254780611
RNA polymerase factor sigma-32
| GeneID in NCBI database: | 8209610 | Locus tag: | CLIBASIA_02490 |
| Protein GI in NCBI database: | 254780611 | Protein Accession: | YP_003065024.1 |
| Gene range: | -(664409, 665317) | Protein Length: | 302aa |
| Gene description: | RNA polymerase factor sigma-32 | ||
| COG prediction: | [K] DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) | ||
| KEGG prediction: | rpoH; RNA polymerase factor sigma-32; K03089 RNA polymerase sigma-32 factor | ||
| SEED prediction: | RNA polymerase sigma factor RpoH | ||
| Pathway involved in KEGG: | RNA polymerase [PATH:las03020] | ||
| Subsystem involved in SEED: | Transcription initiation, bacterial sigma factors;
Heat shock dnaK gene cluster extended | ||
| sequence | sequence profile | ||
Prediction of Local Sequence Properties
| Source | Summary | Result |
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Close Homologs Detected by BLAST or PSI-BLAST
Homolog within the Genome Detected by BLAST
Original result of BLAST against C. L. asiaticus genome
| Identity | Alignment graph | Length | Definition | E-value | |
| Target | 302 | RNA polymerase factor sigma-32 [Candidatus Liberibacter | |||
| 254780289 | 682 | RNA polymerase sigma factor RpoD [Candidatus Liber | 5e-23 |
| >gi|254780289|ref|YP_003064702.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter asiaticus str. psy62] Length = 682 | Back alignment |
|---|
Score = 99.8 bits (247), Expect = 5e-23, Method: Compositional matrix adjust.
Identities = 85/289 (29%), Positives = 138/289 (47%), Gaps = 49/289 (16%)
Query: 7 SIIVNGEIGLSRYIHEIRKIPMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
SI V I +S + H + M+ K E E +AK+ +V ++LRLV+ +A
Sbjct: 415 SISVETGISISEFRH---IVSMVRKGECEASIAKK-----------EMVEANLRLVISVA 460
Query: 66 MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
Y GL +++ EGNIGLM+A +KFD G++ +TY+MWW+K A+ I ++
Sbjct: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520
Query: 126 IGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVIS 175
I K ++ RR+ ++ PE++ + K L +++ E IS
Sbjct: 521 IPVHMRDKIHKVVRTARRMSNKIK----REPTPEEIAKKLAMPVEGVRKVLKITK-EPIS 575
Query: 176 MNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
+ + GDE + L + DKN+ D + + N R TR ++
Sbjct: 576 LETPI-GDEDTSHLGDFIEDKNAVSPLDSAI---------------QANLRETTTRVLAS 619
Query: 235 LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
L PRE R+ R TLE + +F V+RER+RQIEA+A +K++
Sbjct: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668
|
Close Homologs Detected BLAST or PSI-BLAST in the First 2 Iterations
Original result of PSI-BLAST first 2 iterations
| Identity | Alignment graph | Length | Definition | Round | E-value |
| Target | 302 | RNA polymerase factor sigma-32 [Candidatus Liberibacter | |||
| 315121811 | 300 | RNA polymerase factor sigma-32 [Candidatus Liberibacter | 1 | 1e-145 | |
| 190893168 | 302 | RNA polymerase sigma factor protein (sigma-70) [Rhizobi | 1 | 1e-124 | |
| 327190963 | 332 | RNA polymerase sigma factor protein (sigma-70) [Rhizobi | 1 | 1e-124 | |
| 222086841 | 302 | alternative sigma factor RpoH [Agrobacterium radiobacte | 1 | 1e-124 | |
| 74099847 | 302 | RpoH [Rhizobium leguminosarum] Length = 302 | 1 | 1e-124 | |
| 15889716 | 300 | RNA polymerase factor sigma-32 [Agrobacterium tumefacie | 1 | 1e-123 | |
| 325293796 | 300 | RNA polymerase sigma-32 factor [Agrobacterium sp. H13-3 | 1 | 1e-123 | |
| 86358940 | 302 | RNA polymerase factor sigma-32 [Rhizobium etli CFN 42] | 1 | 1e-123 | |
| 116253507 | 302 | RNA polymerase factor sigma-32 [Rhizobium leguminosarum | 1 | 1e-123 | |
| 209550663 | 302 | RNA polymerase factor sigma-32 [Rhizobium leguminosarum | 1 | 1e-123 |
| >gi|315121811|ref|YP_004062300.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter solanacearum CLso-ZC1] Length = 300 | Back alignment and organism information |
|---|
Score = 519 bits (1337), Expect = e-145, Method: Compositional matrix adjust.
Identities = 247/289 (85%), Positives = 269/289 (93%)
Query: 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
M+R+NMSI+++GEIGL RYIHEI+KIPMLEKQEEY+LAKRY EH DL+A H+LVTSHLRL
Sbjct: 1 MSRRNMSIMIDGEIGLRRYIHEIKKIPMLEKQEEYMLAKRYHEHHDLNAVHKLVTSHLRL 60
Query: 61 VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
VVKIAMGYRGYGLPISEV+SEGNIGLMQAVKKFDPERGFRLATY +WWIKAA+QEYILRS
Sbjct: 61 VVKIAMGYRGYGLPISEVISEGNIGLMQAVKKFDPERGFRLATYGIWWIKAAIQEYILRS 120
Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
WSLVKIGTTANQKRLFFNLRRLKG LQA+ D NLKPEQVV IA KLNVSE+EVISMNCRL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRRLKGRLQAVNDTNLKPEQVVEIATKLNVSEAEVISMNCRL 180
Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
+GDESLN L+NSSDK+SSQWQD LVY+HD QEQ LI+KEERKNRRNMLTRSMS LNPRER
Sbjct: 181 SGDESLNVLMNSSDKDSSQWQDLLVYNHDSQEQTLIDKEERKNRRNMLTRSMSTLNPRER 240
Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
RIFEARRL ENP TLENLSSEF VSRER+RQIEARAF+KVQ S+QKQ E
Sbjct: 241 RIFEARRLNENPSTLENLSSEFAVSRERIRQIEARAFEKVQASVQKQTE 289
|
Species: Candidatus Liberibacter solanacearum Genus: Candidatus Liberibacter Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|190893168|ref|YP_001979710.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT 652] Length = 302 | Back alignment and organism information |
|---|
Score = 449 bits (1156), Expect = e-124, Method: Compositional matrix adjust.
Identities = 213/288 (73%), Positives = 247/288 (85%)
Query: 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
M R + I GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD AAH+LVTSHLRL
Sbjct: 1 MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60
Query: 61 VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61 VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120
Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V IA KLNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180
Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
+GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E + RR ML+++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELETRRRMLSKAMSVLNERER 240
Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
RIFEARRL E PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+
Sbjct: 241 RIFEARRLAEEPVTLEDLSAEFDISRERVRQIEVRAFEKVQDAVRKEA 288
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Species: Rhizobium etli Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|327190963|gb|EGE58017.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CNPAF512] Length = 332 | Back alignment and organism information |
|---|
Score = 449 bits (1155), Expect = e-124, Method: Compositional matrix adjust.
Identities = 213/288 (73%), Positives = 247/288 (85%)
Query: 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
M R + I GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD AAH+LVTSHLRL
Sbjct: 31 MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 90
Query: 61 VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 91 VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 150
Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V IA KLNVSE EVISMN RL
Sbjct: 151 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 210
Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
+GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E + RR ML+++MSVLN RER
Sbjct: 211 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELETRRRMLSKAMSVLNERER 270
Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
RIFEARRL E PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+
Sbjct: 271 RIFEARRLAEEPVTLEDLSAEFDISRERVRQIEVRAFEKVQDAVRKEA 318
|
Species: Rhizobium etli Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|222086841|ref|YP_002545375.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84] Length = 302 | Back alignment and organism information |
|---|
Score = 448 bits (1153), Expect = e-124, Method: Compositional matrix adjust.
Identities = 216/288 (75%), Positives = 242/288 (84%)
Query: 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
M R + I GE GL+RY+ EIRK PMLE QEEY+LAKRY EH D AAHRLVTSHLRL
Sbjct: 1 MARNTLPSIAAGEAGLNRYLDEIRKFPMLEPQEEYMLAKRYAEHADREAAHRLVTSHLRL 60
Query: 61 VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61 VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120
Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
WSLVK+GTTANQKRLFFNLRRLKG +QAI + +LKPE V IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDEGDLKPEHVSEIATKLKVSEEEVISMNRRL 180
Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
+GD SLNA I +S+ S QWQDWLV DH+ QE VLIE++E RR ML R+MSVLN RER
Sbjct: 181 SGDASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELDTRRRMLARAMSVLNDRER 240
Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
RIFEARRL E+PVTLE+LSSEF++SRERVRQIE RAF+KVQE++QK
Sbjct: 241 RIFEARRLSEDPVTLEDLSSEFDISRERVRQIEVRAFEKVQEAVQKDA 288
|
Species: Agrobacterium tumefaciens Genus: Agrobacterium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|74099847|gb|AAZ99132.1| RpoH [Rhizobium leguminosarum] Length = 302 | Back alignment and organism information |
|---|
Score = 447 bits (1150), Expect = e-124, Method: Compositional matrix adjust.
Identities = 212/288 (73%), Positives = 245/288 (85%)
Query: 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
M R + I GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD AAH+LVTSHLRL
Sbjct: 1 MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60
Query: 61 VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFD ERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61 VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRS 120
Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V IA KLNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180
Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
+GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERER 240
Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+
Sbjct: 241 RIFEARRLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEA 288
|
Species: Rhizobium leguminosarum Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|15889716|ref|NP_355397.1| RNA polymerase factor sigma-32 [Agrobacterium tumefaciens str. C58] Length = 300 | Back alignment and organism information |
|---|
Score = 446 bits (1147), Expect = e-123, Method: Compositional matrix adjust.
Identities = 214/288 (74%), Positives = 242/288 (84%)
Query: 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
M R ++ I GE GL+RY+ EIRK PMLE QEEY+L KRY EHGD AAH+LVTSHLRL
Sbjct: 1 MARNSLPTITAGEAGLNRYLDEIRKFPMLEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRL 60
Query: 61 VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61 VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120
Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVISMNRRL 180
Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
GD SLNA I +S+ S QWQDWLV DH+ QE VLIE++E + RR ML ++M VLN RER
Sbjct: 181 HGDASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNERER 240
Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
RIFEARRL E+PVTLE LSSEF++SRERVRQIE RAF+KVQE++QK+
Sbjct: 241 RIFEARRLAEDPVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEA 288
|
Species: Agrobacterium tumefaciens Genus: Agrobacterium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|325293796|ref|YP_004279660.1| RNA polymerase sigma-32 factor [Agrobacterium sp. H13-3] Length = 300 | Back alignment and organism information |
|---|
Score = 446 bits (1147), Expect = e-123, Method: Compositional matrix adjust.
Identities = 214/288 (74%), Positives = 242/288 (84%)
Query: 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
M R ++ I GE GL+RY+ EIRK PMLE QEEY+L KRY EHGD AAH+LVTSHLRL
Sbjct: 1 MARNSLPTITAGEAGLNRYLDEIRKFPMLEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRL 60
Query: 61 VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61 VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120
Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVISMNRRL 180
Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
GD SLNA I +S+ S QWQDWLV DH+ QE VLIE++E + RR ML ++M VLN RER
Sbjct: 181 HGDASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNDRER 240
Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
RIFEARRL E+PVTLE LSSEF++SRERVRQIE RAF+KVQE++QK+
Sbjct: 241 RIFEARRLAEDPVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEA 288
|
Species: Agrobacterium sp. H13-3 Genus: Agrobacterium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|86358940|ref|YP_470832.1| RNA polymerase factor sigma-32 [Rhizobium etli CFN 42] Length = 302 | Back alignment and organism information |
|---|
Score = 446 bits (1147), Expect = e-123, Method: Compositional matrix adjust.
Identities = 211/288 (73%), Positives = 246/288 (85%)
Query: 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
M R + I GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD AAH+LVTSHLRL
Sbjct: 1 MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60
Query: 61 VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61 VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120
Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
WS VK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V IA KLNVSE EVISMN RL
Sbjct: 121 WSAVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180
Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
+GD SLNA I +++ +S QWQDWLV DH+ QE VLIE++E + RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHESQEDVLIEQDELETRRRMLAKAMSVLNERER 240
Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+
Sbjct: 241 RIFEARRLAEDPVTLEDLSAEFDISRERVRQIEVRAFEKVQDAVRKEA 288
|
Species: Rhizobium etli Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|116253507|ref|YP_769345.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv. viciae 3841] Length = 302 | Back alignment and organism information |
|---|
Score = 446 bits (1146), Expect = e-123, Method: Compositional matrix adjust.
Identities = 211/288 (73%), Positives = 244/288 (84%)
Query: 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
M R + I GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD AAH+LVTSHLRL
Sbjct: 1 MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60
Query: 61 VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFD ERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61 VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRS 120
Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V IA KLNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180
Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
+GD SLNA I +++ + QWQDWLV DHD QE VLIE++E RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDGGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERER 240
Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+
Sbjct: 241 RIFEARRLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEA 288
|
Species: Rhizobium leguminosarum Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
| >gi|209550663|ref|YP_002282580.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv. trifolii WSM2304] Length = 302 | Back alignment and organism information |
|---|
Score = 446 bits (1146), Expect = e-123, Method: Compositional matrix adjust.
Identities = 211/289 (73%), Positives = 245/289 (84%)
Query: 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
M R + I GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD AAH+LVTSHLRL
Sbjct: 1 MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60
Query: 61 VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFD ERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61 VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRS 120
Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLKVSEEEVISMNRRL 180
Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
+GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERER 240
Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ +
Sbjct: 241 RIFEARRLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEAQ 289
|
Species: Rhizobium leguminosarum Genus: Rhizobium Family: Rhizobiaceae Order: Rhizobiales Class: Alphaproteobacteria Phylum: Proteobacteria Superkingdom: Bacteria |
Conserved Domains in CDD Database
Detected by RPS-BLAST and HHsearch
Conserved Domains in CDD Database Detected by RPS-BLAST
Original result of RPS-BLAST against CDD database part I
Original result of RPS-BLASTagainst CDD database part II
| Identity | Alignment graph | Length | Definition | E-value |
| Target | 302 | RNA polymerase factor sigma-32 [Candidatus Liberibacter | ||
| PRK06596 | 284 | PRK06596, PRK06596, RNA polymerase factor sigma-32; Rev | 1e-130 | |
| TIGR02392 | 270 | TIGR02392, rpoH_proteo, alternative sigma factor RpoH | 1e-107 | |
| PRK07500 | 289 | PRK07500, rpoH2, RNA polymerase factor sigma-32; Review | 1e-71 | |
| TIGR02394 | 285 | TIGR02394, rpoS_proteo, RNA polymerase sigma factor Rpo | 4e-32 | |
| PRK05657 | 325 | PRK05657, PRK05657, RNA polymerase sigma factor RpoS; V | 2e-29 | |
| TIGR02997 | 298 | TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor | 9e-28 | |
| COG1191 | 247 | COG1191, FliA, DNA-directed RNA polymerase specialized | 7e-18 | |
| PRK07921 | 324 | PRK07921, PRK07921, RNA polymerase sigma factor SigB; R | 3e-17 | |
| PRK05949 | 327 | PRK05949, PRK05949, RNA polymerase sigma factor; Valida | 4e-14 | |
| PRK08583 | 257 | PRK08583, PRK08583, RNA polymerase sigma factor SigB; V | 2e-09 | |
| TIGR02941 | 255 | TIGR02941, Sigma_B, RNA polymerase sigma-B factor | 4e-09 | |
| TIGR02850 | 254 | TIGR02850, spore_sigG, RNA polymerase sigma-G factor | 2e-08 | |
| PRK06288 | 268 | PRK06288, PRK06288, RNA polymerase sigma factor WhiG; R | 4e-08 | |
| PRK08215 | 258 | PRK08215, PRK08215, sporulation sigma factor SigG; Revi | 1e-07 | |
| COG0568 | 342 | COG0568, RpoD, DNA-directed RNA polymerase, sigma subun | 1e-62 | |
| TIGR02393 | 238 | TIGR02393, RpoD_Cterm, RNA polymerase sigma factor RpoD | 3e-24 | |
| PRK07598 | 415 | PRK07598, PRK07598, RNA polymerase sigma factor SigC; V | 3e-18 | |
| TIGR02980 | 227 | TIGR02980, SigBFG, RNA polymerase sigma-70 factor, sigm | 6e-13 | |
| TIGR02479 | 224 | TIGR02479, FliA_WhiG, RNA polymerase sigma factor, FliA | 2e-11 | |
| TIGR02885 | 231 | TIGR02885, spore_sigF, RNA polymerase sigma-F factor | 4e-06 | |
| PRK07408 | 256 | PRK07408, PRK07408, RNA polymerase sigma factor SigF; R | 5e-05 | |
| PRK07670 | 251 | PRK07670, PRK07670, RNA polymerase sigma factor SigD; V | 2e-04 | |
| PRK05572 | 252 | PRK05572, PRK05572, sporulation sigma factor SigF; Vali | 8e-04 | |
| PRK06986 | 236 | PRK06986, fliA, flagellar biosynthesis sigma factor; Va | 0.002 | |
| PRK05911 | 257 | PRK05911, PRK05911, RNA polymerase sigma factor sigma-2 | 0.002 | |
| PRK09210 | 367 | PRK09210, PRK09210, RNA polymerase sigma factor RpoD; V | 8e-21 | |
| PRK05901 | 509 | PRK05901, PRK05901, RNA polymerase sigma factor; Provis | 1e-15 | |
| PRK07406 | 373 | PRK07406, PRK07406, RNA polymerase sigma factor RpoD; V | 2e-13 | |
| PRK07405 | 317 | PRK07405, PRK07405, RNA polymerase sigma factor SigD; V | 5e-11 | |
| TIGR02835 | 234 | TIGR02835, spore_sigmaE, RNA polymerase sigma-E factor | 7e-11 | |
| PRK08301 | 234 | PRK08301, PRK08301, sporulation sigma factor SigE; Revi | 1e-10 | |
| TIGR02846 | 227 | TIGR02846, spore_sigmaK, RNA polymerase sigma-K factor | 6e-10 | |
| PRK05803 | 233 | PRK05803, PRK05803, sporulation sigma factor SigK; Revi | 7e-10 | |
| TIGR02937 | 158 | TIGR02937, sigma70-ECF, RNA polymerase sigma factor, si | 7e-06 | |
| pfam04542 | 71 | pfam04542, Sigma70_r2, Sigma-70 region 2 | 2e-14 | |
| PRK05658 | 619 | PRK05658, PRK05658, RNA polymerase sigma factor RpoD; V | 5e-13 | |
| pfam04545 | 50 | pfam04545, Sigma70_r4, Sigma-70, region 4 | 5e-07 | |
| cd06171 | 55 | cd06171, Sigma70_r4, Sigma70, region (SR) 4 refers to t | 5e-06 | |
| PRK05658 | 619 | PRK05658, PRK05658, RNA polymerase sigma factor RpoD; V | 1e-04 | |
| PRK07406 | 373 | PRK07406, PRK07406, RNA polymerase sigma factor RpoD; V | 2e-04 | |
| TIGR02937 | 158 | TIGR02937, sigma70-ECF, RNA polymerase sigma factor, si | 2e-04 | |
| PRK09210 | 367 | PRK09210, PRK09210, RNA polymerase sigma factor RpoD; V | 3e-04 | |
| PRK05901 | 509 | PRK05901, PRK05901, RNA polymerase sigma factor; Provis | 3e-04 | |
| PRK07405 | 317 | PRK07405, PRK07405, RNA polymerase sigma factor SigD; V | 0.003 |
| >gnl|CDD|180635 PRK06596, PRK06596, RNA polymerase factor sigma-32; Reviewed | Back alignment and domain information |
|---|
Score = 459 bits (1184), Expect = e-130
Identities = 139/287 (48%), Positives = 187/287 (65%), Gaps = 6/287 (2%)
Query: 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
M + + ++ E L YI + KIPML +EEY+LAKR REHGDL AA +LV SHLR
Sbjct: 1 MTKALQLLALSPEGNLDAYIQAVNKIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRF 60
Query: 61 VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
VV IA GYRGYGLP ++++ EGNIGLM+AVK+FDPE G RL ++++ WIKA + EYILR+
Sbjct: 61 VVHIARGYRGYGLPQADLIQEGNIGLMKAVKRFDPEVGVRLVSFAVHWIKAEIHEYILRN 120
Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
W +VK+ TT Q++LFFNLR+ K L L PE+V +A++L VSE EV M RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKKRLGW-----LNPEEVEMVAEELGVSEEEVREMESRL 175
Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
+G D SL+A I+ D+ S QD+L VL E RR +L ++ L+ R
Sbjct: 176 SGQDASLDAPIDDDDEESGAPQDYLEDKSSDPADVLEEDNWEDQRRALLADALEGLDERS 235
Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
R I EAR L ++ TL+ L++E+ VS ERVRQIE A KK++ +I+
Sbjct: 236 RDIIEARWLDDDKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIEA 282
|
Length = 284 |
| >gnl|CDD|162835 TIGR02392, rpoH_proteo, alternative sigma factor RpoH | Back alignment and domain information |
|---|
Score = 382 bits (983), Expect = e-107
Identities = 137/268 (51%), Positives = 184/268 (68%), Gaps = 5/268 (1%)
Query: 15 GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
L YI + +IPML +EEY LAKR REHGDL AA +LV SHLR VVKIA GYRGYGLP
Sbjct: 2 SLDAYIRAVNRIPMLTPEEEYQLAKRLREHGDLDAAKKLVLSHLRFVVKIARGYRGYGLP 61
Query: 75 ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
++++ EGNIGLM+AVK+FDPERG RL ++++ WIKA + EYILR+W LVK+ TT Q++
Sbjct: 62 QADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRK 121
Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
LFFNLR++K LQ + PE+V AIA++L VSE EV M RL+G D SLNA I+
Sbjct: 122 LFFNLRKMKKRLQGWLN----PEEVEAIAEELGVSEREVREMESRLSGQDMSLNASIDDD 177
Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
+ + +LV E L E++ + +R L ++ L+ R RRI EAR L ++ +
Sbjct: 178 EDDGGAPIAYLVDKTSDPEDTLEEEQWEELQRQALANALGSLDARSRRIIEARWLDDDKL 237
Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
TL+ L++E+ VS ER+RQIE A KK++
Sbjct: 238 TLQELAAEYGVSAERIRQIEKNAMKKLK 265
|
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. Length = 270 |
| >gnl|CDD|181003 PRK07500, rpoH2, RNA polymerase factor sigma-32; Reviewed | Back alignment and domain information |
|---|
Score = 264 bits (678), Expect = 1e-71
Identities = 115/264 (43%), Positives = 178/264 (67%), Gaps = 1/264 (0%)
Query: 25 KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
K P LE++EE+ LA R+++H D A HR++++H+RLV+ +A +R +GLP+++++ EG +
Sbjct: 17 KAPYLEREEEHALAYRWKDHRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYV 76
Query: 85 GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
GL++A +F+P+R R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+
Sbjct: 77 GLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRA 136
Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDW 203
L + K E IA L VS S+V M+ RL+G D SLNA + D+ S+ D+
Sbjct: 137 RLAQADEELTKQEIHREIATALGVSLSDVEMMDARLSGPDASLNAPQSEEDEGRSERMDF 196
Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
LV D ++ + + + RR LT+++ LN RE RI RRL+E+ TLE L E
Sbjct: 197 LVDDSPLPDEQVESSIDGERRRRWLTQALQTLNERELRIIRERRLREDGATLEALGEELG 256
Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
+S+ERVRQIEARA +K++ ++ Q
Sbjct: 257 ISKERVRQIEARALEKLRRALLSQ 280
|
Length = 289 |
| >gnl|CDD|131447 TIGR02394, rpoS_proteo, RNA polymerase sigma factor RpoS | Back alignment and domain information |
|---|
Score = 134 bits (338), Expect = 4e-32
Identities = 84/279 (30%), Positives = 139/279 (49%), Gaps = 29/279 (10%)
Query: 19 YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
Y+ EI P+L +EE A+R GD A ++ S+LRLVV IA Y GLP+ ++
Sbjct: 18 YLREIGFKPLLTAEEEIAYARRALA-GDFEARKVMIESNLRLVVSIAKHYVNRGLPLLDL 76
Query: 79 VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
+ EGN+GLM AV+KFDPERGFR +TY+ WWI+ ++ I+ +++ K L
Sbjct: 77 IEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHV-IKELNVY 135
Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
LR + L+ E++ +++ L ++E + S++ L D S + L
Sbjct: 136 LRAAR-QLEKKLGREPSVEEIAELLDKPVEDVSRVLALNER-ITSLDAPLDDDSSKSLLD 193
Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RL 248
+D+ E ++ + ++ L LN R+R + R L
Sbjct: 194 TIADEQ-----------SIDPESLVQNDDLKQLIEAWLAE----LNERQREVLARRFGLL 238
Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
P TLE +++E ++RERVRQI+ A KK++ +++
Sbjct: 239 GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILERD 277
|
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). Length = 285 |
| >gnl|CDD|180185 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated | Back alignment and domain information |
|---|
Score = 125 bits (315), Expect = 2e-29
Identities = 91/289 (31%), Positives = 144/289 (49%), Gaps = 49/289 (16%)
Query: 19 YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
Y++EI P+L +EE A+R GD +A R++ S+LRLVVKIA Y GL + ++
Sbjct: 58 YLNEIGYSPLLTAEEEVYFARRALR-GDFAARQRMIESNLRLVVKIAKRYLNRGLALLDL 116
Query: 79 VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
+ EGN+GL++AV+KFDPERGFR +TY+ WWI+ ++ I+ NQ R
Sbjct: 117 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM------------NQTR---T 161
Query: 139 LR-------------RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE- 184
+R R L+ D+ E+ IA+ L+ +V M LA +E
Sbjct: 162 IRLPVHVVKELNVYLRAARELEHKLDHEPSAEE---IAELLDKPVDDVSRM---LALNER 215
Query: 185 --SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERR 241
SL+ + D S D L + + + + ++ K L LN ++R
Sbjct: 216 ITSLDTPL-GGDPEKS-LLDILADEQENGPEDTTQDDDMKQSIVKWLFE----LNDKQRE 269
Query: 242 IFEARRLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
+ RR TLE+++ E ++RERVRQI+ A ++++E +Q Q
Sbjct: 270 VLA-RRFGLLGYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQTQ 317
|
Length = 325 |
| >gnl|CDD|163097 TIGR02997, Sig70-cyanoRpoD, RNA polymerase sigma factor, cyanobacterial RpoD-like family | Back alignment and domain information |
|---|
Score = 119 bits (301), Expect = 9e-28
Identities = 87/316 (27%), Positives = 143/316 (45%), Gaps = 80/316 (25%)
Query: 19 YIHEIRKIPMLEKQEEYVLAKRYRE---------------HGDLS--------------- 48
Y+ EI ++P+L +EE LA++ ++ + S
Sbjct: 6 YLQEIGRVPLLTPEEEIELARQVQQMMVLEELREELEEQLGREPSKEEWAAAAGLSEAEL 65
Query: 49 ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
A +++ ++LRLVV +A Y+ GL + +++ EG++GL +AV+KFDP RG+
Sbjct: 66 RQRLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGSLGLERAVEKFDPTRGY 125
Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPE 157
+ +TY+ WWI+ + I ANQ R RL H IT+ N +K
Sbjct: 126 KFSTYAYWWIRQGITRAI------------ANQSRTI----RLPIH---ITEKLNKIKKV 166
Query: 158 Q------------VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
Q IA+ L + +V + R SL+A + + ++ D L
Sbjct: 167 QRELSQKLGRTPSEAEIAEALELEPEQVRELLQRARQPVSLDAPVGDEED--TELGDLLE 224
Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFE 263
D + E+ + ER++ R L ++ L PRER++ R P+TL +
Sbjct: 225 DDGESPEEQV----ERESLRQDLESLLAELTPRERQVLRLRFGLDGGEPLTLAEIGRRLN 280
Query: 264 VSRERVRQIEARAFKK 279
+SRERVRQIEA+A +K
Sbjct: 281 LSRERVRQIEAKALRK 296
|
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). Length = 298 |
| >gnl|CDD|31384 COG1191, FliA, DNA-directed RNA polymerase specialized sigma subunit [Transcription] | Back alignment and domain information |
|---|
Score = 86.5 bits (214), Expect = 7e-18
Identities = 59/262 (22%), Positives = 120/262 (45%), Gaps = 19/262 (7%)
Query: 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIG 85
L K+EE L + Y E + A RL+ +L LV IA + G +++ G IG
Sbjct: 4 QPLSKEEEEKLLEYYAEGDE--EARRLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIG 61
Query: 86 LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
L++A++++DP +G + +TY++ I+ + +Y LR VK+ + L RR++
Sbjct: 62 LIKAIERYDPSKGTKFSTYAVRRIRGEILDY-LRKNDSVKV-----PRSLRELGRRIEEA 115
Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
+ + + IA++L + + E I + G + L+ + + D
Sbjct: 116 IDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQLLSLDEDVLKDDDDDVDD--- 172
Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
Q + + E++ +L ++ L RE+ + R +E +T + ++ +S
Sbjct: 173 -----QIENPDDGVEKEELLEILKEAIEPLPEREKLVLVLRYKEE--LTQKEIAEVLGIS 225
Query: 266 RERVRQIEARAFKKVQESIQKQ 287
RV ++ +A KK+++ + K
Sbjct: 226 ESRVSRLHKKAIKKLRKELNKA 247
|
Length = 247 |
| >gnl|CDD|181169 PRK07921, PRK07921, RNA polymerase sigma factor SigB; Reviewed | Back alignment and domain information |
|---|
Score = 84.4 bits (209), Expect = 3e-17
Identities = 89/314 (28%), Positives = 135/314 (42%), Gaps = 82/314 (26%)
Query: 19 YIHEIRKIPMLEKQEEYVLAKR-----YREH-----GDLSAAHR---------------- 52
Y++ I K +L +E LAKR Y EH LS A +
Sbjct: 31 YLNGIGKTALLTAADEVELAKRIEAGLYAEHLLETRKRLSEARKRDLAAVVRDGEAARRH 90
Query: 53 LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
L+ ++LRLVV +A Y G G+P+ +++ EGN+GL++A++KFD +GF+ +TY+ WWI+ A
Sbjct: 91 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 150
Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
I R A+Q R RL HL EQV KL + E
Sbjct: 151 ----ITRG--------MADQSRTI----RLPVHLV---------EQV----NKLARIKRE 181
Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD--------GQEQV-----LIEKE 219
++ +L + + L S + D L + D G ++ IE
Sbjct: 182 ---LHQQLGREATDEELAEESGIPEEKIADLLEHSRDPVSLDMPVGSDEEAPLGDFIEDS 238
Query: 220 ERKNRRNMLTRSM------SVLNPRERRIFEARRLQ-----ENPVTLENLSSEFEVSRER 268
E + N + + SVL + R + RL+ P TL+ + F +SRER
Sbjct: 239 EATSAENAVIAGLLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRER 298
Query: 269 VRQIEARAFKKVQE 282
VRQIE K++
Sbjct: 299 VRQIEREVMSKLRN 312
|
Length = 324 |
| >gnl|CDD|180321 PRK05949, PRK05949, RNA polymerase sigma factor; Validated | Back alignment and domain information |
|---|
Score = 74.1 bits (182), Expect = 4e-14
Identities = 68/299 (22%), Positives = 136/299 (45%), Gaps = 52/299 (17%)
Query: 19 YIHEIRKIPMLEKQEEYVLAKR--------------------------YREHGDLS---- 48
Y+HEI ++P+L ++E V K+ + E +LS
Sbjct: 23 YLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWAEAVNLSETEL 82
Query: 49 ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
A +++ ++LRLVV IA Y+ + +++ EG +GL + V+KFDP RG+
Sbjct: 83 KQTLKQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGY 142
Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
+ +TY+ WWI+ A+ I + +++ +K L ++K + ++ +
Sbjct: 143 KFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNKIKKTQRELSQKLGRSATP 197
Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
IAK+L + S++ + ++ + D ++ + L + +Q + ++
Sbjct: 198 AEIAKELELEPSQI--REYLSMARQPISLDVRVGDNQDTELSELLEDEGPSPDQYITQEL 255
Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
R++ N+L L P++R + R E+ ++L + +SRERVRQ+E +A
Sbjct: 256 LRQDLNNLLAE----LTPQQREVLTLRFGLEDGKELSLAKVGERLNLSRERVRQLEHQA 310
|
Length = 327 |
| >gnl|CDD|181489 PRK08583, PRK08583, RNA polymerase sigma factor SigB; Validated | Back alignment and domain information |
|---|
Score = 58.6 bits (142), Expect = 2e-09
Identities = 64/272 (23%), Positives = 124/272 (45%), Gaps = 40/272 (14%)
Query: 29 LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE-VVSEGNIGLM 87
L K+E Y+E+ D A +LV + LV +A Y G E +V G +GL+
Sbjct: 10 LTKEEVNKWIAEYQENQDEEAQEKLVKHYKNLVESLAYKY-SKGQSHHEDLVQVGMVGLL 68
Query: 88 QAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWS------LVKIGTTANQKRLFFNLR 140
A++++DP G +++ I ++ Y+ ++WS + ++G
Sbjct: 69 GAIRRYDPSFGRSFEAFAVPTIIGEIKRYLRDKTWSVHVPRRIKELGP------------ 116
Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQ 199
++K + +T + ++ IA +L VSE EV+ + +S AL ++ S + S
Sbjct: 117 KIKKAVDELTTELQRSPKISEIADRLGVSEEEVLEA---MEMGKSYQALSVDHSIEADSD 173
Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
+ D GQ++ + E +R +L + + VL+ RE+ I + +ENLS
Sbjct: 174 GSTVTLLDIVGQQE---DGYELTEQRMILEKILPVLSDREKSIIQC-------TFIENLS 223
Query: 260 SE-----FEVSRERVRQIEARAFKKVQESIQK 286
+ +S+ V +++ +A KK++E+
Sbjct: 224 QKETGERLGISQMHVSRLQRQAIKKLREAAFL 255
|
Length = 257 |
| >gnl|CDD|131987 TIGR02941, Sigma_B, RNA polymerase sigma-B factor | Back alignment and domain information |
|---|
Score = 57.6 bits (139), Expect = 4e-09
Identities = 58/270 (21%), Positives = 120/270 (44%), Gaps = 36/270 (13%)
Query: 29 LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
L K++ ++++ + A +LV + LV IA Y G ++V G +GL+
Sbjct: 10 LTKEDVIQWIAEFQQNQNGEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLG 69
Query: 89 AVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
A++++D G +++ I ++ Y+ ++WS+ +R+ ++K +
Sbjct: 70 AIRRYDYSIGNAFEPFAIPTIIGEIKRYLRDKTWSV------HVPRRIKELGPKIKKAID 123
Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI------NSSDKNSSQWQ 201
+TD+ + +++ IA L +SE EV+ + + +S AL SD ++
Sbjct: 124 ELTDHLQRSPKIIEIADHLGLSEEEVLEI---MEMGQSYRALSVDDVIEADSDGSTVARL 180
Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
D + DG +Q RR +L + + +L+ RE+ I ENLS +
Sbjct: 181 DSVGEVEDGYDQT--------ERRMVLEKILPILSEREKSIIHC-------TFEENLSQK 225
Query: 262 -----FEVSRERVRQIEARAFKKVQESIQK 286
+S+ V +++ +A K++E+
Sbjct: 226 ETGERLGISQMHVSRLQRQAISKLKEAAFL 255
|
This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus. Length = 255 |
| >gnl|CDD|131897 TIGR02850, spore_sigG, RNA polymerase sigma-G factor | Back alignment and domain information |
|---|
Score = 55.6 bits (134), Expect = 2e-08
Identities = 66/266 (24%), Positives = 114/266 (42%), Gaps = 29/266 (10%)
Query: 25 KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
K+P+L+ QE L R + GD +A +L+ +LRLV+ + + G + ++ G I
Sbjct: 12 KLPVLKNQEMRELFIRMQS-GDTTAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 70
Query: 85 GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
GLM+++ FD + + +TY++ I ++ Y I S SL I A Q R
Sbjct: 71 GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 126
Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
+ N K V IAK+L V + EV+ + SL I + +
Sbjct: 127 --------DKLISENSKEPTVSEIAKELKVPQEEVVFALDAIQDPVSLFEPIYNDGGDPI 178
Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
D + + + Q L L +M LN RE+ I R + T +
Sbjct: 179 YVMDQISDEKNKDSQWLEGIA--------LKEAMKRLNEREKMILNMRFFEGK--TQMEV 228
Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
+ E +S+ +V ++E A K +++ +
Sbjct: 229 AEEIGISQAQVSRLEKAALKHMRKYV 254
|
Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor. Length = 254 |
| >gnl|CDD|180512 PRK06288, PRK06288, RNA polymerase sigma factor WhiG; Reviewed | Back alignment and domain information |
|---|
Score = 54.3 bits (131), Expect = 4e-08
Identities = 70/260 (26%), Positives = 119/260 (45%), Gaps = 21/260 (8%)
Query: 24 RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVV 79
KIP +Q+E L + Y++ GD L+ + LV +A G G+P ++V
Sbjct: 7 GKIPKYAQQDETELWREYKKTGDPKIREYLILKYSPLVKYVA-GRIAVGMPQNVEFDDLV 65
Query: 80 SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
S G GL+ A++KFDPER + TY++ I+ A+ + LR S+ I + QK +
Sbjct: 66 SYGVFGLIDAIEKFDPEREIKFKTYAVTRIRGAIFDE-LR--SIDWIPRSVRQKAR--QI 120
Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNS 197
R L+A E+ IA +L +S E S+ +L+G SLN L D+
Sbjct: 121 ERAIAMLEARLGRTPSDEE---IADELGISLEEYNSLLSKLSGTSVVSLNDLWFGGDEGD 177
Query: 198 S-QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
D L + E+EE K ++ ++ L RE+++ ++ +TL+
Sbjct: 178 EVSLMDTLESPAALNPDEIAEREEIK---RVIVEAIKTLPEREKKVLILYYYED--LTLK 232
Query: 257 NLSSEFEVSRERVRQIEARA 276
+ V+ R+ Q+ +A
Sbjct: 233 EIGKVLGVTESRISQLHTKA 252
|
Length = 268 |
| >gnl|CDD|181296 PRK08215, PRK08215, sporulation sigma factor SigG; Reviewed | Back alignment and domain information |
|---|
Score = 52.3 bits (126), Expect = 1e-07
Identities = 75/281 (26%), Positives = 128/281 (45%), Gaps = 57/281 (20%)
Query: 25 KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
K+P+L+ +E L +R + GD A +L+ +LRLV+ + + G + ++ G I
Sbjct: 15 KLPVLKNEEMRELFERMQN-GDKEAREKLINGNLRLVLSVIQRFNNRGENVDDLFQVGCI 73
Query: 85 GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-------SWSLVKIGTTANQKRLFF 137
GLM+A+ FD + + +TY++ I ++ Y LR S SL I A Q R
Sbjct: 74 GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRDIAYKALQVR--- 129
Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
+ + + N K V IAK+L V EV+ +L+A+
Sbjct: 130 ---------EKLINENSKEPTVEEIAKELEVPREEVV---------FALDAI-------- 163
Query: 198 SQWQDWL-----VYDHDG------QEQVLIEKEERKN-RRNM-LTRSMSVLNPRERRIFE 244
QD + +Y HDG +Q+ EK + +N + L +M LN RE+ I
Sbjct: 164 ---QDPVSLFEPIY-HDGGDPIYVMDQISDEKNKDENWLEEIALKEAMKKLNDREKLIL- 218
Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
R + +E ++ E +S+ +V ++E A K +++ IQ
Sbjct: 219 NLRFFQGKTQME-VAEEIGISQAQVSRLEKAALKHMRKYIQ 258
|
Length = 258 |
| >gnl|CDD|30914 COG0568, RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] | Back alignment and domain information |
|---|
Score = 235 bits (600), Expect = 1e-62
Identities = 106/295 (35%), Positives = 151/295 (51%), Gaps = 14/295 (4%)
Query: 2 NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG-DLSAAHRLVTSHLRL 60
R+ LS YI I P+L +EE LA+R + DL A +LV S+LRL
Sbjct: 55 GREPSERARRPAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGERDLDAKKKLVESNLRL 114
Query: 61 VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
VV IA Y G GLP +++ EGNIGLM+AV+KFDPE+GF+ +TY+ WWI+ A+ I
Sbjct: 115 VVSIAKKYTGRGLPFLDLIQEGNIGLMKAVEKFDPEKGFKFSTYATWWIRQAITRAIADQ 174
Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
++I +Q L LRR+K L + IA++L VS +V M R
Sbjct: 175 ARTIRIPV--HQVELINKLRRVKRELLQ---ELGREPTPEEIAEELGVSPDKVREMLKRA 229
Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDG-QEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
+ SL+ I + S+ D+L D E + + +++ +L L RE
Sbjct: 230 SEPISLDTPIGDDE--DSELGDFLEDDKSVSPEDAVERESLKEDLNEVLA---EALTERE 284
Query: 240 RRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
RR+ R P TLE L EF +SRERVRQIEA+A +K++ ++ L S
Sbjct: 285 RRVIRLRFGLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLRRHPERSALLRS 339
|
Length = 342 |
| >gnl|CDD|162836 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor RpoD, C-terminal domain | Back alignment and domain information |
|---|
Score = 107 bits (270), Expect = 3e-24
Identities = 73/238 (30%), Positives = 119/238 (50%), Gaps = 22/238 (9%)
Query: 49 AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
A +LV S+LRLVV IA Y GL +++ EGNIGLM+AV+KFD +G++ +TY+ WW
Sbjct: 1 AKKQLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWW 60
Query: 109 IKAAMQEYILRSWSLVKI----GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
I+ A+ I ++I T N+ L + + L E+ +A+
Sbjct: 61 IRQAITRAIADQARTIRIPVHMVETINK------LIKAERQLTQELGREPTDEE---LAE 111
Query: 165 KLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
++ + +V + ++A + SL I + S D+ + D + + ++
Sbjct: 112 RMGMPAEKVREIK-KIAQEPISLETPIGEEED--SFLGDF-IEDTSIESP--DDYAAKEL 165
Query: 224 RRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
R L + L RER++ R L P TLE + EF V+RER+RQIE++A +K
Sbjct: 166 LREQLDEVLETLTERERKVLRMRYGLLDGRPHTLEEVGKEFNVTRERIRQIESKALRK 223
|
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. Length = 238 |
| >gnl|CDD|181056 PRK07598, PRK07598, RNA polymerase sigma factor SigC; Validated | Back alignment and domain information |
|---|
Score = 88.0 bits (218), Expect = 3e-18
Identities = 67/238 (28%), Positives = 127/238 (53%), Gaps = 13/238 (5%)
Query: 47 LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
L A ++ ++LRLVV +A Y+ GL + ++V EG +GL +AV+KFDP +G+R +TY+
Sbjct: 174 LRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAY 233
Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
WWI+ + I +++ +K L ++K + I+ + + IA++L
Sbjct: 234 WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEKGRTPTIEDIAQEL 288
Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
++ ++V + R+ SL + DK+ ++ D L D E++L+ R++ +
Sbjct: 289 EMTPTQVREVLLRVPRSVSLETKV-GKDKD-TELGDLLETDDISPEEMLM----RESLQR 342
Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
L ++ L RER + R + +L + ++SRERVRQIE++A +K+++
Sbjct: 343 DLQHLLADLTSRERDVIRMRFGLADGHTYSLAEIGRALDLSRERVRQIESKALQKLRQ 400
|
Length = 415 |
| >gnl|CDD|163094 TIGR02980, SigBFG, RNA polymerase sigma-70 factor, sigma-B/F/G subfamily | Back alignment and domain information |
|---|
Score = 70.3 bits (173), Expect = 6e-13
Identities = 64/240 (26%), Positives = 112/240 (46%), Gaps = 25/240 (10%)
Query: 52 RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
+LV +L LV IA +R G P ++V G IGL++A+ +FDP G + +T+++ I
Sbjct: 7 KLVELNLPLVRSIARRFRNRGEPHEDLVQVGTIGLVKAIDRFDPSYGVKFSTFAVPTIMG 66
Query: 112 AMQEYILR--SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
++ + R +W+ V++ + L ++ + +T + + IA++L VS
Sbjct: 67 EIKRF-FRDDTWA-VRVPRRLKELGL-----KINKATEELTQRLGRSPTIAEIAEELGVS 119
Query: 170 ESEVISMNCRLAGD----ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
E EV+ AG+ SL+A I D + D L + D E V R
Sbjct: 120 EEEVVE--ALEAGNSYSALSLDAPIEDDDGDPIALLDTLGDEDDALETVE--------DR 169
Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
L ++ L RERRI R ++ T ++ +S+ V ++ RA KK++E +
Sbjct: 170 LALKPLLAALPERERRILLLRFFED--KTQSEIAERLGISQMHVSRLLRRALKKLREQLL 227
|
This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage. Length = 227 |
| >gnl|CDD|162877 TIGR02479, FliA_WhiG, RNA polymerase sigma factor, FliA/WhiG family | Back alignment and domain information |
|---|
Score = 65.4 bits (160), Expect = 2e-11
Identities = 59/236 (25%), Positives = 103/236 (43%), Gaps = 21/236 (8%)
Query: 53 LVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
L+ +L LV +IA GLP S +++ G GL+ A++++DP RG + TY++
Sbjct: 1 LIRRYLPLVKRIAGRLSV-GLPSSVELDDLIQAGMFGLLDAIERYDPSRGAKFETYAVQR 59
Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
I+ AM + LR V ++ L R L+A E+ IA++L +
Sbjct: 60 IRGAMLDE-LRRLDWVPRSLRQKARK----LERAIRELEARLGREPTEEE---IAEELGM 111
Query: 169 SESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
E + SL+ L+ S D S + E+ L ER+ R
Sbjct: 112 DLKEYRQALNEINALSLVSLDELLESGDDGGSLIDRIEDDKSEDPEEEL----EREELRE 167
Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
L ++ L+ RE+ + +E + L+ + ++ RV QI ++A KK++
Sbjct: 168 ALAEAIESLSEREQLVLSLYYYEE--LNLKEIGEVLGLTESRVSQIHSQALKKLRA 221
|
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. Length = 224 |
| >gnl|CDD|131931 TIGR02885, spore_sigF, RNA polymerase sigma-F factor | Back alignment and domain information |
|---|
Score = 47.4 bits (113), Expect = 4e-06
Identities = 58/241 (24%), Positives = 111/241 (46%), Gaps = 18/241 (7%)
Query: 45 GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
GD A +L+ +LRLV I + G ++ G IGL++A+ KFD + +TY
Sbjct: 8 GDKEARDKLIECNLRLVWSIVKRFLNRGYEPEDLFQIGCIGLVKAIDKFDLSYDVKFSTY 67
Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IA 163
++ I ++ + LR ++K+ + K L +R +K L L E + +A
Sbjct: 68 AVPMIMGEIKRF-LRDDGIIKVSRSL--KELARKIRYMKEELS----KELGREPTINELA 120
Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
+ L VS E++ +SL ++ D + D + D ++ +EK
Sbjct: 121 EALGVSPEEIVMALESARSPQSLYDTVHQDDGDPIYLLDQIA-DKGSEDSDWLEKI---- 175
Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
L ++S L+ RER+I R ++ T +++ +S+ +V ++E + KK++E
Sbjct: 176 ---ALKEAISKLDERERQIIMLRYFKDK--TQTEVANMLGISQVQVSRLEKKVLKKMKEK 230
Query: 284 I 284
+
Sbjct: 231 L 231
|
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. Length = 231 |
| >gnl|CDD|180965 PRK07408, PRK07408, RNA polymerase sigma factor SigF; Reviewed | Back alignment and domain information |
|---|
Score = 44.1 bits (105), Expect = 5e-05
Identities = 57/236 (24%), Positives = 110/236 (46%), Gaps = 32/236 (13%)
Query: 37 LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDP 95
L + Y+++ ++ ++LV +L LV K A + P ++V G++GL++A+++FDP
Sbjct: 14 LLRAYQQNPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLVQVGSLGLIRAIERFDP 73
Query: 96 ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL-RRLKGHLQAITDNNL 154
+G +++++ +I+ +Q Y+ V+I R + L R+ K Q +
Sbjct: 74 SKGHAFSSFAIPYIRGEIQHYLRDKSPTVRI------PRRWQELQRQAKKVRQELRQELG 127
Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDE----SLNALINSSDKNSSQWQDWLVYDHDG 210
+ IA+ L++S E +LA SL+A +N + S+ D L+ D
Sbjct: 128 RQPTDQEIAQALDISLEEWQE--IKLALQNRTPLSLDAPVNQDEDGSTSLGD-LLPDPRY 184
Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE------------ARRLQENPVT 254
+ L +++ R L ++++ L R R + E A RL +PVT
Sbjct: 185 RSFQLAQED-----RIRLQQALAQLEERTREVLEFVFLHDLTQKEAAERLGISPVT 235
|
Length = 256 |
| >gnl|CDD|181075 PRK07670, PRK07670, RNA polymerase sigma factor SigD; Validated | Back alignment and domain information |
|---|
Score = 42.0 bits (99), Expect = 2e-04
Identities = 64/281 (22%), Positives = 127/281 (45%), Gaps = 63/281 (22%)
Query: 33 EEYVLAKRYREHGDLSAAHRLVTSHLRLVV----KIAMGYRGYGLPIS----EVVSEGNI 84
EE L R++E D AA L+ ++ LV +I++G LP S ++ S G +
Sbjct: 7 EEQKLWDRWKEERDPDAADELIRRYMPLVHYHVQRISVG-----LPKSVSKDDLKSLGML 61
Query: 85 GLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTTANQKRLFFN 138
GL A++KFDP R + TY+ + I+ A+ ++++ RS K K++
Sbjct: 62 GLYDALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDWLPRS-MREKT------KKVEAA 114
Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV------------ISMNCRLAG-DES 185
+ +L+ N+ P++V A +L ++E EV +S++ + D+
Sbjct: 115 IEKLEQRYM----RNVTPKEV---AAELGMTEEEVEATMNEGFFANLLSIDEKTHDQDDG 167
Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
N + D + ++ L+ ++ LIE+ L + L+ +E+ +
Sbjct: 168 ENVSVTIRDDKTPTPEEKLL------KEELIEE---------LAEKIKQLSEKEQLVISL 212
Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
+E +TL + +S R+ QI ++A K+++ ++K
Sbjct: 213 FYKEE--LTLTEIGQVLNLSTSRISQIHSKALFKLKKLLEK 251
|
Length = 251 |
| >gnl|CDD|180137 PRK05572, PRK05572, sporulation sigma factor SigF; Validated | Back alignment and domain information |
|---|
Score = 40.0 bits (94), Expect = 8e-04
Identities = 65/262 (24%), Positives = 119/262 (45%), Gaps = 41/262 (15%)
Query: 37 LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
L K+ ++ GD A LV +LRLV + + G ++ G IGL++AV KFD
Sbjct: 22 LIKKSQD-GDQEARDTLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLS 80
Query: 97 RGFRLATYSMWWIKAAMQEYILRSWSLVK----IGTTANQKRLFFNLRRLKGHLQAITDN 152
+ +TY++ I +Q + LR VK + TAN+ +R+ K L
Sbjct: 81 YDVKFSTYAVPMIIGEIQRF-LRDDGTVKVSRSLKETANK------IRKDKDELSKE--L 131
Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
+P + +A+ L V+ EV+ LA + S S Q V+++DG
Sbjct: 132 GREP-TIEELAEYLGVTPEEVV-----LAQEAS----------RSPQSIHETVHENDGDP 175
Query: 213 QVLIEK-----EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
L+++ EE + L ++ L+ RER I R ++ T ++ +S+
Sbjct: 176 ITLLDQIADQSEEDWFDKIALKEAIRELDERERLIVYLRYFKDK--TQSEVAKRLGISQV 233
Query: 268 RVRQIEARAFKKVQESIQKQVE 289
+V ++E KK+ + ++++++
Sbjct: 234 QVSRLE----KKILKQMKEKLD 251
|
Length = 252 |
| >gnl|CDD|180784 PRK06986, fliA, flagellar biosynthesis sigma factor; Validated | Back alignment and domain information |
|---|
Score = 38.7 bits (91), Expect = 0.002
Identities = 62/251 (24%), Positives = 108/251 (43%), Gaps = 40/251 (15%)
Query: 51 HRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
LV + LV +IA+ + LP S +++ G IGL++A +++D E+G TY+
Sbjct: 11 DELVEQYAPLVKRIALRLKAR-LPASVDLDDLIQAGMIGLLEAARRYDGEQGASFETYAG 69
Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-AITDNNLKPEQVVAIAKK 165
I+ AM + LRS V N + + +R+L+ L TD +A+K
Sbjct: 70 QRIRGAMLDE-LRSLDWVPRSVRRNAREVAQAIRQLEQELGREPTDTE--------VAEK 120
Query: 166 LNVSESEVISMNCRLAGDESLNALINSS----DKNSSQWQDWLVYDHDGQEQVLIEKEER 221
L +S E M L S D+ + D ++ D Q++ +++ E
Sbjct: 121 LGLSLEEYREM---------LLDTNISQLFSIDELRGEHGDSILVTEDHQDEDPLQQLED 171
Query: 222 KNRRNMLTRSMSVLNPRERRI-----FEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
+ R L ++ L RE+ + E L+E L VS RV QI ++A
Sbjct: 172 EELREALVEAIESLPEREQLVLSLYYQEELNLKEIGAVL-------GVSESRVSQIHSQA 224
Query: 277 FKKVQESIQKQ 287
K+++ + +
Sbjct: 225 IKRLRARLGEW 235
|
Length = 236 |
| >gnl|CDD|135656 PRK05911, PRK05911, RNA polymerase sigma factor sigma-28; Reviewed | Back alignment and domain information |
|---|
Score = 38.4 bits (89), Expect = 0.002
Identities = 55/251 (21%), Positives = 111/251 (44%), Gaps = 44/251 (17%)
Query: 53 LVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
L+ +L LV +A G+P ++ + G GL++AV++FDPE+ R Y+++
Sbjct: 28 LIEFYLPLVKNVAHRLIS-GMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYALFL 86
Query: 109 IKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
IKAA+ + + + W + AN +L + ++ + K + + LN
Sbjct: 87 IKAAIIDDLRKQDWVPRSVHQKAN---------KLADAMDSLRQSLGKEPTDGELCEYLN 137
Query: 168 VSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG-----QEQVLIEKEE 220
+S+ E+ + R A SLN +++ D +E++ E+ E
Sbjct: 138 ISQQELSGWFSSARPALILSLN-------------EEFPCQSDDEAGLALEERIADERAE 184
Query: 221 -------RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
+K ++L ++ L +ER++ +E + L+ + VS RV QI
Sbjct: 185 TGYDVVDKKEFSSILAEAILALEEKERKVMALYYYEE--LVLKEIGKILGVSESRVSQIH 242
Query: 274 ARAFKKVQESI 284
++A K++ ++
Sbjct: 243 SKALLKLRATL 253
|
Length = 257 |
| >gnl|CDD|181701 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated | Back alignment and domain information |
|---|
Score = 96.6 bits (241), Expect = 8e-21
Identities = 46/94 (48%), Positives = 65/94 (69%), Gaps = 1/94 (1%)
Query: 19 YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
Y+ EI ++P+L +EE LAKR E GD A RL ++LRLVV IA Y G G+ ++
Sbjct: 101 YLKEIGRVPLLTAEEEIELAKRI-EEGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDL 159
Query: 79 VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
+ EGN+GLM+AV+KFD +GF+ +TY+ WWI+ A
Sbjct: 160 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQA 193
|
Length = 367 |
| >gnl|CDD|180310 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Score = 79.3 bits (196), Expect = 1e-15
Identities = 40/120 (33%), Positives = 62/120 (51%), Gaps = 26/120 (21%)
Query: 19 YIHEIRKIPMLEKQEEYVLAKR----------YREHGDLSAAHR---------------- 52
Y+ +I K+ +L +EE LAKR E L R
Sbjct: 216 YLKQIGKVKLLNAEEEVELAKRIEAGLYAEELLAEGEKLDPELRRDLQWIGRDGKRAKNH 275
Query: 53 LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
L+ ++LRLVV +A Y GL +++ EGN+GL++AV+KFD +G++ +TY+ WWI+ A
Sbjct: 276 LLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQA 335
|
Length = 509 |
| >gnl|CDD|180964 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated | Back alignment and domain information |
|---|
Score = 71.7 bits (176), Expect = 2e-13
Identities = 34/97 (35%), Positives = 54/97 (55%)
Query: 21 HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
E E + + R R A ++V S+LRLVV IA Y GL +++
Sbjct: 109 REPSDKEWAELVDMPLPKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQ 168
Query: 81 EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
EG++GL++A +KFD E+G++ +TY+ WWI+ A+ I
Sbjct: 169 EGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAI 205
|
Length = 373 |
| >gnl|CDD|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; Validated | Back alignment and domain information |
|---|
Score = 63.6 bits (155), Expect = 5e-11
Identities = 36/138 (26%), Positives = 63/138 (45%), Gaps = 39/138 (28%)
Query: 19 YIHEIRKIPMLEKQEEYVLAKRYREHGDLS------------------------------ 48
Y+ EI ++P+L +EE + K+ + L
Sbjct: 13 YLREIGRVPLLTHEEEILYGKQVQRLVALQEIREELAEELGREPTDAEWAKAAKLSEEEL 72
Query: 49 ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
A ++V ++LRLVV +A Y + + +++ EG IG+ + V+KFDP +G+
Sbjct: 73 RSAIAEGEAAKRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGY 132
Query: 100 RLATYSMWWIKAAMQEYI 117
R +TY+ WWI+ A+ I
Sbjct: 133 RFSTYAYWWIRQAITRAI 150
|
Length = 317 |
| >gnl|CDD|131882 TIGR02835, spore_sigmaE, RNA polymerase sigma-E factor | Back alignment and domain information |
|---|
Score = 63.3 bits (154), Expect = 7e-11
Identities = 37/100 (37%), Positives = 57/100 (57%), Gaps = 2/100 (2%)
Query: 21 HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
E P+ ++EE +L K GD SA L+ +LRLVV IA + G+ I ++VS
Sbjct: 27 SEALPPPLTGEEEEALLQKL--TQGDESAKSTLIERNLRLVVYIARKFENTGIGIEDLVS 84
Query: 81 EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
G IGL++AV F+P + +LATY+ I+ + Y+ R+
Sbjct: 85 IGTIGLIKAVNTFNPSKKIKLATYASRCIENEILMYLRRN 124
|
Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active. Length = 234 |
| >gnl|CDD|181367 PRK08301, PRK08301, sporulation sigma factor SigE; Reviewed | Back alignment and domain information |
|---|
Score = 62.6 bits (153), Expect = 1e-10
Identities = 32/78 (41%), Positives = 47/78 (60%), Gaps = 1/78 (1%)
Query: 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
P L K+EE L + GD + L+ +LRLVV IA + G+ I +++S G IGL
Sbjct: 32 PPLSKEEEEYLLNKL-PKGDEAVRSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 90
Query: 87 MQAVKKFDPERGFRLATY 104
++AV F+PE+ +LATY
Sbjct: 91 IKAVNTFNPEKKIKLATY 108
|
Length = 234 |
| >gnl|CDD|131893 TIGR02846, spore_sigmaK, RNA polymerase sigma-K factor | Back alignment and domain information |
|---|
Score = 60.1 bits (146), Expect = 6e-10
Identities = 31/79 (39%), Positives = 50/79 (63%), Gaps = 2/79 (2%)
Query: 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
P+ E++E+ L R +E GD A + L+ +LRLV I + G + +++S G IGL
Sbjct: 29 PLSEEEEKKYL-DRLKE-GDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGL 86
Query: 87 MQAVKKFDPERGFRLATYS 105
++A+ FDP++G RLATY+
Sbjct: 87 IKAIDSFDPDKGTRLATYA 105
|
The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K. Length = 227 |
| >gnl|CDD|180266 PRK05803, PRK05803, sporulation sigma factor SigK; Reviewed | Back alignment and domain information |
|---|
Score = 60.0 bits (146), Expect = 7e-10
Identities = 28/78 (35%), Positives = 47/78 (60%), Gaps = 2/78 (2%)
Query: 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
P+ E++E L + +E GD A + L+ +LRLV I + G + +++S G IGL
Sbjct: 30 PLSEEEERKYL-ELMKE-GDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGL 87
Query: 87 MQAVKKFDPERGFRLATY 104
++A++ FD +G +LATY
Sbjct: 88 IKAIESFDAGKGTKLATY 105
|
Length = 233 |
| >gnl|CDD|163078 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70 family | Back alignment and domain information |
|---|
Score = 47.0 bits (112), Expect = 7e-06
Identities = 17/70 (24%), Positives = 33/70 (47%), Gaps = 2/70 (2%)
Query: 48 SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
A L +L L+ + A Y G ++V E + L++A+ +FDPE F+ +
Sbjct: 1 EAFEELYERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPEGSFK--AWLFR 58
Query: 108 WIKAAMQEYI 117
+ + +Y+
Sbjct: 59 IARNLILDYL 68
|
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. Length = 158 |
| >gnl|CDD|146937 pfam04542, Sigma70_r2, Sigma-70 region 2 | Back alignment and domain information |
|---|
Score = 74.9 bits (185), Expect = 2e-14
Identities = 25/69 (36%), Positives = 41/69 (59%)
Query: 53 LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
LV +L LV +A Y G G ++V EG +GL++AV++FDPERG +T+ I+ A
Sbjct: 1 LVERYLPLVYSLARRYLGDGADAEDLVQEGFLGLLRAVERFDPERGVSFSTWLYTIIRNA 60
Query: 113 MQEYILRSW 121
+ + + +
Sbjct: 61 IIDALRKQR 69
|
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. Length = 71 |
| >gnl|CDD|180186 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated | Back alignment and domain information |
|---|
Score = 70.2 bits (173), Expect = 5e-13
Identities = 32/69 (46%), Positives = 46/69 (66%), Gaps = 4/69 (5%)
Query: 52 RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
+V ++LRLV+ IA Y GL +++ EGNIGLM+AV KF+ RG++ +TY+ WWI+
Sbjct: 384 EMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQ 443
Query: 112 AMQEYILRS 120
A I RS
Sbjct: 444 A----ITRS 448
|
Length = 619 |
| >gnl|CDD|146939 pfam04545, Sigma70_r4, Sigma-70, region 4 | Back alignment and domain information |
|---|
Score = 50.5 bits (122), Expect = 5e-07
Identities = 21/51 (41%), Positives = 32/51 (62%), Gaps = 2/51 (3%)
Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
++ L PRER + R + +TLE + +SRERVRQIE RA +K+++
Sbjct: 2 LASLPPREREVLVLRFGEG--LTLEEIGERLGISRERVRQIEKRALRKLRK 50
|
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. Length = 50 |
| >gnl|CDD|100119 cd06171, Sigma70_r4, 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) | Back alignment and domain information |
|---|
Score = 47.1 bits (113), Expect = 5e-06
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 2/57 (3%)
Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
R L ++ L RER + R + ++ E ++ +SR VRQ RA KK++
Sbjct: 1 RERLEEALDKLPEREREVILLRFGEG--LSYEEIAEILGISRSTVRQRLHRALKKLR 55
|
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).. Length = 55 |
| >gnl|CDD|180186 PRK05658, PRK05658, RNA polymerase sigma factor RpoD; Validated | Back alignment and domain information |
|---|
Score = 42.5 bits (101), Expect = 1e-04
Identities = 23/59 (38%), Positives = 36/59 (61%), Gaps = 2/59 (3%)
Query: 223 NRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKK 279
+ R T ++ L PRE ++ R + N TLE + +F+V+RER+RQIEA+A +K
Sbjct: 545 SLREATTDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 603
|
Length = 619 |
| >gnl|CDD|180964 PRK07406, PRK07406, RNA polymerase sigma factor RpoD; Validated | Back alignment and domain information |
|---|
Score = 42.1 bits (99), Expect = 2e-04
Identities = 22/51 (43%), Positives = 31/51 (60%), Gaps = 10/51 (19%)
Query: 235 LNPRERRIFEAR------RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
L+PRER + R R++ TLE + F V+RER+RQIEA+A +K
Sbjct: 312 LSPRERDVLRLRYGLDDGRMK----TLEEIGQIFNVTRERIRQIEAKALRK 358
|
Length = 373 |
| >gnl|CDD|163078 TIGR02937, sigma70-ECF, RNA polymerase sigma factor, sigma-70 family | Back alignment and domain information |
|---|
Score = 41.6 bits (98), Expect = 2e-04
Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
E+ E++ R L ++ L RER + R L+ ++ + ++ +S V++ RA
Sbjct: 93 EELEQEEEREALREALEKLPEREREVLVLRYLEG--LSYKEIAEILGISVGTVKRRLKRA 150
Query: 277 FKKVQESI 284
KK++E +
Sbjct: 151 RKKLRELL 158
|
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. Length = 158 |
| >gnl|CDD|181701 PRK09210, PRK09210, RNA polymerase sigma factor RpoD; Validated | Back alignment and domain information |
|---|
Score = 41.1 bits (97), Expect = 3e-04
Identities = 15/26 (57%), Positives = 20/26 (76%)
Query: 254 TLENLSSEFEVSRERVRQIEARAFKK 279
TLE + F V+RER+RQIEA+A +K
Sbjct: 327 TLEEVGKVFGVTRERIRQIEAKALRK 352
|
Length = 367 |
| >gnl|CDD|180310 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Score = 41.1 bits (97), Expect = 3e-04
Identities = 14/37 (37%), Positives = 25/37 (67%)
Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
P TL+ + + V+RER+RQIE++ +K++ + QV
Sbjct: 467 PKTLDEIGQVYGVTRERIRQIESKTLRKLRHPSRSQV 503
|
Length = 509 |
| >gnl|CDD|180963 PRK07405, PRK07405, RNA polymerase sigma factor SigD; Validated | Back alignment and domain information |
|---|
Score = 38.2 bits (89), Expect = 0.003
Identities = 21/61 (34%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
+ L R M L P+++ + R E+ P+TL + +SRERVRQIE A K+++
Sbjct: 247 QLDLERLMEDLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRK 306
Query: 283 S 283
Sbjct: 307 R 307
|
Length = 317 |
Conserved Domains in CDD Database Detected by HHsearch
Original result of HHsearch against CDD database
| Identity | Alignment graph | Length | Definition | Probability |
| Target | 302 | RNA polymerase factor sigma-32 [Candidatus Liberibacter | ||
| TIGR02997 | 336 | Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacte | 100.0 | |
| PRK06596 | 284 | RNA polymerase factor sigma-32; Reviewed | 100.0 | |
| TIGR02392 | 279 | rpoH_proteo alternative sigma factor RpoH; InterPro: IP | 100.0 | |
| TIGR02394 | 292 | rpoS_proteo RNA polymerase sigma factor RpoS; InterPro: | 100.0 | |
| PRK05657 | 328 | RNA polymerase sigma factor RpoS; Validated | 100.0 | |
| PRK07500 | 289 | rpoH2 RNA polymerase factor sigma-32; Reviewed | 100.0 | |
| PRK09210 | 368 | RNA polymerase sigma factor RpoD; Validated | 100.0 | |
| PRK07921 | 320 | RNA polymerase sigma factor SigB; Reviewed | 100.0 | |
| PRK07405 | 318 | RNA polymerase sigma factor SigD; Validated | 100.0 | |
| PRK05901 | 398 | RNA polymerase sigma factor; Provisional | 100.0 | |
| PRK05949 | 327 | RNA polymerase sigma factor; Validated | 100.0 | |
| PRK07406 | 385 | RNA polymerase sigma factor RpoD; Validated | 100.0 | |
| PRK07598 | 410 | RNA polymerase sigma factor SigC; Validated | 100.0 | |
| PRK05658 | 620 | RNA polymerase sigma factor RpoD; Validated | 100.0 | |
| COG0568 | 342 | RpoD DNA-directed RNA polymerase, sigma subunit (sigma7 | 100.0 | |
| PRK08215 | 257 | sporulation sigma factor SigG; Reviewed | 100.0 | |
| PRK08583 | 257 | RNA polymerase sigma factor SigB; Validated | 100.0 | |
| PRK07408 | 256 | RNA polymerase sigma factor SigF; Reviewed | 100.0 | |
| PRK05572 | 251 | sporulation sigma factor SigF; Validated | 100.0 | |
| PRK06288 | 261 | RNA polymerase sigma factor WhiG; Reviewed | 100.0 | |
| PRK07122 | 263 | RNA polymerase sigma factor SigF; Reviewed | 100.0 | |
| PRK05911 | 257 | RNA polymerase sigma factor sigma-28; Reviewed | 100.0 | |
| PRK07670 | 250 | RNA polymerase sigma factor SigD; Validated | 100.0 | |
| PRK05803 | 228 | sporulation sigma factor SigK; Reviewed | 100.0 | |
| PRK08301 | 239 | sporulation sigma factor SigE; Reviewed | 100.0 | |
| TIGR02885 | 231 | spore_sigF RNA polymerase sigma-F factor; InterPro: IPR | 100.0 | |
| COG1191 | 247 | FliA DNA-directed RNA polymerase specialized sigma subu | 100.0 | |
| TIGR02941 | 256 | Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014 | 100.0 | |
| TIGR02846 | 228 | spore_sigmaK RNA polymerase sigma-K factor; InterPro: I | 100.0 | |
| TIGR02850 | 254 | spore_sigG RNA polymerase sigma-G factor; InterPro: IPR | 100.0 | |
| TIGR02835 | 234 | spore_sigmaE RNA polymerase sigma-E factor; InterPro: I | 99.97 | |
| PRK08295 | 209 | RNA polymerase factor sigma-70; Validated | 99.97 | |
| PRK11922 | 231 | RNA polymerase sigma factor; Provisional | 99.8 | |
| PRK12531 | 194 | RNA polymerase sigma factor; Provisional | 99.8 | |
| PRK12534 | 187 | RNA polymerase sigma factor; Provisional | 99.79 | |
| PRK12519 | 194 | RNA polymerase sigma factor; Provisional | 99.78 | |
| PRK09652 | 192 | RNA polymerase sigma factor RpoE; Provisional | 99.78 | |
| PRK11923 | 193 | algU RNA polymerase sigma factor AlgU; Provisional | 99.78 | |
| PRK09641 | 187 | RNA polymerase sigma factor SigW; Provisional | 99.78 | |
| PRK12513 | 194 | RNA polymerase sigma factor; Provisional | 99.77 | |
| PRK09646 | 194 | RNA polymerase sigma factor SigK; Reviewed | 99.77 | |
| PRK13919 | 187 | putative RNA polymerase sigma E protein; Provisional | 99.77 | |
| PRK06811 | 185 | RNA polymerase factor sigma-70; Validated | 99.76 | |
| PRK09648 | 187 | RNA polymerase sigma factor SigD; Reviewed | 99.76 | |
| PRK05602 | 186 | RNA polymerase sigma factor; Reviewed | 99.75 | |
| PRK12543 | 190 | RNA polymerase sigma factor; Provisional | 99.73 | |
| PRK11924 | 180 | RNA polymerase sigma factor; Provisional | 99.73 | |
| PRK12514 | 179 | RNA polymerase sigma factor; Provisional | 99.73 | |
| PRK12526 | 206 | RNA polymerase sigma factor; Provisional | 99.73 | |
| PRK12524 | 196 | RNA polymerase sigma factor; Provisional | 99.72 | |
| PRK12515 | 189 | RNA polymerase sigma factor; Provisional | 99.72 | |
| PRK12537 | 184 | RNA polymerase sigma factor; Provisional | 99.71 | |
| PRK12538 | 233 | RNA polymerase sigma factor; Provisional | 99.71 | |
| PRK09643 | 197 | RNA polymerase sigma factor SigM; Reviewed | 99.71 | |
| PRK09638 | 177 | RNA polymerase sigma factor SigY; Reviewed | 99.7 | |
| PRK12512 | 184 | RNA polymerase sigma factor; Provisional | 99.7 | |
| PRK09647 | 222 | RNA polymerase sigma factor SigE; Reviewed | 99.68 | |
| PRK12539 | 184 | RNA polymerase sigma factor; Provisional | 99.64 | |
| PRK09415 | 177 | RNA polymerase factor sigma C; Reviewed | 99.64 | |
| PRK12518 | 175 | RNA polymerase sigma factor; Provisional | 99.64 | |
| PRK09640 | 188 | RNA polymerase sigma factor SigX; Reviewed | 99.63 | |
| PRK12536 | 178 | RNA polymerase sigma factor; Provisional | 99.62 | |
| TIGR02859 | 198 | spore_sigH RNA polymerase sigma-H factor; InterPro: IPR | 99.59 | |
| PRK12535 | 195 | RNA polymerase sigma factor; Provisional | 99.56 | |
| PRK09649 | 185 | RNA polymerase sigma factor SigC; Reviewed | 99.55 | |
| pfam07638 | 185 | Sigma70_ECF ECF sigma factor. These proteins are probab | 99.54 | |
| TIGR02948 | 187 | SigW_bacill RNA polymerase sigma-W factor; InterPro: IP | 99.32 | |
| TIGR02952 | 171 | Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 f | 99.25 | |
| PRK08241 | 341 | RNA polymerase factor sigma-70; Validated | 99.13 | |
| TIGR02954 | 173 | Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 f | 99.0 | |
| TIGR02999 | 194 | Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family | 98.72 | |
| TIGR02939 | 192 | RpoE_Sigma70 RNA polymerase sigma factor RpoE; InterPro | 98.55 | |
| TIGR02947 | 193 | SigH_actino RNA polymerase sigma-70 factor, TIGR02947 f | 90.59 | |
| TIGR02393 | 240 | RpoD_Cterm RNA polymerase sigma factor RpoD; InterPro: | 100.0 | |
| TIGR02980 | 229 | SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subf | 100.0 | |
| PRK06986 | 234 | fliA flagellar biosynthesis sigma factor; Validated | 100.0 | |
| PRK12427 | 229 | flagellar biosynthesis sigma factor; Provisional | 100.0 | |
| TIGR02479 | 227 | FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family | 100.0 | |
| PRK06759 | 154 | RNA polymerase factor sigma-70; Validated | 99.93 | |
| TIGR02937 | 162 | sigma70-ECF RNA polymerase sigma factor, sigma-70 famil | 99.92 | |
| PRK12542 | 185 | RNA polymerase sigma factor; Provisional | 99.67 | |
| PRK12544 | 207 | RNA polymerase sigma factor; Provisional | 99.59 | |
| PRK12522 | 173 | RNA polymerase sigma factor; Provisional | 99.57 | |
| PRK12520 | 191 | RNA polymerase sigma factor; Provisional | 99.56 | |
| PRK12532 | 195 | RNA polymerase sigma factor; Provisional | 99.56 | |
| PRK12533 | 217 | RNA polymerase sigma factor; Provisional | 99.56 | |
| TIGR02984 | 190 | Sig-70_plancto1 RNA polymerase sigma-70 factor, Plancto | 99.55 | |
| PRK12545 | 201 | RNA polymerase sigma factor; Provisional | 99.54 | |
| PRK09645 | 171 | RNA polymerase sigma factor SigL; Provisional | 99.51 | |
| PRK12517 | 188 | RNA polymerase sigma factor; Provisional | 99.5 | |
| PRK09637 | 181 | RNA polymerase sigma factor SigZ; Provisional | 99.47 | |
| PRK12516 | 190 | RNA polymerase sigma factor; Provisional | 99.47 | |
| PRK09644 | 165 | RNA polymerase sigma factor SigM; Provisional | 99.46 | |
| PRK12541 | 161 | RNA polymerase sigma factor; Provisional | 99.46 | |
| COG1595 | 182 | RpoE DNA-directed RNA polymerase specialized sigma subu | 99.45 | |
| PRK09642 | 160 | RNA polymerase sigma factor SigW; Reviewed | 99.44 | |
| PRK12530 | 191 | RNA polymerase sigma factor; Provisional | 99.43 | |
| PRK12546 | 188 | RNA polymerase sigma factor; Provisional | 99.43 | |
| PRK07037 | 183 | extracytoplasmic-function sigma-70 factor; Validated | 99.41 | |
| PRK12547 | 164 | RNA polymerase sigma factor; Provisional | 99.39 | |
| PRK09639 | 166 | RNA polymerase sigma factor SigX; Provisional | 99.39 | |
| PRK09651 | 172 | RNA polymerase sigma factor FecI; Provisional | 99.37 | |
| PRK12540 | 181 | RNA polymerase sigma factor; Provisional | 99.31 | |
| TIGR02985 | 167 | Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bactero | 99.25 | |
| PRK12523 | 172 | RNA polymerase sigma factor; Reviewed | 99.24 | |
| PRK12511 | 182 | RNA polymerase sigma factor; Provisional | 99.23 | |
| PRK12528 | 167 | RNA polymerase sigma factor; Provisional | 99.07 | |
| PRK12525 | 168 | RNA polymerase sigma factor; Provisional | 99.02 | |
| PRK12529 | 178 | RNA polymerase sigma factor; Provisional | 98.94 | |
| PRK09636 | 289 | RNA polymerase sigma factor SigJ; Provisional | 98.78 | |
| TIGR02989 | 163 | Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirell | 98.69 | |
| PRK09635 | 290 | sigI RNA polymerase sigma factor SigI; Provisional | 98.5 | |
| TIGR02983 | 165 | SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E | 98.41 | |
| TIGR02957 | 287 | SigX4 RNA polymerase sigma-70 factor, TIGR02957 family; | 98.1 | |
| PRK09191 | 261 | two-component response regulator; Provisional | 94.07 | |
| PRK08311 | 237 | putative RNA polymerase sigma factor SigI; Reviewed | 99.69 | |
| pfam04542 | 71 | Sigma70_r2 Sigma-70 region 2. Region 2 of sigma-70 is t | 99.11 | |
| TIGR02895 | 225 | spore_sigI RNA polymerase sigma-I factor; InterPro: IPR | 98.56 | |
| PRK09047 | 161 | RNA polymerase factor sigma-70; Validated | 99.42 | |
| PRK12527 | 159 | RNA polymerase sigma factor; Reviewed | 99.27 | |
| pfam04545 | 50 | Sigma70_r4 Sigma-70, region 4. Region 4 of sigma-70 lik | 98.99 | |
| cd06171 | 55 | Sigma70_r4 Sigma70, region (SR) 4 refers to the most C- | 98.76 | |
| PRK06930 | 170 | positive control sigma-like factor; Validated | 98.46 | |
| TIGR03001 | 249 | Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcale | 98.37 | |
| pfam08281 | 54 | Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 l | 98.15 | |
| TIGR02233 | 106 | Myxo_sigma_rel Myxococcus probable DNA-binding regulato | 97.96 | |
| PRK00118 | 105 | putative DNA-binding protein; Validated | 97.74 | |
| PRK03975 | 139 | tfx putative transcriptional regulator; Provisional | 97.71 | |
| pfam04297 | 101 | UPF0122 Putative helix-turn-helix protein, YlxM / p13 l | 97.7 | |
| TIGR02959 | 170 | SigZ RNA polymerase sigma factor, SigZ family; InterPro | 97.48 | |
| TIGR00721 | 142 | tfx DNA-binding protein, Tfx family; InterPro: IPR00464 | 97.45 | |
| TIGR02960 | 329 | SigX5 RNA polymerase sigma-70 factor, TIGR02960 family; | 97.38 | |
| TIGR02950 | 162 | SigM_subfam RNA polymerase sigma factor, SigM family; I | 97.28 | |
| PRK09958 | 204 | DNA-binding transcriptional activator EvgA; Provisional | 97.18 | |
| pfam00196 | 58 | GerE Bacterial regulatory proteins, luxR family. | 97.12 | |
| COG3413 | 215 | Predicted DNA binding protein [General function predict | 97.08 | |
| PRK09483 | 216 | response regulator; Provisional | 96.95 | |
| smart00421 | 58 | HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (ac | 96.92 | |
| PRK10840 | 216 | transcriptional regulator RcsB; Provisional | 96.9 | |
| PRK10403 | 215 | transcriptional regulator NarP; Provisional | 96.84 | |
| PRK12469 | 475 | RNA polymerase factor sigma-54; Provisional | 96.82 | |
| PRK10651 | 216 | transcriptional regulator NarL; Provisional | 96.82 | |
| PRK09935 | 210 | transcriptional regulator FimZ; Provisional | 96.81 | |
| cd06170 | 57 | LuxR_C_like C-terminal DNA-binding domain of LuxR-like | 96.8 | |
| pfam07374 | 100 | DUF1492 Protein of unknown function (DUF1492). This fam | 96.79 | |
| TIGR03020 | 247 | EpsA transcriptional regulator EpsA. Proteins in this f | 96.74 | |
| PRK10360 | 196 | DNA-binding transcriptional activator UhpA; Provisional | 96.74 | |
| PRK10188 | 240 | DNA-binding transcriptional activator SdiA; Provisional | 96.68 | |
| pfam04967 | 53 | HTH_10 HTH DNA binding domain. | 96.67 | |
| PRK11475 | 205 | DNA-binding transcriptional activator BglJ; Provisional | 96.65 | |
| COG2739 | 105 | Uncharacterized protein conserved in bacteria [Function | 96.64 | |
| TIGR03541 | 232 | reg_near_HchA LuxR family transcriptional regulatory, c | 96.62 | |
| PRK09390 | 202 | fixJ response regulator FixJ; Provisional | 96.62 | |
| PRK06704 | 228 | RNA polymerase factor sigma-70; Validated | 96.59 | |
| COG2197 | 211 | CitB Response regulator containing a CheY-like receiver | 96.53 | |
| TIGR01637 | 139 | phage_arpU phage transcriptional regulator, ArpU family | 96.45 | |
| COG4566 | 202 | TtrR Response regulator [Signal transduction mechanisms | 96.33 | |
| pfam02001 | 100 | DUF134 Protein of unknown function DUF134. This family | 96.32 | |
| PRK13870 | 234 | transcriptional regulator TraR; Provisional | 96.28 | |
| COG1356 | 143 | tfx Transcriptional regulator [DNA replication, recombi | 96.24 | |
| PRK10100 | 216 | DNA-binding transcriptional regulator CsgD; Provisional | 96.12 | |
| PRK05932 | 461 | RNA polymerase factor sigma-54; Reviewed | 95.82 | |
| PRK04217 | 110 | hypothetical protein; Provisional | 95.73 | |
| PRK04841 | 903 | transcriptional regulator MalT; Provisional | 95.54 | |
| TIGR03209 | 142 | P21_Cbot clostridium toxin-associated regulator BotR. S | 94.86 | |
| COG1342 | 99 | Predicted DNA-binding proteins [General function predic | 94.83 | |
| COG2771 | 65 | CsgD DNA-binding HTH domain-containing proteins [Transc | 94.64 | |
| PRK13558 | 674 | bacterio-opsin activator; Provisional | 94.28 | |
| COG1508 | 444 | RpoN DNA-directed RNA polymerase specialized sigma subu | 93.81 | |
| pfam05263 | 130 | DUF722 Protein of unknown function (DUF722). This famil | 93.42 | |
| pfam01726 | 65 | LexA_DNA_bind LexA DNA binding domain. This is the DNA | 92.99 | |
| pfam01371 | 88 | Trp_repressor Trp repressor protein. This protein binds | 92.69 | |
| COG3355 | 126 | Predicted transcriptional regulator [Transcription] | 92.46 | |
| PRK01381 | 99 | Trp operon repressor; Provisional | 91.29 | |
| pfam09862 | 113 | DUF2089 Protein of unknown function(DUF2089). This doma | 90.49 | |
| PRK09863 | 585 | putative frv operon regulatory protein; Provisional | 90.3 | |
| pfam00140 | 37 | Sigma70_r1_2 Sigma-70 factor, region 1.2. | 98.07 | |
| PRK09954 | 362 | hypothetical protein; Provisional | 95.95 | |
| pfam04539 | 78 | Sigma70_r3 Sigma-70 region 3. Region 3 forms a discrete | 98.02 | |
| TIGR02612 | 150 | mob_myst_A mobile mystery protein A; InterPro: IPR01343 | 91.71 | |
| PRK05658 | 620 | RNA polymerase sigma factor RpoD; Validated | 97.91 | |
| TIGR02943 | 194 | Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 f | 97.66 | |
| COG2390 | 321 | DeoR Transcriptional regulator, contains sigma factor-r | 95.53 | |
| PRK11564 | 426 | stationary phase inducible protein CsiE; Provisional | 93.12 | |
| smart00419 | 48 | HTH_CRP helix_turn_helix, cAMP Regulatory protein. | 91.47 | |
| cd00092 | 67 | HTH_CRP helix_turn_helix, cAMP Regulatory protein C-ter | 90.29 | |
| COG1510 | 177 | Predicted transcriptional regulators [Transcription] | 93.05 | |
| PRK12423 | 202 | LexA repressor; Provisional | 91.68 | |
| smart00344 | 108 | HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenou | 90.88 | |
| pfam04552 | 160 | Sigma54_DBD Sigma-54, DNA binding domain. This DNA bind | 90.33 |
| >TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=603.79 Aligned_cols=257 Identities=28% Similarity=0.522 Sum_probs=240.0 Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHH----------------H---------------------------------- Q ss_conf 05999999840799999899999999999----------------8---------------------------------- Q gi|254780611|r 14 IGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------E---------------------------------- 43 (302) Q Consensus 14 ~~~~~yl~~i~~~~~Lt~eee~~l~~~~~----------------~---------------------------------- 43 (302) T Consensus 1 D~Vr~YL~eIGRvPLLt~eEEI~LArqVQry~~LLa~r~~~~~~~~~~~l~~~~~~l~~~~g~~ps~~ewA~~~~~~~~~ 80 (336) T TIGR02997 1 DLVRLYLQEIGRVPLLTPEEEIELARQVQRYEALLAVRDKADEKVQMMALEELREELEEQLGREPSKEEWAAALGLSEAE 80 (336) T ss_pred CCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHH T ss_conf 92004445056678987688999989999999998875327889999999988999998508999878999871899889 Q ss_pred -----H--------------------CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC Q ss_conf -----2--------------------859999999994307787565555799998889999998889989862185345 Q gi|254780611|r 44 -----H--------------------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98 (302) Q Consensus 44 -----~--------------------gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG 98 (302) T Consensus 81 l~~~l~G~~aWA~~a~l~leLk~~~r~G~RAK~kMi~ANLRLVVSvAKKYq~RglElLDLIQEG~lGL~RAVEKFDPtrG 160 (336) T TIGR02997 81 LRQRLRGLQAWAEAAQLELELKLVLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRG 160 (336) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCC T ss_conf 99998765788998422589999999789999999876022688999985136883356887634312211233577778 Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCC Q ss_conf 68999757789999998532024600110230035899999999788786624478882467788861898321100000 Q gi|254780611|r 99 FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178 (302) Q Consensus 99 ~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~ 178 (302) T Consensus 161 YKFSTYAYWWIRQ~ITRAIA~qSRTIRLPiH~~E-----KLnkiKK~qReL~q~lGR~Ps~~EiAe~lel~~~qvR~~l~ 235 (336) T TIGR02997 161 YKFSTYAYWWIRQGITRAIANQSRTIRLPIHITE-----KLNKIKKVQRELSQKLGRRPSEAEIAEALELEPEQVRELLQ 235 (336) T ss_pred CCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH T ss_conf 8633012468756889998436883247410766-----66899899899999838897868999883889889999999 Q ss_pred CCCCCCCHHHHC-CCCCCCCCCHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCC Q ss_conf 012234335520-2323453200000123-56870565566666667779999996219999999999982788--8889 Q gi|254780611|r 179 RLAGDESLNALI-NSSDKNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVT 254 (302) Q Consensus 179 ~~~~~~SLd~~i-~~~d~~~~~~~d~l~~-~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~--~~~T 254 (302) T Consensus 236 ~~~~p~SLd~~VrG~--e~dt~LgdLl~d~~~~~P~~~~~----~~~l~~dL~~lL~~L~p~e~~VL~LRfGL~~~~~~T 309 (336) T TIGR02997 236 RARQPVSLDTRVRGD--EEDTELGDLLEDEDGESPEEQVE----QESLRQDLESLLAELTPRERQVLRLRFGLDDGEPLT 309 (336) T ss_pred HHCCCCCCCCCCCCC--CCCCHHHHHCCCCCCCCCHHHHH----HHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCC T ss_conf 707874457732688--85422654326888998278999----999999999988637988999999857899897532 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH Q ss_conf 899999977899999999999999999 Q gi|254780611|r 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281 (302) Q Consensus 255 l~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302) T Consensus 310 L~eiG~~l~lSRERVRQiE~~AL~kLR 336 (336) T TIGR02997 310 LAEIGERLNLSRERVRQIEAKALRKLR 336 (336) T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHCC T ss_conf 789998838836888899999975349 |
|
| >PRK06596 RNA polymerase factor sigma-32; Reviewed | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=541.09 Aligned_cols=273 Identities=50% Similarity=0.800 Sum_probs=251.8 Q ss_pred CCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH Q ss_conf 58740599999984079999989999999999982859999999994307787565555799998889999998889989 Q gi|254780611|r 10 VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89 (302) Q Consensus 10 ~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~A 89 (302) T Consensus 10 ~~~~~sl~~Yl~~i~~~plLt~eeE~~La~r~~~~gd~~A~~~Li~sNLRLVvsiAkky~~~gl~l~DLIQEGniGLikA 89 (284) T PRK06596 10 PSPEGNLDAYIQAVNRIPMLTAEEEYMLAKRLREHGDLEAAKQLVLSHLRFVVHIARGYRGYGLPQADLIQEGNIGLMKA 89 (284) T ss_pred CCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH T ss_conf 99997099999996578999999999999999977899999999998679999999846789999899999989999999 Q ss_pred HHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCC Q ss_conf 86218534568999757789999998532024600110230035899999999788786624478882467788861898 Q gi|254780611|r 90 VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169 (302) Q Consensus 90 i~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis 169 (302) T Consensus 90 vekFDp~kG~rFSTYA~wWIrq~I~r~i~~~~r~Vrip~~~~~rkl~~~lr~~~~~~~~-----~~~~~~~eiA~~l~~~ 164 (284) T PRK06596 90 VKRFDPEVGVRLVSFAVHWIKAEIHEYILRNWRIVKVATTKAQRKLFFNLRKAKKRLGW-----LNPEEVEMIAEELGVS 164 (284) T ss_pred HHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHC-----CCCCCHHHHHHHHCCC T ss_conf 97058998998186799999999999998745613788899999999999999998714-----5986299999997919 Q ss_pred CCCCCCCCCCCC-CCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHC Q ss_conf 321100000012-2343355202323453200000123568705655666666677799999962199999999999827 Q gi|254780611|r 170 ESEVISMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248 (302) Q Consensus 170 ~~~v~~l~~~~~-~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~ 248 (302) T Consensus 165 ~~~v~~~~~~l~~~~~SLd~~~~~~~~~~~~~~d~l~d~~~~~~~~~~~~~~~~~~~~~L~~al~~L~~REr~Il~~Ry~ 244 (284) T PRK06596 165 EEEVREMESRLSGQDASLDAPIDDDDGESGAPQDYLEDKSSDPAAVLEEDNWEDQRRELLADALETLDERSRDIIEARWL 244 (284) T ss_pred HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCC T ss_conf 99999999985379820237888887775424665146789867899999999999999999986099999999999767 Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 888889899999977899999999999999999999974 Q gi|254780611|r 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 249 ~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 245 ~d~~~TL~EIg~~lgiSrERVRQIe~kAL~KLR~~L~~~ 283 (284) T PRK06596 245 DDDKSTLQELAAEYGVSAERIRQIEKNAMKKLKAAIEAA 283 (284) T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 999948999999979799999999999999999998802 |
|
| >TIGR02392 rpoH_proteo alternative sigma factor RpoH; InterPro: IPR012759 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=543.43 Aligned_cols=272 Identities=49% Similarity=0.803 Sum_probs=260.0 Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHC Q ss_conf 05999999840799999899999999999828599999999943077875655557999988899999988899898621 Q gi|254780611|r 14 IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93 (302) Q Consensus 14 ~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kF 93 (302) T Consensus 1 g~L~~Yi~~vn~~P~L~~EEE~~LA~r~r~~~Dl~AA~~Lv~SHLRfVv~iArgY~GYGL~~aDLIQEGNIGLMkAVkRF 80 (279) T TIGR02392 1 GSLDAYIRAVNRIPMLTAEEEQELAKRLREEGDLDAAKKLVLSHLRFVVKIARGYRGYGLPQADLIQEGNIGLMKAVKRF 80 (279) T ss_pred CCHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHC T ss_conf 97788999997178999889999999865423778999874662478755320367777442443422226655334421 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCC Q ss_conf 85345689997577899999985320246001102300358999999997887866244788824677888618983211 Q gi|254780611|r 94 DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173 (302) Q Consensus 94 Dp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v 173 (302) T Consensus 81 dP~~GvRLvSfAvHWIkAeIHEyILrnWRlVKvATTkaQrKLFFNLRk~K~ki~~l~~gw~~~~e~~~~A~~L~V~~~eV 160 (279) T TIGR02392 81 DPERGVRLVSFAVHWIKAEIHEYILRNWRLVKVATTKAQRKLFFNLRKMKKKITRLQDGWLNPEEVEAIAEELGVSEEEV 160 (279) T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCHHHH T ss_conf 78987220478889999998668997555988852776788876588899986310157989899999997638988899 Q ss_pred CCCCCCCCC-CCCHHHHCCCCCCCCC---CHHCCCCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHC Q ss_conf 000000122-3433552023234532---000001235-68705655666666677799999962199999999999827 Q gi|254780611|r 174 ISMNCRLAG-DESLNALINSSDKNSS---QWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248 (302) Q Consensus 174 ~~l~~~~~~-~~SLd~~i~~~d~~~~---~~~d~l~~~-~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~ 248 (302) T Consensus 161 ~eMe~RlsG~D~~L~~~~~~~~~~~~~~~~~~~yL~D~~~~~~~~~l~~~~~~~~~~~~L~~AL~~Ld~RsR~I~~~RwL 240 (279) T TIGR02392 161 LEMESRLSGRDISLNASIDDDEDDGGSDFAPIAYLADKATSDPEATLEEEQWEELQTQKLANALESLDARSRRIIEARWL 240 (279) T ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 88751455377334788765534563114578863047777888999998999999999999988522887999987302 Q ss_pred CCC-CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 888-8898999999778999999999999999999999 Q gi|254780611|r 249 QEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302) Q Consensus 249 ~~~-~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302) T Consensus 241 ~d~~~~TL~~LA~eygvSaERiRQiE~~Am~K~k~~~~ 278 (279) T TIGR02392 241 DDDGKLTLHELAAEYGVSAERIRQIEKNAMKKLKAALA 278 (279) T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC T ss_conf 78899647899988487466799999999999999841 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the proteobacterial clade of sigma factors called RpoH. 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.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0008270 zinc ion binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent, 0009408 response to heat. |
| >TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS; InterPro: IPR012761 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=547.16 Aligned_cols=273 Identities=30% Similarity=0.473 Sum_probs=242.9 Q ss_pred CCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH Q ss_conf 45587405999999840799999899999999999828599999999943077875655557999988899999988899 Q gi|254780611|r 8 IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87 (302) Q Consensus 8 ~~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi 87 (302) T Consensus 7 ~~~~~~D~~Q~YL~eIg~~PLLt~~EE~~~Arra~-~GD~eAR~~MIE~NLRLVV~IAk~Y~nRGlpLlDLIEEGNLGLm 85 (292) T TIGR02394 7 TETRVADVTQLYLREIGFKPLLTAEEELAYARRAL-AGDFEARKKMIESNLRLVVSIAKHYVNRGLPLLDLIEEGNLGLM 85 (292) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH-CCCHHHHHHHHHHHCHHHHHHHHHCCCCCCHHHHHHHHHHHHHH T ss_conf 22233026888788860155889889999988865-07888988877640126767864404765145777765335665 Q ss_pred HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCC---CCHHHHHHHH Q ss_conf 8986218534568999757789999998532024600110230035899999999788786624478---8824677888 Q gi|254780611|r 88 QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL---KPEQVVAIAK 164 (302) Q Consensus 88 ~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~---~~~~~~eiA~ 164 (302) T Consensus 86 ~AvEKFDPeRGFRFSTYATWWIRQtIERAIMNQaRTiRLPvHV~-kEL-Nv~LRa~r~L~~ns~~~~E~~~EpS~eeiA~ 163 (292) T TIGR02394 86 HAVEKFDPERGFRFSTYATWWIRQTIERAIMNQARTIRLPVHVV-KEL-NVYLRAARQLEKNSAKLDEEEREPSVEEIAE 163 (292) T ss_pred HHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEECCHHHH-HHH-HHHHHHHHHHHHHHHHCCCCCCCCCHHHHHH T ss_conf 42104588999844301113665327865313544110531434-677-7999988876556763373357788789998 Q ss_pred HCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH Q ss_conf 61898321100000012234335520232345320000012356870565566666667779999996219999999999 Q gi|254780611|r 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244 (302) Q Consensus 165 ~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~ 244 (302) T Consensus 164 ~~~kpvedv~~~L~Lne~~~S~D~Pl~~D-~n~~Sl~d~~ADe~~~~P~~~~---~~~~l~~~~~~~L~~Lne~~R~V~~ 239 (292) T TIGR02394 164 LLDKPVEDVSKVLALNERIASLDAPLDED-SNSKSLLDTIADEQSIDPESLV---QNDDLKQLIEAWLAELNERQREVLA 239 (292) T ss_pred HHCCCHHHHHHHHHHCCCCEEEECCCCCC-CCCHHHHHCCCCCCCCCHHHHH---HHHHHHHHHHHHHHHHCHHHHEEHH T ss_conf 83898889999984179952530577877-4301210004788877807642---1899999999988610632112101 Q ss_pred HHHCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 98278--88889899999977899999999999999999999974 Q gi|254780611|r 245 ARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 245 ~ry~~--~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 240 rRFGL~g~E~~TLE~va~~~gLTRERvRQIQ~eaL~~Lr~~L~~~ 284 (292) T TIGR02394 240 RRFGLRGYEKATLEEVAKELGLTRERVRQIQVEALKKLRRILERK 284 (292) T ss_pred HHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 003766542666999998728810478998899999999999864 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry 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 principal sigma factor at that time.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >PRK05657 RNA polymerase sigma factor RpoS; Validated | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=529.99 Aligned_cols=265 Identities=30% Similarity=0.471 Sum_probs=235.2 Q ss_pred CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 74059999998407999998999999999998285999999999430778756555579999888999999888998986 Q gi|254780611|r 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91 (302) Q Consensus 12 ~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~ 91 (302) T Consensus 54 ~~d~~~~YL~eI~~~pLLt~eEE~~La~~~~-~GD~~Ar~~LI~sNLRLVvsIAkkY~~~Gl~l~DLIQEGniGLikAve 132 (328) T PRK05657 54 VLDATQLYLNEIGYSPLLTAEEEVYFARRAL-RGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVE 132 (328) T ss_pred CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 0556999999956789999999999999998-178999999999818999999985568998989999886899999999 Q ss_pred HCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCC Q ss_conf 21853456899975778999999853202460011023003589999999978878662447888246778886189832 Q gi|254780611|r 92 KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171 (302) Q Consensus 92 kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~ 171 (302) T Consensus 133 KFDp~rG~RFSTYA~WWIRq~I~raI~~~~r~IRlP~~~~~-----~l~~i~ra~~~l~~~~gr~pt~eEIA~~lg~~~~ 207 (328) T PRK05657 133 KFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK-----ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVD 207 (328) T ss_pred HCCCCCCCCEEEEEHHHHHHHHHHHHHHCCCCCCCCCHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHH T ss_conf 71976699842300999999999999965777775611999-----9999999999999984899989999999695999 Q ss_pred CCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCC-- Q ss_conf 110000001223433552023234532000001235687056556666666777999999621999999999998278-- Q gi|254780611|r 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-- 249 (302) Q Consensus 172 ~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~-- 249 (302) T Consensus 208 ~v~~~l~~~~~~~SLD~pv~~--d~~~tl~d~l~D~~~~~pd~~~---~~~~l~~~l~~~L~~L~~REr~II~~RfGL~~ 282 (328) T PRK05657 208 DVSRMLALNERITSLDAPLGG--DPEKSLLDILADDQENGPEDTT---QDDDLKQSIVKWLFELNDKQREVIERRFGLNG 282 (328) T ss_pred HHHHHHHHCCCCCCCCCCCCC--CCCCHHHHHHCCCCCCCHHHHH---HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCC T ss_conf 999999745876344453589--9851178886277899999999---99999999999980699999999999808899 Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 88889899999977899999999999999999999974 Q gi|254780611|r 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 250 ~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 283 ~e~~TL~EIg~~lgvSRERVRQIE~~AL~KLR~~l~~~ 320 (328) T PRK05657 283 YEAATLEEVAREIGLTRERVRQIQVEALRRLREILQTQ 320 (328) T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 89605999998969799999999999999987999986 |
|
| >PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=526.68 Aligned_cols=278 Identities=41% Similarity=0.677 Sum_probs=257.6 Q ss_pred CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 74059999998407999998999999999998285999999999430778756555579999888999999888998986 Q gi|254780611|r 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91 (302) Q Consensus 12 ~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~ 91 (302) T Consensus 4 ~~~~~~~y~~~~~~~plLt~eeE~~L~~~~~~~gD~~Ar~~LI~~NLRLV~~iA~ry~~~g~~l~DLIQeG~iGLi~Ave 83 (289) T PRK07500 4 DASADRSMIRSAMKAPYLEREEEHALAYRWKDTRDEDALHRIISAHMRLVISMAGKFRRFGLPMNDLIQEGYVGLLEAAA 83 (289) T ss_pred CCHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 53468999999633799999999999999987779999999999858999999987458998978999986999999997 Q ss_pred HCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCC Q ss_conf 21853456899975778999999853202460011023003589999999978878662447888246778886189832 Q gi|254780611|r 92 KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171 (302) Q Consensus 92 kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~ 171 (302) T Consensus 84 kFDp~rG~rFSTYA~wWIr~aI~r~i~~~~~~iR~p~~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~eiA~~l~~~~~ 163 (289) T PRK07500 84 RFDPDRDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLAQSDEQLTKHEIHREIATALGVSLS 163 (289) T ss_pred CCCCCCCCCEEEHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCHH T ss_conf 36988899721101999999998877736651000038878999999999999999861545655439999988099999 Q ss_pred CCCCCCCCCC-CCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC Q ss_conf 1100000012-234335520232345320000012356870565566666667779999996219999999999982788 Q gi|254780611|r 172 EVISMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250 (302) Q Consensus 172 ~v~~l~~~~~-~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~ 250 (302) T Consensus 164 ~v~~~~~~~~~~~~SL~~~~~~d~~~~~~~~d~l~d~~~~p~~~~e~~~~~~~~~~~L~~~l~~L~eREr~Ii~~r~~~~ 243 (289) T PRK07500 164 DVEMMDARLSGPDSSLNAPQSEEDEGRSERMDFLVDDSPLPDEIVESSIDGERRRQWLTQALQTLNERELFIIRERRLRE 243 (289) T ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC T ss_conf 99999999737986666806787777401555404688983899999999999999999998549999999999976689 Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 888989999997789999999999999999999997401 Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289 (302) Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~~ 289 (302) T Consensus 244 e~~TL~EIg~~lgvSreRVRQIe~kAL~KLR~~L~~~~~ 282 (289) T PRK07500 244 DGATLEALGEELGISKERVRQIEARALEKLRRALLSQSP 282 (289) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCH T ss_conf 985899999997979999999999999999999998477 |
|
| >PRK09210 RNA polymerase sigma factor RpoD; Validated | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=528.39 Aligned_cols=266 Identities=29% Similarity=0.457 Sum_probs=234.7 Q ss_pred CCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 87405999999840799999899999999999828599999999943077875655557999988899999988899898 Q gi|254780611|r 11 NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90 (302) Q Consensus 11 ~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai 90 (302) T Consensus 94 ~~~d~v~~YL~eI~~~pLLt~eEE~~La~r~~-~GD~~Ar~~Li~aNLRLVVsIAkkY~~~Gl~l~DLIQEGNiGLmkAV 172 (368) T PRK09210 94 KINDPVRMYLKEIGRVPLLTAEEEIELAKRIE-EGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAV 172 (368) T ss_pred CCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH T ss_conf 55858999999956788999999999999988-15799999999983899999998666899898999998679999999 Q ss_pred HHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCC Q ss_conf 62185345689997577899999985320246001102300358999999997887866244788824677888618983 Q gi|254780611|r 91 KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170 (302) Q Consensus 91 ~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~ 170 (302) T Consensus 173 eKFDp~rG~RFSTYA~WWIRqaI~raI~~q~r~IRiPvh~~e-----~~~kl~r~~r~L~q~lGrePt~eEIA~~lgi~~ 247 (368) T PRK09210 173 EKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE-----TINKLIRVQRQLLQELGRDPTPEEIAEEMDMPP 247 (368) T ss_pred HHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCH T ss_conf 972987799533466999999999999982785135424999-----999999999999998389998899998949989 Q ss_pred CCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC Q ss_conf 21100000012234335520232345320000012356870565566666667779999996219999999999982788 Q gi|254780611|r 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250 (302) Q Consensus 171 ~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~ 250 (302) T Consensus 248 e~V~~i~~~~~~~~SLd~pvg~e--~~s~l~d~i~D~~~~~p~e---~~~~~~l~~~l~~~L~~L~~REr~Il~~RfGL~ 322 (368) T PRK09210 248 EKVREILKIAQEPVSLETPIGEE--DDSHLGDFIEDQDATSPAD---HAAYELLKEQLEEVLDTLTDREENVLRLRFGLD 322 (368) T ss_pred HHHHHHHHHCCCCCCCCCCCCCC--CCCHHHHHHCCCCCCCHHH---HHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC T ss_conf 99999998538885668867887--7552875524899999899---999999999999998179999999999975999 Q ss_pred --CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf --8889899999977899999999999999999999974 Q gi|254780611|r 251 --NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 251 --~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 323 ~~~~~TLeEIg~~lgvSRERVRQIE~kAL~KLR~~~~~~ 361 (368) T PRK09210 323 DGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361 (368) T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHH T ss_conf 689614999998969798999999999999976736878 |
|
| >PRK07921 RNA polymerase sigma factor SigB; Reviewed | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=520.72 Aligned_cols=272 Identities=24% Similarity=0.402 Sum_probs=238.0 Q ss_pred CCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHC---------------------------CHHHHHHHHHH Q ss_conf 655745587405999999840799999899999999999828---------------------------59999999994 Q gi|254780611|r 4 KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG---------------------------DLSAAHRLVTS 56 (302) Q Consensus 4 ~~~~~~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~g---------------------------d~~Ar~~Li~~ 56 (302) T Consensus 12 ~~~~~~~p~~D~~~~Yl~ei~~~~lLt~eeE~~La~~i~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~A~~~lI~a 90 (320) T PRK07921 12 SDLDAQSPAADLVRVYLNGIGKTALLTAADEVELAKRIEA-GLYAEHLLETRKRLGEARKRDLAAVVRDGEAARRHLLEA 90 (320) T ss_pred HCCCCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHH-HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 4489999898819999997188789899999999999997-377898875111001677889998776069999999998 Q ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHH Q ss_conf 30778756555579999888999999888998986218534568999757789999998532024600110230035899 Q gi|254780611|r 57 HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136 (302) Q Consensus 57 nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~ 136 (302) T Consensus 91 NLRLVvsIAk~Y~~~Gl~~~DLIQEGniGLirAvekFDp~rG~rFSTYA~wWIRq~I~r~i~~~~r~IRlP~~~~~---- 166 (320) T PRK07921 91 NLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVE---- 166 (320) T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH---- T ss_conf 1899999998565899998999998389999888516899998128777999999999999970862147188999---- Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHH Q ss_conf 99999978878662447888246778886189832110000001223433552023234532000001235687056556 Q gi|254780611|r 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216 (302) Q Consensus 137 ~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~ 216 (302) T Consensus 167 -~~~ki~~~~~~l~~~lGR~Pt~eEIA~~lgi~~~~v~~~l~~~~~~~SLD~~vg~--d~~~~l~d~i~D~~~~~~e~~- 242 (320) T PRK07921 167 -QVNKLARIKREMHQHLGREATDEELAEESGIPEEKINDLLEHSRDPVSLDMPVGS--DEEAPLGDFIEDAEAMSAENA- 242 (320) T ss_pred -HHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCC--CCCCCHHHHHHCCCCCCHHHH- T ss_conf -9999999999999983899989999988199999999999972888366776688--875303324405678998999- Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 6666667779999996219999999999982788--888989999997789999999999999999999997 Q gi|254780611|r 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 217 e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~--~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 243 --~~~~~l~~~L~~~L~~L~eREr~IL~~RfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~~~~~ 312 (320) T PRK07921 243 --VIAELLHTDIRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMSKLRHGERA 312 (320) T ss_pred --HHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCHHHH T ss_conf --9999999999999975999999999997489998974799999897969999999999999997072888 |
|
| >PRK07405 RNA polymerase sigma factor SigD; Validated | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=513.91 Aligned_cols=265 Identities=25% Similarity=0.457 Sum_probs=233.9 Q ss_pred CCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH---------------------------------------HCCHHH Q ss_conf 55874059999998407999998999999999998---------------------------------------285999 Q gi|254780611|r 9 IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------------------HGDLSA 49 (302) Q Consensus 9 ~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~---------------------------------------~gd~~A 49 (302) T Consensus 4 ~~~~~d~~~~Yl~ei~~~~LLt~eeE~~la~~i~~~~~~~~~~~~l~~~~~~~~~~~~~a~a~~~~~~~l~~~~~~g~~A 83 (318) T PRK07405 4 AKTATDLVRTYLREIGRVPLLTHEEEILYGKQVQRLMALQEIRESLAEELGREPSDLEWAKAAKLSEEELRRAIAEGEAA 83 (318) T ss_pred CCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHH T ss_conf 87898759999998177679999999999999999988899999999871678746788876045689999987627999 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC Q ss_conf 99999943077875655557999988899999988899898621853456899975778999999853202460011023 Q gi|254780611|r 50 AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129 (302) Q Consensus 50 r~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302) T Consensus 84 ~~~lv~~NLRLVv~iAk~y~~~gl~~~DLIQEGniGLi~AvekFDp~rG~rFSTYA~wWIrq~I~r~i~~~~r~IRlP~~ 163 (318) T PRK07405 84 KRKMVEANLRLVVSVAKKYLKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIH 163 (318) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHHHHHHCCCCCCCCHH T ss_conf 99999981999999998665799798899998689999999970976598022200999999999999976985168778 Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC Q ss_conf 00358999999997887866244788824677888618983211000000122343355202323453200000123568 Q gi|254780611|r 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209 (302) Q Consensus 130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~ 209 (302) T Consensus 164 ~~~-----~~~ki~~~~~~L~~~lGr~Pt~~EIAe~lgi~~e~V~~~l~~~~~~~SLD~~v~d~--~~~~l~dll~D~~~ 236 (318) T PRK07405 164 ITE-----KLNKIKKAQRQLSQQLGRAATIGELAEELELTPKQVREYLERARQPLSLDLRVGDN--QDTELGELLEDDGA 236 (318) T ss_pred HHH-----HHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCC--CCCHHHHHHCCCCC T ss_conf 999-----99999999999998718986489999885999999999999807886768888999--86405667547889 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 7056556666666777999999621999999999998278--88889899999977899999999999999999999 Q gi|254780611|r 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302) Q Consensus 210 ~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~--~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302) T Consensus 237 ~pe~~~~----~~~l~~~L~~~L~~L~eREr~II~lRfGl~~~~~~TL~EIg~~lgvSrERVRQIE~~AL~KLR~~~ 309 (318) T PRK07405 237 SPEDFAT----QSSLRRDLERLMADLTPQQKEVIALRFGLEDGQPLTLAKIGERLNISRERVRQIEREALSKLRKRK 309 (318) T ss_pred CHHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH T ss_conf 8799999----999999999999629998999999980778989747999998979599999999999999998728 |
|
| >PRK05901 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=508.18 Aligned_cols=267 Identities=25% Similarity=0.424 Sum_probs=232.9 Q ss_pred CCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHC------------------CHHHHHHHHHHHHHHHHHHHHHHCCC Q ss_conf 587405999999840799999899999999999828------------------59999999994307787565555799 Q gi|254780611|r 10 VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG------------------DLSAAHRLVTSHLRLVVKIAMGYRGY 71 (302) Q Consensus 10 ~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~g------------------d~~Ar~~Li~~nlrlV~~iA~~y~~~ 71 (302) T Consensus 104 ~~tdd~v~~yl~~~g~~~ll~~~~e~~~a~~~~~-~~~~~~~~~~~~~~~~~~~~~~Ar~~Li~aNLRLVvsIAkkY~~~ 182 (398) T PRK05901 104 TATADPVKAYLKQIGKVKLLNAEEEVELAKRIEA-GLYAEELLEKRDLRWIARDGKRAKNHLLEANLRLVVSLAKRYTNR 182 (398) T ss_pred CCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 8889719999986275548887999999999984-045676676777777530539999999997069999999764689 Q ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHC Q ss_conf 99888999999888998986218534568999757789999998532024600110230035899999999788786624 Q gi|254780611|r 72 GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151 (302) Q Consensus 72 g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~ 151 (302) T Consensus 183 Gl~l~DLIQEGniGLirAvekFDp~rG~rFSTYA~wWIRqaI~rai~~~~r~IRiP~h~~e--~---~~k~~r~~~~l~~ 257 (398) T PRK05901 183 GLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--T---INKLGRIERELLQ 257 (398) T ss_pred CCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHCCCEEECCHHHHH--H---HHHHHHHHHHHHH T ss_conf 9898899998689999999971977799542114999999999999966873523323999--9---9999999999999 Q ss_pred CCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 47888246778886189832110000001223433552023234532000001235687056556666666777999999 Q gi|254780611|r 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231 (302) Q Consensus 152 ~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~ 231 (302) T Consensus 258 ~~gr~Pt~eEiA~~lg~~~~~v~~~~~~~~~~~SLd~~vg~--d~~~~l~d~i~D~~~~~p~~---~~~~~~l~~~l~~~ 332 (398) T PRK05901 258 ELGREPTPEELAEEMDFTPEKVREIQKYAREPISLDKTIGD--EGDSQFGDFIEDSEAVSPVD---AVSFTLLQDQLQEV 332 (398) T ss_pred HHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCC--CCCCCHHHHCCCCCCCCHHH---HHHHHHHHHHHHHH T ss_conf 84899999999988199999999999972898556787789--98651866416999999999---99999999999999 Q ss_pred HHCCCHHHHHHHHHHHCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 621999999999998278--88889899999977899999999999999999999974 Q gi|254780611|r 232 MSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 232 l~~L~~rEr~II~~ry~~--~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 333 L~~L~~REr~Ii~~RyGL~~~~~~TL~eIg~~lgvSrERVRQIE~kAL~KLR~~~~~~ 390 (398) T PRK05901 333 LETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIESKTMRKLRHPSRSQ 390 (398) T ss_pred HCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHH T ss_conf 8389999999999975899989603999998979699999999999999967837887 |
|
| >PRK05949 RNA polymerase sigma factor; Validated | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=508.25 Aligned_cols=264 Identities=24% Similarity=0.451 Sum_probs=231.3 Q ss_pred CCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH---------------------------------------HCCHHH Q ss_conf 55874059999998407999998999999999998---------------------------------------285999 Q gi|254780611|r 9 IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------------------HGDLSA 49 (302) Q Consensus 9 ~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~---------------------------------------~gd~~A 49 (302) T Consensus 13 ~~~~~D~~~~YL~ei~~~pLLt~eeE~~La~~iq~~~~~~~~~~~l~~~~~~~~~~~ewa~~~~~~~~~l~~~~~~g~~A 92 (327) T PRK05949 13 PTFTADMVRTYLHEIGRVPLLTHEQEIVYGKQVQQMMSLLEAKEALAKKLGREPSLPEWADAVNLSETELKQALKQGKRA 92 (327) T ss_pred CCCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf 98998819999998278668899999999999999998899999999983789756889987266789999998758999 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC Q ss_conf 99999943077875655557999988899999988899898621853456899975778999999853202460011023 Q gi|254780611|r 50 AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129 (302) Q Consensus 50 r~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302) T Consensus 93 ~~~LI~sNLRLVvsIAkrY~~~Gl~~~DLIQEGniGLirAvekFDp~rG~RFSTYA~wWIRq~I~r~i~~~~r~IRlP~~ 172 (327) T PRK05949 93 KQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIH 172 (327) T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEHHHHHHHHHHHHHHHCCCCCCCCHH T ss_conf 99999981999999998643699898999998589999999980965597134200999989999999982887446378 Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC Q ss_conf 00358999999997887866244788824677888618983211000000122343355202323453200000123568 Q gi|254780611|r 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209 (302) Q Consensus 130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~ 209 (302) T Consensus 173 ~~~-----~~~ki~~~~~~l~~~lgr~pt~~EiA~~l~i~~~~v~~~l~~~~~~~SLD~~v~d--~~~~~l~dll~d~~~ 245 (327) T PRK05949 173 ITE-----KLNKIKKTQRELSQKLGRSATPAEIAKALELEPSQIREYLSMARQPISLDVRVGD--NQDTELSELLEDEGV 245 (327) T ss_pred HHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCC--CCCCHHHHHHCCCCC T ss_conf 999-----9999999999999981889988999989499999999999841887223674699--974026667336889 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 70565566666667779999996219999999999982788--888989999997789999999999999999999 Q gi|254780611|r 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302) Q Consensus 210 ~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~--~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302) T Consensus 246 ~pe~~~----~~~~lr~~l~~~L~~L~~REr~Ii~~RfGl~~~~~~TL~EIg~~lgiSrERVRQIE~rAL~KLR~~ 317 (327) T PRK05949 246 SPDQYI----TQELLRQDLNNLLAELTPQQREVLTLRFGLEDGKELSLAKVGQRLNLSRERVRQLEHQALAHLRRR 317 (327) T ss_pred CHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC T ss_conf 999999----999999999999856999999999997189996985799999998959999999999999998625 |
|
| >PRK07406 RNA polymerase sigma factor RpoD; Validated | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=509.14 Aligned_cols=265 Identities=28% Similarity=0.463 Sum_probs=232.6 Q ss_pred CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH---------------------------------------HCCHHHHHH Q ss_conf 74059999998407999998999999999998---------------------------------------285999999 Q gi|254780611|r 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------------------HGDLSAAHR 52 (302) Q Consensus 12 ~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~---------------------------------------~gd~~Ar~~ 52 (302) T Consensus 73 t~D~vr~YL~eIg~~~LLt~~eEi~La~~i~~~~~le~~~~~l~~~~~~~p~~~ewa~~~~~~~~~l~~~~~~g~~Ar~~ 152 (385) T PRK07406 73 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLELEELREQFESELGHFPSVEEWAELVDMPLPKFRRRLMLGRRAKEK 152 (385) T ss_pred CCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHH T ss_conf 88849999986277679999999999999999999999999988741665427999988088889999999879999999 Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHH Q ss_conf 99943077875655557999988899999988899898621853456899975778999999853202460011023003 Q gi|254780611|r 53 LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132 (302) Q Consensus 53 Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~ 132 (302) T Consensus 153 LI~aNLRLVVsIAkkY~~rGl~l~DLIQEGniGLirAvEKFDp~rG~RFSTYA~WWIRqaI~RaI~~~sr~IRlP~h~~- 231 (385) T PRK07406 153 MVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLY- 231 (385) T ss_pred HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEHHHHHHHHHHHHHHHHCCCEECCHHHHH- T ss_conf 9999899999999865689989889999858999999998196548822110299999999999997386120208999- Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCH Q ss_conf 58999999997887866244788824677888618983211000000122343355202323453200000123568705 Q gi|254780611|r 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212 (302) Q Consensus 133 r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~ 212 (302) T Consensus 232 ----e~l~ki~k~~~~L~~~lGr~Pt~eEIA~~l~i~~e~v~~~~~~~~~~vSLD~pvg~~~--ds~l~D~i~~d~~~pe 305 (385) T PRK07406 232 ----ETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPIGKEE--DSRLGDFIEADGETPE 305 (385) T ss_pred ----HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCC--CCCHHHHHHCCCCCHH T ss_conf ----9999999999999987089986999999939999999999985489865458888765--3318889863599999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 65566666667779999996219999999999982788--8889899999977899999999999999999999974 Q gi|254780611|r 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 213 ~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~--~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 306 ~~~----~~~~lr~~L~~~L~~L~eREr~II~lRfGL~dg~~~TL~EIg~~lgISRERVRQIE~rAL~KLR~p~r~~ 378 (385) T PRK07406 306 DDV----SKNLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNS 378 (385) T ss_pred HHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHHH T ss_conf 999----9999999999998649999999999975899999646999998979599999999999999967717789 |
|
| >PRK07598 RNA polymerase sigma factor SigC; Validated | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=507.48 Aligned_cols=269 Identities=28% Similarity=0.495 Sum_probs=234.5 Q ss_pred CCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH------------------------------------------- Q ss_conf 7455874059999998407999998999999999998------------------------------------------- Q gi|254780611|r 7 SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------------------- 43 (302) Q Consensus 7 ~~~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~------------------------------------------- 43 (302) T Consensus 48 ~~~~~s~D~vr~YL~eIgrvpLLt~eeEv~la~~ve~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~ 127 (410) T PRK07598 48 SRNRRSTDLVRLYLQEIGRVPLLGRDEEVSEAQKVQRYMKLVVLANAAKEGDEVIKPYLRLIEVRDRLTAELGHRPSLER 127 (410) T ss_pred CCCCCCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHH T ss_conf 77999997199999982877789858999999999999999999876520220245667788899999987356851788 Q ss_pred --------------------------------------HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH Q ss_conf --------------------------------------285999999999430778756555579999888999999888 Q gi|254780611|r 44 --------------------------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85 (302) Q Consensus 44 --------------------------------------~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iG 85 (302) T Consensus 128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~el~~~~~~G~~Ar~kLI~aNLRLVVsIAkkY~~rGl~l~DLIQEGniG 207 (410) T PRK07598 128 WAAIADISLADLKPTLAEGKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLG 207 (410) T ss_pred HHHHCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH T ss_conf 87740331234556655445556664014699999999999999999999989999999986578998989999874899 Q ss_pred HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHH Q ss_conf 99898621853456899975778999999853202460011023003589999999978878662447888246778886 Q gi|254780611|r 86 LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165 (302) Q Consensus 86 Li~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~ 165 (302) T Consensus 208 LirAVEKFDp~rG~RFSTYA~WWIRQaI~RaI~~~~r~IRlP~h~~e-----~l~ki~r~~r~L~q~lGR~Pt~eEIA~~ 282 (410) T PRK07598 208 LERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITE-----KLNKIKKAQRKISQEKGRTPTIEDIAQE 282 (410) T ss_pred HHHHHHHCCCCCCCEEEEEEHHHHHHHHHHHHHHHCCEECCCCHHHH-----HHHHHHHHHHHHHHHCCCCCCHHHHHHH T ss_conf 99999970965597257621899999999999980880204602999-----9999999999999875999979999988 Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH Q ss_conf 18983211000000122343355202323453200000123568705655666666677799999962199999999999 Q gi|254780611|r 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245 (302) Q Consensus 166 Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ 245 (302) T Consensus 283 lg~s~e~V~~~l~~~~~~vSLd~pvg~--d~d~~l~dll~~~~~~pee~~~----~~~l~~~L~~lL~~L~~REr~IL~l 356 (410) T PRK07598 283 LEMTPTQVREVLLRVPRSVSLETKVGK--DKDTELGDLLETDDVSPEEMLM----RESLQRDLQQLLADLTSRERDVIRM 356 (410) T ss_pred CCCCHHHHHHHHHHCCCCCCCCCCCCC--CCCCCHHHHHCCCCCCHHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHH T ss_conf 099999999999872788553678888--8864188874458999899999----9999999999983699999999999 Q ss_pred HHCC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 8278--8888989999997789999999999999999999997 Q gi|254780611|r 246 RRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 246 ry~~--~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 357 RfGL~dg~~~TL~EIG~~lgISRERVRQIE~kAL~KLR~p~r~ 399 (410) T PRK07598 357 RFGLADGRTYSLAEIGRALDLSRERVRQIEAKALQKLRQPKRR 399 (410) T ss_pred HCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCHHH T ss_conf 6489997966899999897969999999999999996773778 |
