|
Name |
Accession |
Description |
Interval |
E-value |
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
181-446 |
3.07e-159 |
|
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: 450.27 E-value: 3.07e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 181 MYLREIGQIPLLSHDEELEYAKRALEGDEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKG 260
Cdd:COG0568 1 AYLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 261 YKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDP 340
Cdd:COG0568 81 FRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 341 ISLETPVGSEEDSELGDFVEDNKMLNPYELTNRSLLREQLDGVLNSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTR 420
Cdd:COG0568 161 VSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSR 240
|
250 260
....*....|....*....|....*.
gi 492559350 421 ERIRQIEVKALRKLRHPSRRKKLEDF 446
Cdd:COG0568 241 ERVRQIEAKALRKLRHPLRSRKLRDY 266
|
|
| PRK09210 |
PRK09210 |
RNA polymerase sigma factor RpoD; Validated |
158-446 |
2.99e-155 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236413 [Multi-domain] Cd Length: 367 Bit Score: 444.04 E-value: 2.99e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 158 DDEYISDDLFTLSGdMKVDEPIKMYLREIGQIPLLSHDEELEYAKRALEGDEWASQQLIEANLRLVVSIAKKHTNRGLKL 237
Cdd:PRK09210 78 EEEELDNDLSVPPG-VKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLF 156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 238 LDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKEARIYLQETGKDATPE 317
Cdd:PRK09210 157 LDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPE 236
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 318 VLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEDNKMLNPYELTNRSLLREQLDGVLNSLSSREEKVLRY 397
Cdd:PRK09210 237 EIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRL 316
|
250 260 270 280
....*....|....*....|....*....|....*....|....*....
gi 492559350 398 RYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 446
Cdd:PRK09210 317 RFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDF 365
|
|
| RpoD_Cterm |
TIGR02393 |
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ... |
211-446 |
4.53e-155 |
|
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: 438.66 E-value: 4.53e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 211 ASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV 290
Cdd:TIGR02393 1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 291 HMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEDNKMLNPYEL 370
Cdd:TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492559350 371 TNRSLLREQLDGVLNSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 446
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDF 236
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
215-285 |
3.51e-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: 3.51e-23
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492559350 215 LIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRT 285
Cdd:pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
377-435 |
1.60e-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: 56.34 E-value: 1.60e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 492559350 377 REQLDGVLNSLSSREEKVLRYRYGLDdgspKTLEEVGKIFKVTRERIRQIEVKALRKLR 435
Cdd:cd06171 1 RERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| PRK05658 |
PRK05658 |
RNA polymerase sigma factor RpoD; Validated |
9-203 |
1.68e-06 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 235549 [Multi-domain] Cd Length: 619 Bit Score: 50.18 E-value: 1.68e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 9 KVLALVRKAMENKCITYEEINDGLKDDFP-VDKIEQLITGMMDQGIEIIRQADIDKNKkiakeiktkeakakktkestpk 87
Cdd:PRK05658 12 QLKKLIKRGKERGYLTYAELNDHLPEDIVdSEQIEDIIAMLNDMGIQVVEEAPDADDL---------------------- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 88 kaakkkekeeleeeNFDEDSFDDFKDEDIDlfekddflddddfddvldgklddfdDDFDHFNPDDLEDIGddeyISDDlf 167
Cdd:PRK05658 70 --------------LLAENEADAQTDEDAE-------------------------EEAAAALSSVESEIG----RTDD-- 104
|
170 180 190
....*....|....*....|....*....|....*.
gi 492559350 168 tlsgdmkvdePIKMYLREIGQIPLLSHDEELEYAKR 203
Cdd:PRK05658 105 ----------PVRMYLREMGTVELLTREGEIEIAKR 130
|
|
| Sigma70_r1_1 |
pfam03979 |
Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is ... |
8-71 |
2.23e-04 |
|
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: 39.48 E-value: 2.23e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492559350 8 EKVLALVRKAMENKCITYEEINDGLKDDFP-VDKIEQLITGMMDQGIEIIRQADIDKNKKIAKEI 71
Cdd:pfam03979 1 AQLKELIKKGKKKGYLTYDEINDALPDDILdSEQIEDIIEMLNDMGIDVVEEAPDADELLLSDEA 65
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| RpoD |
COG0568 |
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]; DNA-directed RNA ... |
181-446 |
3.07e-159 |
|
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: 450.27 E-value: 3.07e-159
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 181 MYLREIGQIPLLSHDEELEYAKRALEGDEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKG 260
Cdd:COG0568 1 AYLREIGRVPLLTAEEEVELARRIQAGDEEAKRKLVEANLRLVVSIAKKYQGRGLPLLDLIQEGNLGLMKAVEKFDPERG 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 261 YKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDP 340
Cdd:COG0568 81 FRFSTYATWWIRQAITRAIADQWRTIRLPVHMAETLNKLRRAKRQLLQELGREPTPEEIAEELGVPEEKVREMLRLAREP 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 341 ISLETPVGSEEDSELGDFVEDNKMLNPYELTNRSLLREQLDGVLNSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTR 420
Cdd:COG0568 161 VSLDAPVGDDEDSELGDLLEDEEAPSPEEALEEELLREELREALDTLTEREREILRLRFGLDDGEPHTLEEIGKEFGVSR 240
|
250 260
....*....|....*....|....*.
gi 492559350 421 ERIRQIEVKALRKLRHPSRRKKLEDF 446
Cdd:COG0568 241 ERVRQIEAKALRKLRHPLRSRKLRDY 266
|
|
| PRK09210 |
PRK09210 |
RNA polymerase sigma factor RpoD; Validated |
158-446 |
2.99e-155 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236413 [Multi-domain] Cd Length: 367 Bit Score: 444.04 E-value: 2.99e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 158 DDEYISDDLFTLSGdMKVDEPIKMYLREIGQIPLLSHDEELEYAKRALEGDEWASQQLIEANLRLVVSIAKKHTNRGLKL 237
Cdd:PRK09210 78 EEEELDNDLSVPPG-VKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLF 156
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 238 LDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKEARIYLQETGKDATPE 317
Cdd:PRK09210 157 LDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGREPTPE 236
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 318 VLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEDNKMLNPYELTNRSLLREQLDGVLNSLSSREEKVLRY 397
Cdd:PRK09210 237 EIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDATSPADHAAYELLKEQLEDVLDTLTDREENVLRL 316
|
250 260 270 280
....*....|....*....|....*....|....*....|....*....
gi 492559350 398 RYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 446
Cdd:PRK09210 317 RFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKQLKDF 365
|
|
| RpoD_Cterm |
TIGR02393 |
RNA polymerase sigma factor RpoD, C-terminal domain; This model represents the well-conserved ... |
211-446 |
4.53e-155 |
|
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: 438.66 E-value: 4.53e-155
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 211 ASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV 290
Cdd:TIGR02393 1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 291 HMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEDNKMLNPYEL 370
Cdd:TIGR02393 81 HMVETINKLIKAERQLTQELGREPTDEELAERMGMPAEKVREIKKIAQEPISLETPIGEEEDSFLGDFIEDESIESPDDA 160
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492559350 371 TNRSLLREQLDGVLNSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 446
Cdd:TIGR02393 161 AAKELLREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRKLRHPSRSKKLKDF 236
|
|
| PRK05901 |
PRK05901 |
RNA polymerase sigma factor; Provisional |
103-446 |
3.14e-147 |
|
RNA polymerase sigma factor; Provisional
Pssm-ID: 235640 [Multi-domain] Cd Length: 509 Bit Score: 429.03 E-value: 3.14e-147
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 103 FDEDSFDDFKDEDIDLFEKDDFLDDDDFDDVLDGKLDDFDDDFDHFNPDDLEDIGDDEYISDDLFTLSGDMK---VDEPI 179
Cdd:PRK05901 134 DDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQARKDAKltaTADPV 213
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 180 KMYLREIGQIPLLSHDEELEYAKR-------------------ALEGD-EW-------ASQQLIEANLRLVVSIAKKHTN 232
Cdd:PRK05901 214 KAYLKQIGKVKLLNAEEEVELAKRieaglyaeellaegekldpELRRDlQWigrdgkrAKNHLLEANLRLVVSLAKRYTN 293
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 233 RGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKEARIYLQETGK 312
Cdd:PRK05901 294 RGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGR 373
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 313 DATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEDNKMLNPYELTNRSLLREQLDGVLNSLSSREE 392
Cdd:PRK05901 374 EPTPEELAKEMGFTPEKVREIQKYNREPISLDKTIGKEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREA 453
|
330 340 350 360 370
....*....|....*....|....*....|....*....|....*....|....
gi 492559350 393 KVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 446
Cdd:PRK05901 454 GVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQVLRDF 507
|
|
| PRK05658 |
PRK05658 |
RNA polymerase sigma factor RpoD; Validated |
211-446 |
5.20e-142 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 235549 [Multi-domain] Cd Length: 619 Bit Score: 419.58 E-value: 5.20e-142
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 211 ASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV 290
Cdd:PRK05658 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 460
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 291 HMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEDNKMLNPYEL 370
Cdd:PRK05658 461 HMIETINKLNRISRQMLQEIGREPTPEELAERLGMPEDKVRKVLKIAKEPISLETPIGDDEDSHLGDFIEDKNAELPIDA 540
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492559350 371 TNRSLLREQLDGVLNSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 446
Cdd:PRK05658 541 AIQESLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSRKLRSF 616
|
|
| PRK07406 |
PRK07406 |
RNA polymerase sigma factor RpoD; Validated |
176-446 |
1.09e-119 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 236012 [Multi-domain] Cd Length: 373 Bit Score: 354.09 E-value: 1.09e-119
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 176 DEPIKMYLREIGQIPLLSHDEELEYAKR------------ALEGD--------EWASQ--------------------QL 215
Cdd:PRK07406 62 EDSIRVYLQEIGRIRLLRPDEEIELARKiadlleleelreQFESElgrepsdkEWAELvdmplpkfrrrlmlgrrakeKM 141
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 216 IEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIET 295
Cdd:PRK07406 142 VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYET 221
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 296 INKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEdNKMLNPYELTNRSL 375
Cdd:PRK07406 222 ISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIE-ADGETPEDDVAKNL 300
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492559350 376 LREQLDGVLNSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 446
Cdd:PRK07406 301 LREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVLKEY 371
|
|
| Sig70-cyanoRpoD |
TIGR02997 |
RNA polymerase sigma factor, cyanobacterial RpoD-like family; This family includes a number of ... |
178-435 |
1.53e-117 |
|
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: 345.77 E-value: 1.53e-117
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 178 PIKMYLREIGQIPLLSHDEELEYA----------------------------------------KRALEGDEWASQQLIE 217
Cdd:TIGR02997 2 LVRLYLQEIGRVPLLTPEEEIELArqvqqmmvleelreeleeqlgrepskeewaaaaglseaelRQRLRQGQRAKEKMIK 81
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 218 ANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETIN 297
Cdd:TIGR02997 82 ANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAYWWIRQGITRAIANQSRTIRLPIHITEKLN 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 298 KIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEDNKMLnPYELTNRSLLR 377
Cdd:TIGR02997 162 KIKKVQRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEEDTELGDLLEDDGES-PEEQVERESLR 240
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*...
gi 492559350 378 EQLDGVLNSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLR 435
Cdd:TIGR02997 241 QDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLNLSRERVRQIEAKALRKLR 298
|
|
| PRK07921 |
PRK07921 |
RNA polymerase sigma factor SigB; Reviewed |
179-446 |
4.58e-112 |
|
RNA polymerase sigma factor SigB; Reviewed
Pssm-ID: 181169 [Multi-domain] Cd Length: 324 Bit Score: 332.85 E-value: 4.58e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 179 IKMYLREIGQIPLLSHDEELEYAKR----------------------------ALEGDEwASQQLIEANLRLVVSIAKKH 230
Cdd:PRK07921 28 VRVYLNGIGKTALLTAADEVELAKRieaglyaehlletrkrlsearkrdlaavVRDGEA-ARRHLLEANLRLVVSLAKRY 106
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 231 TNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKEARIYLQET 310
Cdd:PRK07921 107 TGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQL 186
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 311 GKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEDNKMLNPYELTNRSLLREQLDGVLNSLSSR 390
Cdd:PRK07921 187 GREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSAENAVIAGLLHTDIRSVLATLDER 266
|
250 260 270 280 290
....*....|....*....|....*....|....*....|....*....|....*.
gi 492559350 391 EEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 446
Cdd:PRK07921 267 EQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRNGERADRLRSY 322
|
|
| rpoS_proteo |
TIGR02394 |
RNA polymerase sigma factor RpoS; A sigma factor is a DNA-binding protein protein that binds ... |
174-443 |
4.27e-95 |
|
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: 287.78 E-value: 4.27e-95
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 174 KVDEPIKMYLREIGQIPLLSHDEELEYAKRALEGDEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVE 253
Cdd:TIGR02394 10 RVADVTQLYLREIGFKPLLTAEEEIAYARRALAGDFEARKVMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLMHAVE 89
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 254 KFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAI 333
Cdd:TIGR02394 90 KFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVIKELNVYLRAARQLEKKLGREPSVEEIAELLDKPVEDVSRV 169
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 334 QEMNQDPISLETPVGSEEDSELGDFVEDNKMLNPYELTNRSLLREQLDGVLNSLSSREEKVLRYRYGLDDGSPKTLEEVG 413
Cdd:TIGR02394 170 LALNERITSLDAPLDDDSSKSLLDTIADEQSIDPESLVQNDDLKQLIEAWLAELNERQREVLARRFGLLGYEPATLEEVA 249
|
250 260 270
....*....|....*....|....*....|
gi 492559350 414 KIFKVTRERIRQIEVKALRKLRHPSRRKKL 443
Cdd:TIGR02394 250 AEVGLTRERVRQIQVEALKKLRRILERDGV 279
|
|
| PRK05657 |
PRK05657 |
RNA polymerase sigma factor RpoS; Validated |
154-435 |
4.66e-91 |
|
RNA polymerase sigma factor RpoS; Validated
Pssm-ID: 235548 [Multi-domain] Cd Length: 325 Bit Score: 279.15 E-value: 4.66e-91
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 154 EDIGDDEYISDDLFTLSGDMKVDEPIKMYLREIGQIPLLSHDEELEYAKRALEGDEWASQQLIEANLRLVVSIAKKHTNR 233
Cdd:PRK05657 30 EEPSDNDLAEEELLSQGATQRVLDATQLYLNEIGYSPLLTAEEEVYFARRALRGDFAARQRMIESNLRLVVKIAKRYLNR 109
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 234 GLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIKKEARIYLQETGKD 313
Cdd:PRK05657 110 GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVKELNVYLRAARELEHKLDHE 189
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 314 ATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEDNKMLNPYELTNRSLLREQLDGVLNSLSSREEK 393
Cdd:PRK05657 190 PSAEEIAELLDKPVDDVSRMLALNERITSLDTPLGGDPEKSLLDILADEQENGPEDTTQDDDMKQSIVKWLFELNDKQRE 269
|
250 260 270 280
....*....|....*....|....*....|....*....|..
gi 492559350 394 VLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLR 435
Cdd:PRK05657 270 VLARRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLR 311
|
|
| PRK07598 |
PRK07598 |
RNA polymerase sigma factor SigC; Validated |
211-446 |
1.89e-85 |
|
RNA polymerase sigma factor SigC; Validated
Pssm-ID: 236067 [Multi-domain] Cd Length: 415 Bit Score: 267.89 E-value: 1.89e-85
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 211 ASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV 290
Cdd:PRK07598 176 AKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPV 255
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 291 HMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEDNKmLNPYEL 370
Cdd:PRK07598 256 HITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQVREVLLRVPRSVSLETKVGKDKDTELGDLLETDD-ISPEEM 334
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 492559350 371 TNRSLLREQLDGVLNSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRKKLEDF 446
Cdd:PRK07598 335 LMRESLQRDLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQPKRRNRIRDY 410
|
|
| PRK07405 |
PRK07405 |
RNA polymerase sigma factor SigD; Validated |
176-435 |
4.13e-83 |
|
RNA polymerase sigma factor SigD; Validated
Pssm-ID: 180963 [Multi-domain] Cd Length: 317 Bit Score: 258.54 E-value: 4.13e-83
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 176 DEPIKMYLREIGQIPLLSHDEELEYAKR----------------------------------------ALEGDEWASQQL 215
Cdd:PRK07405 7 TDLVRTYLREIGRVPLLTHEEEILYGKQvqrlvalqeireelaeelgreptdaewakaaklseeelrsAIAEGEAAKRKM 86
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 216 IEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIET 295
Cdd:PRK07405 87 VEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK 166
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 296 INKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEDNKmLNPYELTNRSL 375
Cdd:PRK07405 167 LNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDNQDTELGELLEDTG-ASPEDFATQSS 245
|
250 260 270 280 290 300
....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 376 LREQLDGVLNSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLR 435
Cdd:PRK07405 246 LQLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLR 305
|
|
| PRK05949 |
PRK05949 |
RNA polymerase sigma factor; Validated |
168-441 |
3.70e-82 |
|
RNA polymerase sigma factor; Validated
Pssm-ID: 180321 [Multi-domain] Cd Length: 327 Bit Score: 256.31 E-value: 3.70e-82
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 168 TLSGDMkvdepIKMYLREIGQIPLLSHDEELEYAK----------------------------------------RALEG 207
Cdd:PRK05949 14 TFSADM-----VRTYLHEIGRVPLLTHEQEIVYGKqvqqmmslleakealakklgrepslpewaeavnlsetelkQTLKQ 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 208 DEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIR 287
Cdd:PRK05949 89 GKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIR 168
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 288 IPVHMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEDNKmLNP 367
Cdd:PRK05949 169 LPIHITEKLNKIKKTQRELSQKLGRSATPAEIAKELELEPSQIREYLSMARQPISLDVRVGDNQDTELSELLEDEG-PSP 247
|
250 260 270 280 290 300 310
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 492559350 368 YELTNRSLLREQLDGVLNSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRhpsRRK 441
Cdd:PRK05949 248 DQYITQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQALAHLR---RRR 318
|
|
| PRK06596 |
PRK06596 |
RNA polymerase factor sigma-32; Reviewed |
182-435 |
1.13e-47 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 235838 [Multi-domain] Cd Length: 284 Bit Score: 164.96 E-value: 1.13e-47
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 182 YLREIGQIPLLSHDEELEYAKRALE-GDEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKG 260
Cdd:PRK06596 19 YIQAVNKIPMLTAEEEYMLAKRLREhGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVG 98
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 261 YKFSTYATWWIRQAITRAIAdqgRTIRIpVHMIET---------INKIKKEARIYLQEtgkdatpEV--LAERLGMEVEK 329
Cdd:PRK06596 99 VRLVSFAVHWIKAEIHEYIL---RNWRI-VKVATTkaqrklffnLRKAKKRLGWLNPE-------EVemVAEELGVSEEE 167
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 330 VKaiqEMN-----QDpISLETPVGSEEDS--ELGDFVEDNKMLNPYELTNRSLL---REQLDGVLNSLSSREEKVLRYRY 399
Cdd:PRK06596 168 VR---EMEsrlsgQD-ASLDAPIDDDDEEsgAPQDYLEDKSSDPADVLEEDNWEdqrRALLADALEGLDERSRDIIEARW 243
|
250 260 270
....*....|....*....|....*....|....*.
gi 492559350 400 gLDDGsPKTLEEVGKIFKVTRERIRQIEVKALRKLR 435
Cdd:PRK06596 244 -LDDD-KSTLQELAAEYGVSAERVRQIEKNAMKKLK 277
|
|
| rpoH_proteo |
TIGR02392 |
alternative sigma factor RpoH; A sigma factor is a DNA-binding protein protein that binds to ... |
182-435 |
4.83e-46 |
|
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: 160.52 E-value: 4.83e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 182 YLREIGQIPLLSHDEELEYAKRALE-GDEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKG 260
Cdd:TIGR02392 6 YIRAVNRIPMLTPEEEYQLAKRLREhGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPERG 85
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 261 YKFSTYATWWIRQAITRAIAdqgRTIRIpVHMIET---------INKIKKeaRIYLQETGKDAtpEVLAERLGMEVEKVK 331
Cdd:TIGR02392 86 VRLVSFAVHWIKAEIHEYIL---RNWRL-VKVATTkaqrklffnLRKMKK--RLQGWLNPEEV--EAIAEELGVSEREVR 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 332 AI-QEMNQDPISLETPVGSEEDS--ELGDFVEDNKMLNPYELTNR---SLLREQLDGVLNSLSSREEKVLRYRYgLDDgS 405
Cdd:TIGR02392 158 EMeSRLSGQDMSLNASIDDDEDDggAPIAYLVDKRSDPEDTLEEEqweELQRQALANALGSLDARSRRIIEARW-LDD-D 235
|
250 260 270
....*....|....*....|....*....|
gi 492559350 406 PKTLEEVGKIFKVTRERIRQIEVKALRKLR 435
Cdd:TIGR02392 236 KLTLQELAAEYGVSAERIRQIEKNAMKKLK 265
|
|
| FliA |
COG1191 |
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA ... |
196-435 |
3.57e-41 |
|
DNA-directed RNA polymerase specialized sigma subunit [Transcription]; DNA-directed RNA polymerase specialized sigma subunit is part of the Pathway/BioSystem: RNA polymerase
Pssm-ID: 440804 [Multi-domain] Cd Length: 236 Bit Score: 146.51 E-value: 3.57e-41
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 196 EELEYAKRALEGDEWASQQLIEANLRLVVSIAKKHTNRGLKLL-DLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQA 274
Cdd:COG1191 1 DLEELLRRYQEGDEEAREELIEEYLPLVKKIASRLAGRLPAELdDLIQVGLIGLIEAIDRFDPSKGVSFETYAVPRIRGA 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 275 ITRAIADQGrtiRIPVHMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEM--NQDPISLETPVGSEED 352
Cdd:COG1191 81 ILDYLRDED---WVPRSVRELARKIEEAIEELEQELGREPTDEEIAEELGISLEEVQEALEAanAYQLLSLDEPLEDGDD 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 353 seLGDFVEDNkmlNPYELTNRSLLREQLDGVLNSLSSREEKVLRYRYGLDdgspKTLEEVGKIFKVTRERIRQIEVKALR 432
Cdd:COG1191 158 --LLDLLESG---DPEEELEHEELREALAEAIEQLPERERLVLSLYYFEE----LTLKEIAEVLGVSESRVSRLHKKALA 228
|
...
gi 492559350 433 KLR 435
Cdd:COG1191 229 RLR 231
|
|
| rpoH2 |
PRK07500 |
RNA polymerase factor sigma-32; Reviewed |
188-435 |
1.73e-37 |
|
RNA polymerase factor sigma-32; Reviewed
Pssm-ID: 236033 [Multi-domain] Cd Length: 289 Bit Score: 138.24 E-value: 1.73e-37
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 188 QIPLLSHDEELEYAKRALEG-DEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTY 266
Cdd:PRK07500 17 KAPYLEREEEHALAYRWKDHrDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAARFEPDREVRFSTY 96
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 267 ATWWIRQAITRAIADQGRTIR---------IPVHMIETINKIKKEARiylqETGKDATPEVLAERLGMEVEKVKAIQ-EM 336
Cdd:PRK07500 97 ATWWIRASIQDYILRNWSIVRggtssaqkaLFFNLRRLRARLAQADE----ELTKQEIHREIATALGVSLSDVEMMDaRL 172
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 337 NQDPISLETPVGSEED--SELGDFVEDNKMLnPYELTNRSL----LREQLDGVLNSLSSREEKVLRYRYGLDDgsPKTLE 410
Cdd:PRK07500 173 SGPDASLNAPQSEEDEgrSERMDFLVDDSPL-PDEQVESSIdgerRRRWLTQALQTLNERELRIIRERRLRED--GATLE 249
|
250 260
....*....|....*....|....*
gi 492559350 411 EVGKIFKVTRERIRQIEVKALRKLR 435
Cdd:PRK07500 250 ALGEELGISKERVRQIEARALEKLR 274
|
|
| PRK05803 |
PRK05803 |
RNA polymerase sporulation sigma factor SigK; |
192-436 |
1.13e-29 |
|
RNA polymerase sporulation sigma factor SigK;
Pssm-ID: 180266 [Multi-domain] Cd Length: 233 Bit Score: 115.43 E-value: 1.13e-29
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 192 LSHDEELEYAKRALEGDEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWI 271
Cdd:PRK05803 31 LSEEEERKYLELMKEGDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIESFDAGKGTKLATYAARCI 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 272 RQAItraiadqgrtiripVHMIETINKIKKEarIYLQE-TGKDatpevlaerlgmevekvkaiQEMNqdPISLETPVGSE 350
Cdd:PRK05803 111 ENEI--------------LMHLRNLKKTKKE--VSLQDpIGVD--------------------KEGN--EISLIDILGSE 152
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 351 EDSELgdfvednkmlnpyELTNRSLLREQLDGVLNSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKA 430
Cdd:PRK05803 153 EDDVI-------------EQVELKMEVEKLYKKIDILDEREKEVIEMRYGLGNGKEKTQREIAKALGISRSYVSRIEKRA 219
|
....*.
gi 492559350 431 LRKLRH 436
Cdd:PRK05803 220 LKKLFK 225
|
|
| spore_sigF |
TIGR02885 |
RNA polymerase sigma-F factor; Members of this protein family are the RNA polymerase sigma ... |
202-435 |
7.98e-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: 107.49 E-value: 7.98e-27
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 202 KRALEGDEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIAD 281
Cdd:TIGR02885 3 KLAQNGDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRFLRD 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 282 QGrTIRIPVHMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDS------EL 355
Cdd:TIGR02885 83 DG-IIKVSRSLKELARKIRYMKEELSKELGREPTINELAEALGVSPEEIVMALESARSPQSLYDTVHQDDGDpiylldQI 161
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 356 GD-FVEDNKMLnpyeltNRSLLREqldgVLNSLSSREEKVLRYRYGLDdgspKTLEEVGKIFKVTRERIRQIEVKALRKL 434
Cdd:TIGR02885 162 ADkGSEDSDWL------EKIALKE----AISKLDERERQIIMLRYFKD----KTQTEVANMLGISQVQVSRLEKKVLKKM 227
|
.
gi 492559350 435 R 435
Cdd:TIGR02885 228 K 228
|
|
| FliA_WhiG |
TIGR02479 |
RNA polymerase sigma factor, FliA/WhiG family; Most members of this family are the flagellar ... |
239-435 |
1.29e-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: 106.97 E-value: 1.29e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 239 DLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAI---TRAIADQGRTIRIPVHMIEtinkikKEARIYLQETGKDAT 315
Cdd:TIGR02479 28 DLIQAGMFGLLDAIERYDPSRGAKFETYAVQRIRGAMldeLRRLDWVPRSLRQKARKLE------RAIRELEARLGREPT 101
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 316 PEVLAERLGMEVEKV-KAIQEMNQDPI-SLETPVGSEEDSE-LGDFVEDNKMLNPYELTNRSLLREQLDGVLNSLSSREE 392
Cdd:TIGR02479 102 EEEIAEELGMDLKEYrQALNEINALSLvSLDELLESGDDGGsLIDRIEDDKSEDPEEELEREELREALAEAIESLSEREQ 181
|
170 180 190 200
....*....|....*....|....*....|....*....|....*
gi 492559350 393 KV--LRYRYGLddgspkTLEEVGKIFKVTRERIRQIEVKALRKLR 435
Cdd:TIGR02479 182 LVlsLYYYEEL------NLKEIGEVLGLTESRVSQIHSQALKKLR 220
|
|
| PRK05572 |
PRK05572 |
RNA polymerase sporulation sigma factor, SigF/SigG family; |
192-435 |
8.72e-26 |
|
RNA polymerase sporulation sigma factor, SigF/SigG family;
Pssm-ID: 180137 [Multi-domain] Cd Length: 252 Bit Score: 105.44 E-value: 8.72e-26
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 192 LSHDEELEYAKRALEGDEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWI 271
Cdd:PRK05572 14 LKDEENKELIKKSQDGDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKFSTYAVPMI 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 272 RQAITRAIADQGrTIRIPVHMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVgSEE 351
Cdd:PRK05572 94 IGEIQRFLRDDG-TVKVSRSLKETANKIRKDKDELSKELGREPTIEELAEYLGVTPEEVVLAQEASRSPQSIHETV-HEN 171
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 352 DSE---LGDFVEDN---KMLnpyeltNRSLLREqldgVLNSLSSREEKVLRYRYGLDdgspKTLEEVGKIFKVTRERIRQ 425
Cdd:PRK05572 172 DGDpitLLDQIADQseeDWF------DKIALKE----AIRELDERERLIVYLRYFKD----KTQSEVAKRLGISQVQVSR 237
|
250
....*....|
gi 492559350 426 IEVKALRKLR 435
Cdd:PRK05572 238 LEKKILKQMK 247
|
|
| PRK08215 |
PRK08215 |
RNA polymerase sporulation sigma factor SigG; |
189-435 |
1.87e-24 |
|
RNA polymerase sporulation sigma factor SigG;
Pssm-ID: 181296 [Multi-domain] Cd Length: 258 Bit Score: 101.56 E-value: 1.87e-24
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 189 IPLLSHDEELEYAKRALEGDEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYAT 268
Cdd:PRK08215 16 LPVLKNEEMRELFERMQNGDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKAIDNFDLSQNVKFSTYAV 95
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 269 WWIRQAITRAIADQgRTIRIPVHMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVG 348
Cdd:PRK08215 96 PMIIGEIRRYLRDN-NPIRVSRSLRDIAYKALQVREKLINENSKEPTVEEIAKELEVPREEVVFALDAIQDPVSLFEPIY 174
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 349 SEEDSEL--GDFVEDNKMLNPYELTNRSlLREqldgVLNSLSSREEKVLRYRYGldDGspKTLEEVGKIFKVTRERIRQI 426
Cdd:PRK08215 175 HDGGDPIyvMDQISDEKNKDENWLEEIA-LKE----AMKKLNDREKLILNLRFF--QG--KTQMEVAEEIGISQAQVSRL 245
|
....*....
gi 492559350 427 EVKALRKLR 435
Cdd:PRK08215 246 EKAALKHMR 254
|
|
| Sigma70_r2 |
pfam04542 |
Sigma-70 region 2; Region 2 of sigma-70 is the most conserved region of the entire protein. ... |
215-285 |
3.51e-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: 3.51e-23
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492559350 215 LIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRT 285
Cdd:pfam04542 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLWRAIERFDPERGVSFSTWLYTIIRNAIIDYLRKQRRT 71
|
|
| Sigma70_r3 |
pfam04539 |
Sigma-70 region 3; Region 3 forms a discrete compact three helical domain within the ... |
294-367 |
2.37e-22 |
|
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: 90.36 E-value: 2.37e-22
10 20 30 40 50 60 70
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 492559350 294 ETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSELGDFVEDNKMLNP 367
Cdd:pfam04539 1 ELLNKIKRAQRELEQELGREPTPEEIAEELGLSPEKVREVLEAAREPVSLDTPVGEEEDGELGDLLEDDDIESP 74
|
|
| PRK06288 |
PRK06288 |
RNA polymerase sigma factor WhiG; Reviewed |
239-447 |
1.10e-21 |
|
RNA polymerase sigma factor WhiG; Reviewed
Pssm-ID: 235770 [Multi-domain] Cd Length: 268 Bit Score: 93.98 E-value: 1.10e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 239 DLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAI---TRAIADQGRTIRIPVHMIETINKIkKEARIylqetGKDAT 315
Cdd:PRK06288 63 DLVSYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIfdeLRSIDWIPRSVRQKARQIERAIAM-LEARL-----GRTPS 136
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 316 PEVLAERLGMEVEKVKAI--QEMNQDPISLETPVGSEEDSE---LGDFVEDNKMLNPYELTNRSLLREQLDGVLNSLSSR 390
Cdd:PRK06288 137 DEEIADELGISLEEYNSLlsKLSGTSVVSLNDLWFGGDEGDevsLMDTLESPAALNPDEIAEREEIKRVIVEAIKTLPER 216
|
170 180 190 200 210
....*....|....*....|....*....|....*....|....*....|....*....
gi 492559350 391 EEKV--LRYRYGLddgspkTLEEVGKIFKVTRERIRQIEVKALRKLRHpsrrkKLEDFK 447
Cdd:PRK06288 217 EKKVliLYYYEDL------TLKEIGKVLGVTESRISQLHTKAVLQLRA-----KLAEIK 264
|
|
| PRK07670 |
PRK07670 |
FliA/WhiG family RNA polymerase sigma factor; |
239-436 |
3.55e-19 |
|
FliA/WhiG family RNA polymerase sigma factor;
Pssm-ID: 181075 [Multi-domain] Cd Length: 251 Bit Score: 86.64 E-value: 3.55e-19
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 239 DLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITraiaDQGRTI-RIPVHMIETINKIKKEARIYLQETGKDATPE 317
Cdd:PRK07670 54 DLKSLGMLGLYDALEKFDPSRDLKFDTYASFRIRGAII----DGLRKEdWLPRSMREKTKKVEAAIEKLEQRYMRNVTPK 129
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 318 VLAERLGMEVEKVKAIqeMNQ----DPISL-ETPVGSEEDSELGDFVEDNKMLNPYELTNRSLLREQLDGVLNSLSSREE 392
Cdd:PRK07670 130 EVAAELGMTEEEVEAT--MNEgffaNLLSIdEKTHDQDDGENVSVTIRDDKTPTPEEKLLKEELIEELAEKIKQLSEKEQ 207
|
170 180 190 200
....*....|....*....|....*....|....*....|....*.
gi 492559350 393 KV--LRYRYGLddgspkTLEEVGKIFKVTRERIRQIEVKALRKLRH 436
Cdd:PRK07670 208 LVisLFYKEEL------TLTEIGQVLNLSTSRISQIHSKALFKLKK 247
|
|
| PRK07408 |
PRK07408 |
RNA polymerase sigma factor SigF; Reviewed |
214-361 |
2.21e-18 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 180965 [Multi-domain] Cd Length: 256 Bit Score: 84.20 E-value: 2.21e-18
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 214 QLIEANLRLVVSIAKKHTNRGLKLL-DLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHM 292
Cdd:PRK07408 29 QLVELNLGLVRKEAHRWSNQCSEPYeDLVQVGSLGLIRAIERFDPSKGHAFSSFAIPYIRGEIQHYLRDKSPTVRIPRRW 108
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 492559350 293 IETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQ--EMNQDPISLETPVGSEEDSE--LGDFVED 361
Cdd:PRK07408 109 QELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKlaLQNRTPLSLDAPVNQDEDGStsLGDLLPD 181
|
|
| PRK08583 |
PRK08583 |
RNA polymerase sigma factor SigB; Validated |
207-435 |
5.42e-16 |
|
RNA polymerase sigma factor SigB; Validated
Pssm-ID: 236306 [Multi-domain] Cd Length: 257 Bit Score: 77.43 E-value: 5.42e-16
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 207 GDEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTI 286
Cdd:PRK08583 26 QDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSV 105
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 287 RIPVHMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGSEEDSE-----LGDFV-- 359
Cdd:PRK08583 106 HVPRRIKELGPKIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEAMEMGKSYQALSVDHSIEADSDgstvtLLDIVgq 185
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 492559350 360 -EDNkmlnpYELTNRSLLreqLDGVLNSLSSREEKVLRYRYgLDDGSPKtleEVGKIFKVTRERIRQIEVKALRKLR 435
Cdd:PRK08583 186 qEDG-----YELTEQRMI---LEKILPVLSDREKSIIQCTF-IENLSQK---ETGERLGISQMHVSRLQRQAIKKLR 250
|
|
| fliA |
PRK06986 |
flagellar biosynthesis sigma factor; Validated |
211-435 |
1.28e-15 |
|
flagellar biosynthesis sigma factor; Validated
Pssm-ID: 235901 [Multi-domain] Cd Length: 236 Bit Score: 76.04 E-value: 1.28e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 211 ASQQLIEANLRLVVSIA---KKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQG---R 284
Cdd:PRK06986 9 DQDELVEQYAPLVKRIAlrlKARLPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAGQRIRGAMLDELRSLDwvpR 88
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 285 TIRIPVHMIEtinkikKEARIYLQETGKDATPEVLAERLGMEVEKvkaIQEMNQDP-----ISLETPVGSEEDSELGDfv 359
Cdd:PRK06986 89 SVRRNAREVA------QAIRQLEQELGREPTDTEVAEKLGLSLEE---YREMLLDTnisqlFSIDELRGEHGDSILVT-- 157
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 492559350 360 EDNKMLNPYELTNRSLLREQLDGVLNSLSSREEKVLR--YRYGLDdgspktLEEVGKIFKVTRERIRQIEVKALRKLR 435
Cdd:PRK06986 158 EDHQDEDPLQQLEDEELREALVEAIESLPEREQLVLSlyYQEELN------LKEIGAVLGVSESRVSQIHSQAIKRLR 229
|
|
| PRK08301 |
PRK08301 |
RNA polymerase sporulation sigma factor SigE; |
190-435 |
4.25e-15 |
|
RNA polymerase sporulation sigma factor SigE;
Pssm-ID: 236228 [Multi-domain] Cd Length: 234 Bit Score: 74.51 E-value: 4.25e-15
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 190 PLLSHDEELEYAKRALEGDEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATw 269
Cdd:PRK08301 32 PPLSKEEEEYLLNKLPKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEKKIKLATYAS- 110
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 270 wirqaitraiadqgRTIRIPVHM-IETINKIKKEARIYlqetgkdatpevlaerlgmevekvkaiQEMNQD----PISLE 344
Cdd:PRK08301 111 --------------RCIENEILMyLRRNNKVKAEVSFD---------------------------EPLNIDwdgnELLLS 149
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 345 TPVGSEEDsELGDFVEDNkmlnpyelTNRSLLREQLDgvlnSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIR 424
Cdd:PRK08301 150 DVLGTDND-IIYKDIEDE--------VDRKLLKKALK----KLSDREKQIMELRFGLNGGEEKTQKEVADMLGISQSYIS 216
|
250
....*....|.
gi 492559350 425 QIEVKALRKLR 435
Cdd:PRK08301 217 RLEKRIIKRLK 227
|
|
| PRK07122 |
PRK07122 |
RNA polymerase sigma factor SigF; Reviewed |
213-435 |
5.84e-14 |
|
RNA polymerase sigma factor SigF; Reviewed
Pssm-ID: 168831 [Multi-domain] Cd Length: 264 Bit Score: 71.73 E-value: 5.84e-14
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 213 QQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHM 292
Cdd:PRK07122 43 DRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRL 122
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 293 IETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKA--IQEMNQDPISLETPVGSEEDSE------LGDfvEDNKM 364
Cdd:PRK07122 123 KELHLRLGRATAELSQRLGRAPTASELAAELGMDREEVVEglVAGSAYNTLSIDSGGGSGDDDAraiadtLGD--VDAGL 200
|
170 180 190 200 210 220 230
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 492559350 365 LNpyeLTNRSLLREqldgVLNSLSSREEKVLRYRYGLDDGSPKTLEEVGkifkVTRERIRQIEVKALRKLR 435
Cdd:PRK07122 201 DQ---IENREALRP----LLAALPERERTVLVLRFFESMTQTQIAERVG----ISQMHVSRLLAKTLARLR 260
|
|
| sigma70-ECF |
TIGR02937 |
RNA polymerase sigma factor, sigma-70 family; This model encompasses all varieties of the ... |
213-435 |
1.43e-13 |
|
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: 68.14 E-value: 1.43e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 213 QQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKgyKFSTYATWWIRQAITRAIADQgRTIRIPVHM 292
Cdd:TIGR02937 4 EELYERYLPLVYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEG--SFKAWLFRIARNLILDYLRRK-RRLRRELDL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 293 IEtinkikkeariylqetgkdatpevlaerlgmevekvkaiqemnQDPISLETPVGSEEDSElgdfvednkmlnpyeltn 372
Cdd:TIGR02937 81 LE-------------------------------------------ELLDSDPSPEEELEQEE------------------ 99
|
170 180 190 200 210 220
....*....|....*....|....*....|....*....|....*....|....*....|...
gi 492559350 373 rslLREQLDGVLNSLSSREEKVLRYRYGLDdgspKTLEEVGKIFKVTRERIRQIEVKALRKLR 435
Cdd:TIGR02937 100 ---EREALREALEKLPEREREVLVLRYLEG----LSYKEIAEILGISVGTVKRRLKRARKKLR 155
|
|
| PRK05911 |
PRK05911 |
RNA polymerase sigma factor sigma-28; Reviewed |
210-435 |
4.27e-13 |
|
RNA polymerase sigma factor sigma-28; Reviewed
Pssm-ID: 235644 [Multi-domain] Cd Length: 257 Bit Score: 68.88 E-value: 4.27e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 210 WASQQ------LIEANLRLVVSIAKKHTN---RGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAItraIA 280
Cdd:PRK05911 17 WSTQEieyrdvLIEFYLPLVKNVAHRLISgmpSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFLIKAAI---ID 93
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 281 DQGRTIRIPVHMIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKA--IQEMNQDPISLETPVGSEEDSELGDF 358
Cdd:PRK05911 94 DLRKQDWVPRSVHQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGwfSSARPALILSLNEEFPCQSDDEAGLA 173
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 359 VE----DNKMLNPYELTNRSLLREQLDGVLNSLSSREEKVLRYRYGLDdgspKTLEEVGKIFKVTRERIRQIEVKALRKL 434
Cdd:PRK05911 174 LEeriaDERAETGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEE----LVLKEIGKILGVSESRVSQIHSKALLKL 249
|
.
gi 492559350 435 R 435
Cdd:PRK05911 250 R 250
|
|
| Sigma70_r4 |
pfam04545 |
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ... |
383-436 |
2.85e-12 |
|
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: 60.90 E-value: 2.85e-12
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....
gi 492559350 383 VLNSLSSREEKVLRYRYGlddgSPKTLEEVGKIFKVTRERIRQIEVKALRKLRH 436
Cdd:pfam04545 1 ALASLPPRERQVLVLRYG----EGLTLEEIGERLGISRERVRQIEKRALRKLRK 50
|
|
| Sigma70_r4 |
cd06171 |
Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in ... |
377-435 |
1.60e-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: 56.34 E-value: 1.60e-10
10 20 30 40 50
....*....|....*....|....*....|....*....|....*....|....*....
gi 492559350 377 REQLDGVLNSLSSREEKVLRYRYGLDdgspKTLEEVGKIFKVTRERIRQIEVKALRKLR 435
Cdd:cd06171 1 RERLEEALDKLPEREREVILLRFGEG----LSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
|
| Sigma70_r1_2 |
pfam00140 |
Sigma-70 factor, region 1.2; |
177-210 |
1.81e-10 |
|
Sigma-70 factor, region 1.2;
Pssm-ID: 425482 [Multi-domain] Cd Length: 34 Bit Score: 55.40 E-value: 1.81e-10
10 20 30
....*....|....*....|....*....|....
gi 492559350 177 EPIKMYLREIGQIPLLSHDEELEYAKRALEGDEW 210
Cdd:pfam00140 1 DSVRLYLKEIGRIPLLTAEEEVELAKRIEAGDEA 34
|
|
| PRK08295 |
PRK08295 |
RNA polymerase sporulation sigma factor SigH; |
195-397 |
1.59e-06 |
|
RNA polymerase sporulation sigma factor SigH;
Pssm-ID: 181361 [Multi-domain] Cd Length: 208 Bit Score: 48.75 E-value: 1.59e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 195 DEEL-EYAKralEGDEWASQQLIEANLRLVVSIAKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWI-R 272
Cdd:PRK08295 11 DEELvELAR---SGDKEALEYLIEKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYDKDKLSSFKSFAELCItR 87
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 273 QAITrAIADQGRTIRIPVHmietinkikkeariylqetgkdatpevlaerlgmevekvkaiqemnqDPISLETPVGSEE- 351
Cdd:PRK08295 88 QIIT-AIKTANRQKHIPLN-----------------------------------------------SYVSLDKPIYDEEs 119
|
170 180 190 200
....*....|....*....|....*....|....*....|....*..
gi 492559350 352 DSELGDFVEDNKMLNPYELT-NRSLLREQLDGVLNSLSSREEKVLRY 397
Cdd:PRK08295 120 DRTLLDVISEAKVTDPEELIiSKEELEDIEEKIEELLSELEKEVLEL 166
|
|
| PRK05658 |
PRK05658 |
RNA polymerase sigma factor RpoD; Validated |
9-203 |
1.68e-06 |
|
RNA polymerase sigma factor RpoD; Validated
Pssm-ID: 235549 [Multi-domain] Cd Length: 619 Bit Score: 50.18 E-value: 1.68e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 9 KVLALVRKAMENKCITYEEINDGLKDDFP-VDKIEQLITGMMDQGIEIIRQADIDKNKkiakeiktkeakakktkestpk 87
Cdd:PRK05658 12 QLKKLIKRGKERGYLTYAELNDHLPEDIVdSEQIEDIIAMLNDMGIQVVEEAPDADDL---------------------- 69
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 492559350 88 kaakkkekeeleeeNFDEDSFDDFKDEDIDlfekddflddddfddvldgklddfdDDFDHFNPDDLEDIGddeyISDDlf 167
Cdd:PRK05658 70 --------------LLAENEADAQTDEDAE-------------------------EEAAAALSSVESEIG----RTDD-- 104
|
170 180 190
....*....|....*....|....*....|....*.
gi 492559350 168 tlsgdmkvdePIKMYLREIGQIPLLSHDEELEYAKR 203
Cdd:PRK05658 105 ----------PVRMYLREMGTVELLTREGEIEIAKR 130
|
|
| Sigma70_r1_1 |
pfam03979 |
Sigma-70 factor, region 1.1; Region 1.1 modulates DNA binding by region 2 and 4 when sigma is ... |
8-71 |
2.23e-04 |
|
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: 39.48 E-value: 2.23e-04
10 20 30 40 50 60
....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 492559350 8 EKVLALVRKAMENKCITYEEINDGLKDDFP-VDKIEQLITGMMDQGIEIIRQADIDKNKKIAKEI 71
Cdd:pfam03979 1 AQLKELIKKGKKKGYLTYDEINDALPDDILdSEQIEDIIEMLNDMGIDVVEEAPDADELLLSDEA 65
|
|
| |
