRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA 109
PRK05901 PRK05901
RNA polymerase sigma factor; Provisional
 113-150 1.87e-07

RNA polymerase sigma factor; Provisional


Pssm-ID: 235640 [Multi-domain]  Cd Length: 509  Bit Score: 54.23  E-value: 1.87e-07
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 736425800 113 ELTDrTDDPVRMYLREMGAVELLSREGEIAIAKRIEAG 150
Cdd:PRK05901 205 KLTA-TADPVKAYLKQIGKVKLLNAEEEVELAKRIEAG 241
PRK08295 PRK08295
RNA polymerase sporulation sigma factor SigH;
414-553 2.44e-05

RNA polymerase sporulation sigma factor SigH;


Pssm-ID: 181361 [Multi-domain]  Cd Length: 208  Bit Score: 45.67  E-value: 2.44e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 414 RIVTQVQKGEREstiAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI-RQA 492
Cdd:PRK08295  13 ELVELARSGDKE---ALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCItRQI 89

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 736425800 493 ITrSIADQARTIRIPVHMIETINKIV---RTSRQILHEI--GREPTPEEL---SSKLSMPLEKVRKVLK 553
Cdd:PRK08295  90 IT-AIKTANRQKHIPLNSYVSLDKPIydeESDRTLLDVIseAKVTDPEELiisKEELEDIEEKIEELLS 157
PRK12427 PRK12427
FliA/WhiG family RNA polymerase sigma factor;
457-653 1.25e-04

FliA/WhiG family RNA polymerase sigma factor;


Pssm-ID: 183523 [Multi-domain]  Cd Length: 231  Bit Score: 44.08  E-value: 1.25e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 457 DLIQEGNIGLMKAVDKFEYRRGyKFSTYATWWIRQAIT---RSIADQARTIRIPVHmietinKIVRTSRQILHEIGREPT 533
Cdd:PRK12427  47 DMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILdelRELDWRPRRLRQKTH------KTNDAIREIAKRLGHEPN 119

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 736425800 534 PEELSSKLSMPLEKVRKVLKI--AKEPISLETPVGDEDDshlGDFIEDRNalLPIDAAIQANLRdtttRVLASLTPREER 611
Cdd:PRK12427 120 FEEISAELNLTAEEYQEYLLLenAGTLESLDELLALEAH---NDILQSRD--LEENIIIEDNLK----QALSQLDEREQL 190

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 736425800 612 VLRMRFGIGMNtdhtLEEVGQQFSVTRERIRQIEAKALRKLK 653
Cdd:PRK12427 191 ILHLYYQHEMS----LKEIALVLDLTEARICQLNKKIAQKIK 228
RpoD COG0568
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ...
 124-155 1.34e-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: 41.19  E-value: 1.34e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 736425800 124 MYLREMGAVELLSREGEIAIAKRIEAG----RETMI 155
Cdd:COG0568    1 AYLREIGRVPLLTAEEEVELARRIQAGdeeaKRKLV 36
PRK07921 PRK07921
RNA polymerase sigma factor SigB; Reviewed
 99-150 4.11e-03

RNA polymerase sigma factor SigB; Reviewed


Pssm-ID: 181169 [Multi-domain]  Cd Length: 324  Bit Score: 39.71  E-value: 4.11e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 736425800  99 VEATSNALVTTAKRELTDR--TDDPVRMYLREMGAVELLSREGEIAIAKRIEAG 150
Cdd:PRK07921   3 ADATARATTSRVDSDLDAQspAADLVRVYLNGIGKTALLTAADEVELAKRIEAG 56
PRK07405 PRK07405
RNA polymerase sigma factor SigD; Validated
 114-148 5.24e-03

RNA polymerase sigma factor SigD; Validated


Pssm-ID: 180963 [Multi-domain]  Cd Length: 317  Bit Score: 39.36  E-value: 5.24e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 736425800 114 LTDRTDDPVRMYLREMGAVELLSREGEIAIAKRIE 148
Cdd:PRK07405   2 TAKTSTDLVRTYLREIGRVPLLTHEEEILYGKQVQ 36
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH