|
Name |
Accession |
Description |
Interval |
E-value |
| PRK05658 |
PRK05658 |
RNA polymerase sigma factor RpoD; Validated |
20-687 |
0e+00 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 235549 [Multi-domain] Cd Length: 619 Bit Score: 1050.54 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 20 DGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTSEQIEDTMAMLSDMGINVIEDEDVEEAgaatssddDDSSD 99
Cdd:PRK05658 2 DSPMLDNPQSQLKKLIKRGKERGYLTYAELNDHLPEDIVDSEQIEDIIAMLNDMGIQVVEEAPDADD--------LLLAE 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 100 DDNGEGGELAPSTGSALATAKKKEPTDRTDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRETMIGGLCESPLTFQALI 179
Cdd:PRK05658 74 NEADAQTDEDAEEEAAAALSSVESEIGRTDDPVRMYLREMGTVELLTREGEIEIAKRIEAGENIMIAALCESPLTIDAIL 153
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 180 IWRDELNEGTTLLREIIDLETtysGPEAKAAPQFQSPEKIEADRKAAEEKEkarrgrspsgDDDITDvggeglpgeeeee 259
Cdd:PRK05658 154 EWYDRLENGERRLRELIDGFV---DPNAEEDPAHVGSELEELDDDEDEEEE----------EDENDD------------- 207
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 260 dedesslSLAAMEAELRPQVMTTLDTIAETYKKLRKLQDQQVEQRLsasgtlssAQERRYKELKDELVKSVKSLSLNQNR 339
Cdd:PRK05658 208 -------SLAADESELPEKVLEKFKALAKQYKKLRKAQEKKVEGRL--------AQHKKYAKLREKLKEELKSLRLTSKQ 272
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 340 IDALVEQLYDINKRLVQNEGRLLRLAESYGVKRDSFLEQYQGAELDPNWMKSIGnLAARGWKEFAKSENTTIRDIRQEIQ 419
Cdd:PRK05658 273 IDELVEQLRDINKRVRGQERELLRLVERLKMPRKDFLKLFQGNELDITWLEKEI-ASGKPWSEFLVRVYDEIKKLQQELE 351
|
410 420 430 440 450 460 470 480
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 420 NLATETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 499
Cdd:PRK05658 352 AIEEETGLTIEELKEINRQISKGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 431
|
490 500 510 520 530 540 550 560
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 500 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPI 579
Cdd:PRK05658 432 KFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPI 511
|
570 580 590 600 610 620 630 640
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 580 SLETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 659
Cdd:PRK05658 512 SLETPIGDDEDSHLGDFIEDKNAELPIDAAIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRE 591
|
650 660
....*....|....*....|....*...
gi 494975592 660 RIRQIEAKALRKLKHPSRSRKLRSFLDS 687
Cdd:PRK05658 592 RIRQIEAKALRKLRHPSRSRKLRSFLDN 619
|
|
| RpoD_Cterm |
TIGR02393 |
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ... |
449-686 |
2.10e-154 |
|
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: 445.98 E-value: 2.10e-154
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 449 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 528
Cdd:TIGR02393 1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 529 HMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDA 608
Cdd:TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 494975592 609 AIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLD 686
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDFLD 238
|
|
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
427-686 |
1.08e-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: 437.56 E-value: 1.08e-150
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 427 ISISEFRRIVHMVQKGEREAriaKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 506
Cdd:COG0568 12 LTAEEEVELARRIQAGDEEA---KRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERGFRFSTYAT 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 507 WWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVG 586
Cdd:COG0568 89 WWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREPVSLDAPVG 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 587 DEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 666
Cdd:COG0568 169 DDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSRERVRQIEA 248
|
250 260
....*....|....*....|
gi 494975592 667 KALRKLKHPSRSRKLRSFLD 686
Cdd:COG0568 249 KALRKLRHPLRSRKLRDYLD 268
|
|
| PRK09210 |
PRK09210 |
RNA polymerase sigma factor RpoD; Validated |
439-686 |
4.24e-144 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236413 [Multi-domain] Cd Length: 367 Bit Score: 424.78 E-value: 4.24e-144
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 439 VQKGEREAriaKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 518
Cdd:PRK09210 123 IEEGDEEA---KQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIA 199
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 519 DQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIE 598
Cdd:PRK09210 200 DQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIE 279
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 599 DKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 678
Cdd:PRK09210 280 DQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 359
|
....*...
gi 494975592 679 RKLRSFLD 686
Cdd:PRK09210 360 KQLKDFLE 367
|
|
| PRK05901 |
PRK05901 |
RNA polymerase sigma factor; Provisional |
444-686 |
7.42e-142 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 424.02 E-value: 7.42e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 444 REARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 523
Cdd:PRK05901 267 RDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQART 346
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 524 IRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNAL 603
Cdd:PRK05901 347 IRIPVHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAV 426
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 604 LPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRS 683
Cdd:PRK05901 427 SPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRD 506
|
...
gi 494975592 684 FLD 686
Cdd:PRK05901 507 FLD 509
|
|
| Sig70-cyanoRpoD |
TIGR02997 |
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ... |
418-673 |
6.89e-111 |
|
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: 336.53 E-value: 6.89e-111
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 418 IQNLATETGISISEFRRIVhmvqkgeREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 497
Cdd:TIGR02997 51 KEEWAAAAGLSEAELRQRL-------RQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTR 123
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 498 GYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKE 577
Cdd:TIGR02997 124 GYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLNKIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQ 203
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 578 PISLETPVGDEEDSHLGDFIEDkNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVT 657
Cdd:TIGR02997 204 PVSLDAPVGDEEDTELGDLLED-DGESPEEQVERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLS 282
|
250
....*....|....*.
gi 494975592 658 RERIRQIEAKALRKLK 673
Cdd:TIGR02997 283 RERVRQIEAKALRKLR 298
|
|
| PRK07406 |
PRK07406 |
RNA polymerase sigma factor RpoD; Validated |
422-685 |
2.33e-110 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236012 [Multi-domain] Cd Length: 373 Bit Score: 338.30 E-value: 2.33e-110
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 422 ATETGISISEFRRIVHmvqkgerEARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 501
Cdd:PRK07406 117 AELVDMPLPKFRRRLM-------LGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKF 189
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 502 STYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 581
Cdd:PRK07406 190 STYATWWIRQAITRAIADQSRTIRLPVHLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISL 269
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 582 ETPVGDEEDSHLGDFIEDKNAlLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 661
Cdd:PRK07406 270 ETPIGKEEDSRLGDFIEADGE-TPEDDVAKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERI 348
|
250 260
....*....|....*....|....
gi 494975592 662 RQIEAKALRKLKHPSRSRKLRSFL 685
Cdd:PRK07406 349 RQIEAKALRKLRHPNRNSVLKEYI 372
|
|
| PRK07921 |
PRK07921 |
RNA polymerase sigma factor SigB; Reviewed |
421-684 |
1.71e-103 |
|
RNA polymerase sigma factor SigB; Reviewed
Pssm-ID: 181169 [Multi-domain] Cd Length: 324 Bit Score: 318.60 E-value: 1.71e-103
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 421 LATETGISISEFRRIVHMVqkgeREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 500
Cdd:PRK07921 63 LETRKRLSEARKRDLAAVV----RDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFK 138
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 501 FSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPIS 580
Cdd:PRK07921 139 FSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVS 218
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 581 LETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 660
Cdd:PRK07921 219 LDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRER 298
|
250 260
....*....|....*....|....
gi 494975592 661 IRQIEAKALRKLKHPSRSRKLRSF 684
Cdd:PRK07921 299 VRQIEREVMSKLRNGERADRLRSY 322
|
|
| rpoS_proteo |
TIGR02394 |
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ... |
439-682 |
1.01e-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: 270.83 E-value: 1.01e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 439 VQKGEREARiakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 518
Cdd:TIGR02394 40 ALAGDFEAR---KVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIM 116
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 519 DQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIE 598
Cdd:TIGR02394 117 NQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRVLALNERITSLDAPLDDDSSKSLLDTIA 196
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 599 DKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 678
Cdd:TIGR02394 197 DEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILER 276
|
....
gi 494975592 679 RKLR 682
Cdd:TIGR02394 277 DGVD 280
|
|
| PRK07598 |
PRK07598 |
RNA polymerase sigma factor SigC; Validated |
402-687 |
4.18e-81 |
|
RNA polymerase sigma factor SigC; Validated
Pssm-ID: 236067 [Multi-domain] Cd Length: 415 Bit Score: 263.65 E-value: 4.18e-81
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 402 EFAKSENTTIRDIRQEIQN----LATETGISISEFRRIVhmvqkgeREARIAKKEMVEANLRLVISIAKKYTNRGLQFLD 477
Cdd:PRK07598 132 RWAKTADISLADLKPTLAEgkrrWAEIAKLTVEELEQIQ-------KQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLD 204
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 478 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEEL 557
Cdd:PRK07598 205 LVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDI 284
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 558 AEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEdKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRF 637
Cdd:PRK07598 285 AQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLE-TDDISPEEMLMRESLQRDLQHLLADLTSRERDVIRMRF 363
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|
gi 494975592 638 GIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFLDS 687
Cdd:PRK07598 364 GLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDYLEL 413
|
|
| PRK05949 |
PRK05949 |
RNA polymerase sigma factor; Validated |
422-687 |
2.31e-76 |
|
RNA polymerase sigma factor; Validated
Pssm-ID: 180321 [Multi-domain] Cd Length: 327 Bit Score: 247.83 E-value: 2.31e-76
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 422 ATETGISISEFRRIVHmvqKGEReariAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 501
Cdd:PRK05949 72 AEAVNLSETELKQTLK---QGKR----AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKF 144
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 502 STYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 581
Cdd:PRK05949 145 STYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISL 224
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 582 ETPVGDEEDSHLGDFIEDkNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 661
Cdd:PRK05949 225 DVRVGDNQDTELSELLED-EGPSPDQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERV 303
|
250 260
....*....|....*....|....*.
gi 494975592 662 RQIEAKALRKLKHpsRSRKLRSFLDS 687
Cdd:PRK05949 304 RQLEHQALAHLRR--RRANVKEYLAS 327
|
|
| PRK05657 |
PRK05657 |
RNA polymerase sigma factor RpoS; Validated |
439-683 |
5.80e-75 |
|
RNA polymerase sigma factor RpoS; Validated
Pssm-ID: 235548 [Multi-domain] Cd Length: 325 Bit Score: 244.09 E-value: 5.80e-75
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 439 VQKGEREARiakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIA 518
Cdd:PRK05657 80 ALRGDFAAR---QRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 519 DQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIE 598
Cdd:PRK05657 157 NQTRTIRLPVHVVKELNVYLRAARELEHKLDHEPSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILA 236
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 599 DKNALLPiDAAIQANLRETTTRV-LASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 677
Cdd:PRK05657 237 DEQENGP-EDTTQDDDMKQSIVKwLFELNDKQREVLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315
|
....*.
gi 494975592 678 SRKLRS 683
Cdd:PRK05657 316 TQGLSI 321
|
|
| PRK07405 |
PRK07405 |
RNA polymerase sigma factor SigD; Validated |
422-673 |
1.86e-73 |
|
RNA polymerase sigma factor SigD; Validated
Pssm-ID: 180963 [Multi-domain] Cd Length: 317 Bit Score: 240.05 E-value: 1.86e-73
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 422 ATETGISISEFRRIVHmvqkgerEARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 501
Cdd:PRK07405 62 AKAAKLSEEELRSAIA-------EGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRF 134
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 502 STYATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISL 581
Cdd:PRK07405 135 STYAYWWIRQAITRAIAEKSRTIRLPIHITEKLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSL 214
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 582 ETPVGDEEDSHLGDFIEDKNAlLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERI 661
Cdd:PRK07405 215 DLRVGDNQDTELGELLEDTGA-SPEDFATQSSLQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERV 293
|
250
....*....|..
gi 494975592 662 RQIEAKALRKLK 673
Cdd:PRK07405 294 RQIEREALSKLR 305
|
|
| FliA |
COG1191 |
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
434-673 |
5.29e-42 |
|
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: 152.29 E-value: 5.29e-42
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 434 RIVHMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFL-DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 512
Cdd:COG1191 1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIASRLAGRLPAELdDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 513 ITRSIADQArtiRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAK--EPISLETPVGDEED 590
Cdd:COG1191 81 ILDYLRDED---WVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAANayQLLSLDEPLEDGDD 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 591 shLGDFIEDKNallPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMntdhTLEEVGQQFSVTRERIRQIEAKALR 670
Cdd:COG1191 158 --LLDLLESGD---PEEELEHEELREALAEAIEQLPERERLVLSLYYFEEL----TLKEIAEVLGVSESRVSRLHKKALA 228
|
...
gi 494975592 671 KLK 673
Cdd:COG1191 229 RLR 231
|
|
| rpoH_proteo |
TIGR02392 |
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ... |
449-673 |
1.17e-33 |
|
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: 130.09 E-value: 1.17e-33
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 449 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIadqARTIRIpV 528
Cdd:TIGR02392 36 AAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYI---LRNWRL-V 111
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 529 HMIETIN--KIVRTSRQMLHEIGREPTPEE---LAEKLAMPLEKVRKV-LKIAKEPISLETPVGDEEDSHLG--DFIEDK 600
Cdd:TIGR02392 112 KVATTKAqrKLFFNLRKMKKRLQGWLNPEEveaIAEELGVSEREVREMeSRLSGQDMSLNASIDDDEDDGGApiAYLVDK 191
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 494975592 601 NAlLPIDAAIQANLRETTT----RVLASLTPREERVLRMRFgigMNTDH-TLEEVGQQFSVTRERIRQIEAKALRKLK 673
Cdd:TIGR02392 192 RS-DPEDTLEEEQWEELQRqalaNALGSLDARSRRIIEARW---LDDDKlTLQELAAEYGVSAERIRQIEKNAMKKLK 265
|
|
| PRK06596 |
PRK06596 |
RNA polymerase factor sigma-32; Reviewed |
449-673 |
2.19e-32 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 235838 [Multi-domain] Cd Length: 284 Bit Score: 126.83 E-value: 2.19e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 449 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIadqARTIRIpV 528
Cdd:PRK06596 49 AAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYI---LRNWRI-V 124
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 529 HMIETIN--KIVRTSRQMLHEIGREpTPEE---LAEKLAMPLEKVRKV-LKIAKEPISLETPVGDEEDSH--LGDFIEDK 600
Cdd:PRK06596 125 KVATTKAqrKLFFNLRKAKKRLGWL-NPEEvemVAEELGVSEEEVREMeSRLSGQDASLDAPIDDDDEESgaPQDYLEDK 203
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 494975592 601 NAlLPIDAAIQANLRETTTRVLA----SLTPREERVLRMRFgigMNTDH-TLEEVGQQFSVTRERIRQIEAKALRKLK 673
Cdd:PRK06596 204 SS-DPADVLEEDNWEDQRRALLAdaleGLDERSRDIIEARW---LDDDKsTLQELAAEYGVSAERVRQIEKNAMKKLK 277
|
|
| rpoH2 |
PRK07500 |
RNA polymerase factor sigma-32; Reviewed |
449-685 |
1.33e-28 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 236033 [Multi-domain] Cd Length: 289 Bit Score: 115.90 E-value: 1.33e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 449 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR--- 525
Cdd:PRK07500 41 ALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRggt 120
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 526 ------IPVHMIETINKIVRTSRQM-LHEIGReptpeELAEKLAMPLEKVRKV-LKIAKEPISLETPVGDEEDSHLG--D 595
Cdd:PRK07500 121 ssaqkaLFFNLRRLRARLAQADEELtKQEIHR-----EIATALGVSLSDVEMMdARLSGPDASLNAPQSEEDEGRSErmD 195
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 596 FIEDkNALLP---IDAAIQ-ANLRETTTRVLASLTPREERVLRMRfgiGMNTD-HTLEEVGQQFSVTRERIRQIEAKALR 670
Cdd:PRK07500 196 FLVD-DSPLPdeqVESSIDgERRRRWLTQALQTLNERELRIIRER---RLREDgATLEALGEELGISKERVRQIEARALE 271
|
250
....*....|....*..
gi 494975592 671 KLKHP--SRSRKLRSFL 685
Cdd:PRK07500 272 KLRRAllSQSPEVAYFA 288
|
|
| Sigma70_ner |
pfam04546 |
Sigma-70, non-essential region; The domain is found in the primary vegetative sigma factor. ... |
269-421 |
8.75e-28 |
|
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: 109.95 E-value: 8.75e-28
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 269 AAMEAELRPQVMTTLDTIAETYKKLRKLQDQQveqrlsasgtlsSAQERRYKELKDELVKSVKSLSLNQNRIDALVEQLY 348
Cdd:pfam04546 29 AADEGPDPEEALERFEELREQYEKLRKAIEKH------------GRSSKKYLKLREELSEEFMQFRLVPKQFDRLVDQLR 96
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 494975592 349 DINKRLVQNEGRLLRL-AESYGVKRDSFLEQYQGAELDPNWMKSIGNlAARGWKEFAKSENTTIRDIRQEIQNL 421
Cdd:pfam04546 97 EMVDRVRAQEREIMRLcVERAKMPRKDFIKSFPGNETNLEWLDKEIA-AGKPWSEKLERVAEDIRRAQQKLADI 169
|
|
| Sigma70_r3 |
pfam04539 |
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ... |
532-609 |
1.55e-27 |
|
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: 106.15 E-value: 1.55e-27
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 494975592 532 ETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLGDFIEDKNALLPIDAA 609
Cdd:pfam04539 1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESPEEAV 78
|
|
| spore_sigF |
TIGR02885 |
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ... |
435-673 |
2.86e-27 |
|
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: 110.58 E-value: 2.86e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 435 IVHMVQKGEREARiakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 514
Cdd:TIGR02885 1 LIKLAQNGDKEAR---DKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIK 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 515 RSIADQArTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSH 592
Cdd:TIGR02885 78 RFLRDDG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVhqDDGDPIY 156
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 593 LGDFIEDKNAlLPIDAAIQANLREtttrVLASLTPREERVLRMRFgigmNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 672
Cdd:TIGR02885 157 LLDQIADKGS-EDSDWLEKIALKE----AISKLDERERQIIMLRY----FKDKTQTEVANMLGISQVQVSRLEKKVLKKM 227
|
.
gi 494975592 673 K 673
Cdd:TIGR02885 228 K 228
|
|
| PRK08215 |
PRK08215 |
RNA polymerase sporulation sigma factor SigG; |
427-673 |
3.63e-27 |
|
RNA polymerase sporulation sigma factor SigG;
Pssm-ID: 181296 [Multi-domain] Cd Length: 258 Bit Score: 110.81 E-value: 3.63e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 427 ISISEFRRIVHMVQKGEREARiakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 506
Cdd:PRK08215 19 LKNEEMRELFERMQNGDKEAR---EKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAV 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 507 WWIRQAITRSIADQaRTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPV- 585
Cdd:PRK08215 96 PMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIy 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 586 -------------GDEEDshlgdfiEDKNALLPIdaaiqaNLRETttrvLASLTPREERVLRMRFGIGmntdHTLEEVGQ 652
Cdd:PRK08215 175 hdggdpiyvmdqiSDEKN-------KDENWLEEI------ALKEA----MKKLNDREKLILNLRFFQG----KTQMEVAE 233
|
250 260
....*....|....*....|.
gi 494975592 653 QFSVTRERIRQIEAKALRKLK 673
Cdd:PRK08215 234 EIGISQAQVSRLEKAALKHMR 254
|
|
| FliA_WhiG |
TIGR02479 |
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ... |
477-673 |
4.80e-27 |
|
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Pssm-ID: 274153 [Multi-domain] Cd Length: 224 Bit Score: 109.67 E-value: 4.80e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 477 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI---TRSIADQARTIRIPVHMIEtinkivRTSRQMLHEIGREPT 553
Cdd:TIGR02479 28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLRQKARKLE------RAIRELEARLGREPT 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 554 PEELAEKLAMPLEKVRKVLK--IAKEPISLETPVGDEEDS-HLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREE 630
Cdd:TIGR02479 102 EEEIAEELGMDLKEYRQALNeiNALSLVSLDELLESGDDGgSLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQ 181
|
170 180 190 200
....*....|....*....|....*....|....*....|...
gi 494975592 631 RVLRMRFGIGMNtdhtLEEVGQQFSVTRERIRQIEAKALRKLK 673
Cdd:TIGR02479 182 LVLSLYYYEELN----LKEIGEVLGLTESRVSQIHSQALKKLR 220
|
|
| PRK05572 |
PRK05572 |
RNA polymerase sporulation sigma factor, SigF/SigG family; |
417-673 |
1.62e-26 |
|
RNA polymerase sporulation sigma factor, SigF/SigG family;
Pssm-ID: 180137 [Multi-domain] Cd Length: 252 Bit Score: 108.91 E-value: 1.62e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 417 EIQNLATETGISISEFRRIVHMVQKGEREARiakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 496
Cdd:PRK05572 4 EVKNKKKKPQLKDEENKELIKKSQDGDQEAR---DTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLS 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 497 RGYKFSTYATWWIRQAITRSIADQArTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAK 576
Cdd:PRK05572 81 YDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASR 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 577 EPISL-ETPVGDEEDS-HLGDFIEDKNALLPIDaaiQANLREtttrVLASLTPREERVLRMRFgigmNTDHTLEEVGQQF 654
Cdd:PRK05572 160 SPQSIhETVHENDGDPiTLLDQIADQSEEDWFD---KIALKE----AIRELDERERLIVYLRY----FKDKTQSEVAKRL 228
|
250
....*....|....*....
gi 494975592 655 SVTRERIRQIEAKALRKLK 673
Cdd:PRK05572 229 GISQVQVSRLEKKILKQMK 247
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
453-523 |
8.44e-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: 8.44e-23
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 494975592 453 MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 523
Cdd:pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
|
|
| PRK07122 |
PRK07122 |
RNA polymerase sigma factor SigF; Reviewed |
450-673 |
5.86e-22 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 168831 [Multi-domain] Cd Length: 264 Bit Score: 96.00 E-value: 5.86e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 450 KKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH 529
Cdd:PRK07122 42 RDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRR 121
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 530 MIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKI--AKEPISLETPVG--DEEDSHLGDFIEDknallp 605
Cdd:PRK07122 122 LKELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEGLVAgsAYNTLSIDSGGGsgDDDARAIADTLGD------ 195
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 606 IDAAI-QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-QQFSVTRerirqIEAKALRKLK 673
Cdd:PRK07122 196 VDAGLdQIENREALRPLLAALPERERTVLVLRFFESMTQTQIAERVGiSQMHVSR-----LLAKTLARLR 260
|
|
| PRK06288 |
PRK06288 |
RNA polymerase sigma factor WhiG; Reviewed |
474-673 |
7.41e-22 |
|
RNA polymerase sigma factor WhiG; Reviewed
Pssm-ID: 235770 [Multi-domain] Cd Length: 268 Bit Score: 95.91 E-value: 7.41e-22
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 474 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI----------TRSIADQARTIRIPVHMIEtinkivrtsrq 543
Cdd:PRK06288 60 EFDDLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIfdelrsidwiPRSVRQKARQIERAIAMLE----------- 128
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 544 mlHEIGREPTPEELAEKLAMPLEKVRKVLK--IAKEPISLET--PVGDEEDS-HLGDFIEDKNALLPIDAAIQANLRETT 618
Cdd:PRK06288 129 --ARLGRTPSDEEIADELGISLEEYNSLLSklSGTSVVSLNDlwFGGDEGDEvSLMDTLESPAALNPDEIAEREEIKRVI 206
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*
gi 494975592 619 TRVLASLTPREERVLRMRFGIGMntdhTLEEVGQQFSVTRERIRQIEAKALRKLK 673
Cdd:PRK06288 207 VEAIKTLPEREKKVLILYYYEDL----TLKEIGKVLGVTESRISQLHTKAVLQLR 257
|
|
| PRK07408 |
PRK07408 |
RNA polymerase sigma factor SigF; Reviewed |
452-599 |
8.83e-21 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 180965 [Multi-domain] Cd Length: 256 Bit Score: 92.29 E-value: 8.83e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 452 EMVEANLRLVISIAKKYTNRGLQ-FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 530
Cdd:PRK07408 29 QLVELNLGLVRKEAHRWSNQCSEpYEDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRW 108
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 494975592 531 IETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVlKIA---KEPISLETPVGDEEDSH--LGDFIED 599
Cdd:PRK07408 109 QELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEI-KLAlqnRTPLSLDAPVNQDEDGStsLGDLLPD 181
|
|
| PRK07670 |
PRK07670 |
FliA/WhiG family RNA polymerase sigma factor; |
477-674 |
3.07e-20 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 181075 [Multi-domain] Cd Length: 251 Bit Score: 90.49 E-value: 3.07e-20
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 477 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITrsiaDQARTI-RIPVHMIETINKIVRTSRQMLHEIGREPTPE 555
Cdd:PRK07670 54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAII----DGLRKEdWLPRSMREKTKKVEAAIEKLEQRYMRNVTPK 129
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 556 ELAEKLAMPLEKVRKVLK--IAKEPISL-ETPVGDEEDSHLGDFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERV 632
Cdd:PRK07670 130 EVAAELGMTEEEVEATMNegFFANLLSIdEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQLV 209
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 494975592 633 LRMRFgigmNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKH 674
Cdd:PRK07670 210 ISLFY----KEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247
|
|
| Sigma70_r1_1 |
pfam03979 |
Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is ... |
29-86 |
2.93e-19 |
|
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: 82.24 E-value: 2.93e-19
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*...
gi 494975592 29 DAVKKMIKAAKKRGYVTMDELNAVLPSEEVTSEQIEDTMAMLSDMGINVIEDEDVEEA 86
Cdd:pfam03979 1 AQLKELIKKGKKKGYLTYDEINDALPDDILDSEQIEDIIEMLNDMGIDVVEEAPDADE 58
|
|
| PRK09210 |
PRK09210 |
RNA polymerase sigma factor RpoD; Validated |
28-162 |
4.01e-19 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236413 [Multi-domain] Cd Length: 367 Bit Score: 89.66 E-value: 4.01e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 28 DDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTSEQIEDTMAMLSDMGINVIEDEDVEEAGAATSSDDDDSSDDdngeggE 107
Cdd:PRK09210 12 EQVVKELIEKGKKRGTLTYDEIAEKLIPFELDSDQIDDLYERLEDAGISIVDEEGNPSSAQVVEEEEEEELDN------D 85
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*
gi 494975592 108 LAPSTGSALatakkkeptdrtDDPVRMYLREMGSVELLSREGEIAIAKRIEAGRE 162
Cdd:PRK09210 86 LSVPPGVKI------------NDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDE 128
|
|
| PRK05803 |
PRK05803 |
RNA polymerase sporulation sigma factor SigK; |
440-674 |
7.35e-19 |
|
RNA polymerase sporulation sigma factor SigK;
Pssm-ID: 180266 [Multi-domain] Cd Length: 233 Bit Score: 86.15 E-value: 7.35e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 440 QKGEREARiakKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAtwwirqaitrsiad 519
Cdd:PRK05803 44 KEGDEEAR---NILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYA-------------- 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 520 qARTIRipvhmietiNKIVrtsrqmlheigreptpeelaeklaMPLEKVRKVlkiaKEPISLETPVG-DEEDSH--LGDF 596
Cdd:PRK05803 107 -ARCIE---------NEIL------------------------MHLRNLKKT----KKEVSLQDPIGvDKEGNEisLIDI 148
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 494975592 597 IEDKNAllPIDAAIQANLR-ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKH 674
Cdd:PRK05803 149 LGSEED--DVIEQVELKMEvEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225
|
|
| fliA |
PRK06986 |
flagellar biosynthesis sigma factor; Validated |
443-673 |
5.50e-16 |
|
flagellar biosynthesis sigma factor; Validated
Pssm-ID: 235901 [Multi-domain] Cd Length: 236 Bit Score: 77.97 E-value: 5.50e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 443 EREARIAKKEMVEANLRLVISIAKKYTNR---GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI------ 513
Cdd:PRK06986 3 TAEGKMDQDELVEQYAPLVKRIALRLKARlpaSVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMldelrs 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 514 ----TRSIADQARTIRIPVhmietinkivrtsRQMLHEIGREPTPEELAEKLAMPLEKVRKVL------KIakepISLET 583
Cdd:PRK06986 83 ldwvPRSVRRNAREVAQAI-------------RQLEQELGREPTDTEVAEKLGLSLEEYREMLldtnisQL----FSIDE 145
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 584 PVGDEEDSHLGdfIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNtdhtLEEVGQQFSVTRERIRQ 663
Cdd:PRK06986 146 LRGEHGDSILV--TEDHQDEDPLQQLEDEELREALVEAIESLPEREQLVLSLYYQEELN----LKEIGAVLGVSESRVSQ 219
|
250
....*....|
gi 494975592 664 IEAKALRKLK 673
Cdd:PRK06986 220 IHSQAIKRLR 229
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
449-673 |
5.89e-16 |
|
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: 75.85 E-value: 5.89e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 449 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRrgYKFSTYATWWIRQAITRSIADQARtiripv 528
Cdd:TIGR02937 2 AFEELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE--GSFKAWLFRIARNLILDYLRRKRR------ 73
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 529 hmietinkIVRTSRQMLHEIGREPTPEELAEKlamplekvrkvlkiakepisletpvgdeedshlgdfIEDKNALLpida 608
Cdd:TIGR02937 74 --------LRRELDLLEELLDSDPSPEEELEQ------------------------------------EEEREALR---- 105
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 494975592 609 aiqanlretttRVLASLTPREERVLRMRFGIGMntdhTLEEVGQQFSVTRERIRQIEAKALRKLK 673
Cdd:TIGR02937 106 -----------EALEKLPEREREVLVLRYLEGL----SYKEIAEILGISVGTVKRRLKRARKKLR 155
|
|
| Sigma70_r4 |
pfam04545 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
621-674 |
7.96e-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: 7.96e-13
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 494975592 621 VLASLTPREERVLRMRFGigmnTDHTLEEVGQQFSVTRERIRQIEAKALRKLKH 674
Cdd:pfam04545 1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
|
|
| PRK08583 |
PRK08583 |
RNA polymerase sigma factor SigB; Validated |
449-673 |
1.59e-11 |
|
RNA polymerase sigma factor SigB; Validated
Pssm-ID: 236306 [Multi-domain] Cd Length: 257 Bit Score: 65.10 E-value: 1.59e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 449 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 528
Cdd:PRK08583 30 AQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPR 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 529 HMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAK--EPISLETPV-GDEEDSHLgdfiedknALLP 605
Cdd:PRK08583 110 RIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKsyQALSVDHSIeADSDGSTV--------TLLD 181
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 494975592 606 I-----DAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVG-QQFSVTRerirqIEAKALRKLK 673
Cdd:PRK08583 182 IvgqqeDGYELTEQRMILEKILPVLSDREKSIIQCTFIENLSQKETGERLGiSQMHVSR-----LQRQAIKKLR 250
|
|
| PRK05911 |
PRK05911 |
RNA polymerase sigma factor sigma-28; Reviewed |
453-673 |
5.31e-11 |
|
RNA polymerase sigma factor sigma-28; Reviewed
Pssm-ID: 235644 [Multi-domain] Cd Length: 257 Bit Score: 63.48 E-value: 5.31e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 453 MVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAItrsIADQARTIRIPVH 529
Cdd:PRK05911 28 LIEFYLPLVKNVAHRLISgmpSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI---IDDLRKQDWVPRS 104
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 530 MIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEP--ISL--ETPVGDEEDS--HLGDFIEDKNAL 603
Cdd:PRK05911 105 VHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPAliLSLneEFPCQSDDEAglALEERIADERAE 184
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 604 LPIDAAIQANLRETTTRVLASLTPREERVLRMRFgigmNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 673
Cdd:PRK05911 185 TGYDVVDKKEFSSILAEAILALEEKERKVMALYY----YEELVLKEIGKILGVSESRVSQIHSKALLKLR 250
|
|
| PRK05901 |
PRK05901 |
RNA polymerase sigma factor; Provisional |
2-160 |
6.48e-11 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 65.40 E-value: 6.48e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 2 ATKVKENEEAEVERDGTSDGPLLDLSDDAVKKMIKAAKKRGYVTMDELNAVLPSEEVTSEQIEDTMAMLSDMGINVIEDE 81
Cdd:PRK05901 91 PAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDE 170
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 494975592 82 DVEEAGAATSSDDDDSSDDDNGEGGELAPSTGSALATAkkkeptdrTDDPVRMYLREMGSVELLSREGEIAIAKRIEAG 160
Cdd:PRK05901 171 EKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAKLTA--------TADPVKAYLKQIGKVKLLNAEEEVELAKRIEAG 241
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
615-673 |
4.36e-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: 55.57 E-value: 4.36e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 494975592 615 RETTTRVLASLTPREERVLRMRFGIGMntdhTLEEVGQQFSVTRERIRQIEAKALRKLK 673
Cdd:cd06171 1 RERLEEALDKLPEREREVILLRFGEGL----SYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| Sigma70_r1_2 |
pfam00140 |
Sigma-70 factor, region 1.2; |
130-162 |
5.78e-10 |
|
Sigma-70 factor, region 1.2;
Pssm-ID: 425482 [Multi-domain] Cd Length: 34 Bit Score: 54.62 E-value: 5.78e-10
10 20 30
....*....|....*....|....*....|...
gi 494975592 130 DPVRMYLREMGSVELLSREGEIAIAKRIEAGRE 162
Cdd:pfam00140 1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAGDE 33
|
|
| PRK08301 |
PRK08301 |
RNA polymerase sporulation sigma factor SigE; |
449-505 |
3.82e-09 |
|
RNA polymerase sporulation sigma factor SigE;
Pssm-ID: 236228 [Multi-domain] Cd Length: 234 Bit Score: 57.56 E-value: 3.82e-09
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*..
gi 494975592 449 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 505
Cdd:PRK08301 53 VRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYA 109
|
|
| PRK08295 |
PRK08295 |
RNA polymerase sporulation sigma factor SigH; |
434-573 |
1.68e-05 |
|
RNA polymerase sporulation sigma factor SigH;
Pssm-ID: 181361 [Multi-domain] Cd Length: 208 Bit Score: 46.44 E-value: 1.68e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 434 RIVHMVQKGEREAriaKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI-RQA 512
Cdd:PRK08295 13 ELVELARSGDKEA---LEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCItRQI 89
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 494975592 513 ITrSIADQARTIRIPVHMIETINKIV---RTSRQMLHEI--GREPTPEEL---AEKLAMPLEKVRKVLK 573
Cdd:PRK08295 90 IT-AIKTANRQKHIPLNSYVSLDKPIydeESDRTLLDVIseAKVTDPEELiisKEELEDIEEKIEELLS 157
|
|
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
134-165 |
1.56e-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: 40.81 E-value: 1.56e-03
10 20 30
....*....|....*....|....*....|....*.
gi 494975592 134 MYLREMGSVELLSREGEIAIAKRIEAG----RETMI 165
Cdd:COG0568 1 AYLREIGRVPLLTAEEEVELARRIQAGdeeaKRKLV 36
|
|
| PRK12427 |
PRK12427 |
FliA/WhiG family RNA polymerase sigma factor; |
477-673 |
1.65e-03 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 183523 [Multi-domain] Cd Length: 231 Bit Score: 40.62 E-value: 1.65e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 477 DLIQEGNIGLMKAVDKFEYRRGyKFSTYATWWIRQAIT---RSIADQARTIRIPVHmietinKIVRTSRQMLHEIGREPT 553
Cdd:PRK12427 47 DMEQIALMGLLEALRRYGHPDE-QFAAYAVHRIRGAILdelRELDWRPRRLRQKTH------KTNDAIREIAKRLGHEPN 119
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 494975592 554 PEELAEKLAMPLEKVRKVLKI--AKEPISLETPVGDEEDshlGDFIEDKNalLPIDAAIQANLRETttrvLASLTPREER 631
Cdd:PRK12427 120 FEEISAELNLTAEEYQEYLLLenAGTLESLDELLALEAH---NDILQSRD--LEENIIIEDNLKQA----LSQLDEREQL 190
|
170 180 190 200
....*....|....*....|....*....|....*....|..
gi 494975592 632 VLRMRFGIGMNtdhtLEEVGQQFSVTRERIRQIEAKALRKLK 673
Cdd:PRK12427 191 ILHLYYQHEMS----LKEIALVLDLTEARICQLNKKIAQKIK 228
|
|
| PRK07405 |
PRK07405 |
RNA polymerase sigma factor SigD; Validated |
125-158 |
7.46e-03 |
|
RNA polymerase sigma factor SigD; Validated
Pssm-ID: 180963 [Multi-domain] Cd Length: 317 Bit Score: 38.97 E-value: 7.46e-03
10 20 30
....*....|....*....|....*....|....
gi 494975592 125 TDRTDDPVRMYLREMGSVELLSREGEIAIAKRIE 158
Cdd:PRK07405 3 AKTSTDLVRTYLREIGRVPLLTHEEEILYGKQVQ 36
|
|
| |