|
| >PRK05658 RNA polymerase sigma factor RpoD; Validated | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=502.02 Aligned_cols=254 Identities=27% Similarity=0.438 Sum_probs=217.3 Q ss_pred HHCCCCCCHHHHHHHHHHHHHHCC---HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 407999998999999999998285---99999999943077875655557999988899999988899898621853456 Q gi|254780611|r 23 IRKIPMLEKQEEYVLAKRYREHGD---LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99 (302) Q Consensus 23 i~~~~~Lt~eee~~l~~~~~~~gd---~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~ 99 (302) T Consensus 354 ie~~~gl~i~elK~i~r~I~~-Ge~~a~~AKkeMiEANLRLVISIAKKYtNRGLqFLDLIQEGNiGLMkAVdKFeyrrGy 432 (620) T PRK05658 354 IEEETGLTIEELKEINRQISK-GEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 432 (620) T ss_pred HHHHHCCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCHHHHHHHHHCCCCCCC T ss_conf 999849799999999999999-8777899999999861899999999831489987899874407999999862845597 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 89997577899999985320246001102300358999999997887866244788824677888618983211000000 Q gi|254780611|r 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179 (302) Q Consensus 100 ~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~ 179 (302) T Consensus 433 KFSTYATWWIRQAITRaIaDqaRTIRiPVHmi-----etinkl~r~~r~l~qe~Grept~eEia~~~~~~~~kvr~vlki 507 (620) T PRK05658 433 KFSTYATWWIRQAITRSIADQARTIRIPVHMI-----ETINKLNRISRQMLQEMGREPTPEELAERLGMPEDKVRKVLKI 507 (620) T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHH-----HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 13577999999999999986177401518899-----9999999999999998289999999998949899999999986 Q ss_pred CCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCC--CCCHHH Q ss_conf 122343355202323453200000123568705655666666677799999962199999999999827888--889899 Q gi|254780611|r 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLEN 257 (302) Q Consensus 180 ~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~--~~Tl~E 257 (302) T Consensus 508 ~~epiSle~pig~~--~ds~lgdfied~~~~~p~---~~~~~~~l~~~~~~vl~~Lt~rE~~vl~~RfGi~~~~~~TLee 582 (620) T PRK05658 508 AKEPISLETPIGDD--EDSHLGDFIEDKNAELPI---DAATQESLREQTTDVLASLTPREAKVLRMRFGIDMNTDHTLEE 582 (620) T ss_pred CCCCCCCCCCCCCC--CCCCCCCCCCCCCCCCHH---HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHH T ss_conf 48980243887888--876400101689999879---9999999999999998479999999999957999999678999 Q ss_pred HHHHHCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 999977899999999999999999999974 Q gi|254780611|r 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 258 Ia~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 583 vg~~f~vtRERiRQIEakalrklrhp~r~~ 612 (620) T PRK05658 583 VGKQFDVTRERIRQIEAKALRKLRHPSRSR 612 (620) T ss_pred HHHHHCCCHHHHHHHHHHHHHHHCCCCHHH T ss_conf 998829768989999999999856872578 |
|
| >COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription] | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=482.39 Aligned_cols=266 Identities=38% Similarity=0.576 Sum_probs=237.9 Q ss_pred CCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHC-CHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH Q ss_conf 87405999999840799999899999999999828-59999999994307787565555799998889999998889989 Q gi|254780611|r 11 NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG-DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89 (302) Q Consensus 11 ~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~g-d~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~A 89 (302) T Consensus 64 ~~~~~~~~~~~~~~~~~~l~~~Ee~~la~~~~~g~~~~~Ak~klv~snLRlVvsIAk~Y~~rGL~~~DLIQEGniGLmkA 143 (342) T COG0568 64 RPAGRLSFYIRAIEAAPLLTPEEEKALARRLKRGERDLDAKKKLVESNLRLVVSIAKKYTGRGLPFLDLIQEGNIGLMKA 143 (342) T ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCCCHHHHHH T ss_conf 13456889998876400159789999999998588559999999999889999999986337986889885250999999 Q ss_pred HHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCC Q ss_conf 86218534568999757789999998532024600110230035899999999788786624478882467788861898 Q gi|254780611|r 90 VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169 (302) Q Consensus 90 i~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis 169 (302) T Consensus 144 VekFdp~rG~kFsTYA~wWIrqaI~raI~~q~rtIRipvh--~~e~~nkl~r~~r~l~q~---~~r~p~~eeia~~l~~~ 218 (342) T COG0568 144 VEKFDPEKGFKFSTYATWWIRQAITRAIADQARTIRIPVH--QVELINKLRRVKRELLQE---LGREPTPEEIAEELGVS 218 (342) T ss_pred HHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHH--HHHHHHHHHHHHHHHHHH---HCCCCCHHHHHHHHCCC T ss_conf 9962966687211099999999999999974234657699--999999999999999998---45899799999995999 Q ss_pred CCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHHHH Q ss_conf 3211000000122343355202323453200000123568-7056556666666777999999621-9999999999982 Q gi|254780611|r 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARR 247 (302) Q Consensus 170 ~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~-~~~~~~~e~~e~~~~~~~L~~~l~~-L~~rEr~II~~ry 247 (302) T Consensus 219 ~~~V~~m~~~~~~~~SLd~~ig~ded~--~l~d~leD~~~~~p~~~~~~~----~~~~~~~~~L~~~Lt~rE~~Vi~~R~ 292 (342) T COG0568 219 PDKVREMLKRASEPISLDTPIGDDEDS--ELGDFLEDDKSVSPEDAVERE----SLKEDLNEVLAEALTERERRVIRLRF 292 (342) T ss_pred HHHHHHHHHHCCCCCCCCCCCCCCCCC--HHHHHHHCCCCCCHHHHHHHH----HHHHHHHHHHHHCCCHHHHHHHHHHH T ss_conf 999999998653676767848888520--788876426878989999988----89999999987159999999999995 Q ss_pred CC--CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 78--88889899999977899999999999999999999974 Q gi|254780611|r 248 LQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 248 ~~--~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 293 gl~~~~~~TLeevg~~~~vsrERvRQIE~kAl~KLr~~~~~~ 334 (342) T COG0568 293 GLDDGEPKTLEELGEEFGISRERVRQIEAKALRKLRRHPERS 334 (342) T ss_pred CCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 567999551999998959869999999999999998706322 |
|
| >PRK08215 sporulation sigma factor SigG; Reviewed | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=472.71 Aligned_cols=257 Identities=25% Similarity=0.362 Sum_probs=219.7 Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH Q ss_conf 98665574558740599999984079999989999999999982859999999994307787565555799998889999 Q gi|254780611|r 1 MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80 (302) Q Consensus 1 ~~~~~~~~~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQ 80 (302) T Consensus 1 ~~~~~~~~~~~----------~~~k~PlLt~EEe~~L~~~~~-~gD~~Ar~~LI~~nLrLV~~iA~ky~~~g~~~~DLiQ 69 (257) T PRK08215 1 MTRNKVEICGV----------NTSKLPVLKNEEMKELFRRMQ-NGDTSAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQ 69 (257) T ss_pred CCCCEEEEECC----------CCCCCCCCCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHH T ss_conf 98650476266----------622489999999999999999-3889999999998789999999876589989889999 Q ss_pred HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHH Q ss_conf 99888998986218534568999757789999998532024600110230035899999999788786624478882467 Q gi|254780611|r 81 EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160 (302) Q Consensus 81 eG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~ 160 (302) T Consensus 70 eG~iGLi~AiekFDp~rG~rFsTYA~~wIr~~I~~~i~~~-~~irip~~~~-----~~~~k~~~~~~~l~~~~~r~pt~~ 143 (257) T PRK08215 70 VGCIGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDN-NPIRVSRSLR-----DIAYKALQVREKLIKENSKEPTVS 143 (257) T ss_pred HHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHHHHHHHC-CCCEEEHHHH-----HHHHHHHHHHHHHHHHHCCCCCHH T ss_conf 8799999999970976799543211999999999999967-9851009999-----999999999999999838999999 Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHH Q ss_conf 78886189832110000001223433552023234532000001235687056556666666777999999621999999 Q gi|254780611|r 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240 (302) Q Consensus 161 eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr 240 (302) T Consensus 144 eiA~~l~i~~~~v~~~l~~~~~~~SL~~~~~~d~~d~~~~~d~~~d~~~~~~~~-~~-------~~~l~~~l~~L~~REr 215 (257) T PRK08215 144 EIAKELEVPREEVVFALDAIQDPVSLFEPIYHDGGDPIFVMDQISDEKNKDEQW-LE-------EIALKEAMKRLNDREK 215 (257) T ss_pred HHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCCCHHH-HH-------HHHHHHHHHCCCHHHH T ss_conf 999880989999999998638986676855578997104422147976550899-99-------9999999964999999 Q ss_pred HHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 99999827888889899999977899999999999999999999 Q gi|254780611|r 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302) Q Consensus 241 ~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302) T Consensus 216 ~Ii~~ry~~~--~Tl~eIa~~lGvSreRVrQie~~AL~kLR~~l 257 (257) T PRK08215 216 MILNLRFFQG--KTQMEVADEIGISQAQVSRLEKAALKHMRKYI 257 (257) T ss_pred HHHHHHHCCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHC T ss_conf 9999994799--98999999989699999999999999998549 |
|
| >PRK08583 RNA polymerase sigma factor SigB; Validated | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=466.37 Aligned_cols=251 Identities=21% Similarity=0.277 Sum_probs=214.6 Q ss_pred HHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC Q ss_conf 99840799999899999999999828599999999943077875655557999988899999988899898621853456 Q gi|254780611|r 20 IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99 (302) Q Consensus 20 l~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~ 99 (302) T Consensus 1 ~~~~~~~~~Lt~eee~~L~~~~~~~gd~~Ar~~Li~~nlrLV~~iA~~y~~~g~~~~DLiQeG~iGLi~AiekFDp~rG~ 80 (257) T PRK08583 1 MKESSQPTKLTKEDVNQWIAEYQENQDEEAQEKLVKHYKNLVESLAYKYSKGQSHHEDLVQVGMVGLLGAIRRYDYSFGR 80 (257) T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCC T ss_conf 98676899999999999999998819999999999984999999999862689886179999999999998706986588 Q ss_pred CHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC Q ss_conf 89997577899999985320246001102300358999999997887866244788824677888618983211000000 Q gi|254780611|r 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179 (302) Q Consensus 100 ~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~ 179 (302) T Consensus 81 rFsTYA~~wIr~~I~~~lr~~~~~ir~P~~~-----~~~~~ki~~~~~~l~~~~~r~pt~~eiA~~l~~s~e~v~~~l~~ 155 (257) T PRK08583 81 SFEAFAVPTIIGEIKRYLRDKTWSVHVPRRI-----KELGPKIKKAVDELTDELQRSPKISEIADRLGVSEEEVLEAMEM 155 (257) T ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHH-----HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf 8398789999999999999648711354999-----99988899999999998089987999998959599999999997 Q ss_pred C--CCCCCHHHHCCCCCC-CCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHH Q ss_conf 1--223433552023234-5320000012356870565566666667779999996219999999999982788888989 Q gi|254780611|r 180 L--AGDESLNALINSSDK-NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256 (302) Q Consensus 180 ~--~~~~SLd~~i~~~d~-~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~ 256 (302) T Consensus 156 ~~~~~~~Sld~~~~~d~d~~~~~~~d~~~~----~e~~~----e~~e~~~~l~~~l~~L~erEr~Ii~lry~~~--~t~~ 225 (257) T PRK08583 156 GKSYQALSVDHSIEADSDGSTVTLLDIVGQ----QEDGY----ELTEQRMILEKILPVLSDREKSIIQCTFIEN--LSQK 225 (257) T ss_pred HCCCCCCCCCCCCCCCCCCCCCCHHHCCCC----CCCHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCHH T ss_conf 516897027888877888771204330489----66247----8999999999999549999999999995799--9999 Q ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999778999999999999999999999 Q gi|254780611|r 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302) Q Consensus 257 EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302) T Consensus 226 eIa~~lGiS~eRVrQi~~~Al~kLR~~~~ 254 (257) T PRK08583 226 ETGERLGISQMHVSRLQRQAIKKLREAAF 254 (257) T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHC T ss_conf 99999896999999999999999877750 |
|
| >PRK07408 RNA polymerase sigma factor SigF; Reviewed | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=454.33 Aligned_cols=247 Identities=21% Similarity=0.294 Sum_probs=214.6 Q ss_pred CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH Q ss_conf 99989999999999982859999999994307787565555799-99888999999888998986218534568999757 Q gi|254780611|r 28 MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY-GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302) Q Consensus 28 ~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~-g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302) T Consensus 5 ~~~keee~eL~~~y~~~gd~~ar~~LI~~nlrLV~~iA~ry~~~~~~~~~DLiQeG~iGLi~AvekFDp~kG~rFsTYA~ 84 (256) T PRK07408 5 ESLKSETMELLRAYQQTPSIALRNQLVELNLGLVRKEAHRWSNQCSEPYEDLEQVGYLGLIRAIERFDPSKGHAFSSFAV 84 (256) T ss_pred CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH T ss_conf 11579999999999884999999999998099999999986157999878999999999999999739733898899999 Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCC--CCCC Q ss_conf 78999999853202460011023003589999999978878662447888246778886189832110000001--2234 Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDE 184 (302) Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~--~~~~ 184 (302) T Consensus 85 ~wIr~~I~~~lr~~~~~iRiP~~~-----~~~~~ki~~~~~~l~~~~gr~pt~~EiA~~l~is~~~v~~~~~~~~~~~~~ 159 (256) T PRK07408 85 PYIRGEIQHYLRDKSPTVRIPRRW-----LELQRQAKKVRQELRQELGRQPTDQEIAQALDISLEEWQEIKLALQNRMPL 159 (256) T ss_pred HHHHHHHHHHHHHHCCCEECCHHH-----HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCE T ss_conf 999999999999808974136999-----999999999999999987899989999989596999999999987278873 Q ss_pred CHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCC Q ss_conf 33552023234532000001235687056556666666777999999621999999999998278888898999999778 Q gi|254780611|r 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264 (302) Q Consensus 185 SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgi 264 (302) T Consensus 160 SLd~~~~~~~d~~~~l~d~l~d~~~~~~~~~~------e~~~~L~~~l~~L~eREr~Il~~ry~~~--~tl~EIa~~lgv 231 (256) T PRK07408 160 SLDAPVSQDEDGSTSLGDLLPDPRYRSFQLAQ------EDRIRLQQALAQLEERTREVLEFVFLHD--LTQKEAAERLGI 231 (256) T ss_pred ECCCCCCCCCCCCCHHHHHCCCCCCCHHHHHH------HHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCHHHHHHHHCC T ss_conf 05664779998761177755899975388999------9999999998569999999999996379--989999989798 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999974 Q gi|254780611|r 265 SRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 265 S~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 232 S~~rVsqi~~~AL~kLR~~L~~~ 254 (256) T PRK07408 232 SPVTVSRRVKKGLQQLKKLLQPQ 254 (256) T ss_pred CHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99999999999999999972133 |
|
| >PRK05572 sporulation sigma factor SigF; Validated | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=450.28 Aligned_cols=247 Identities=21% Similarity=0.327 Sum_probs=209.8 Q ss_pred HHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCH Q ss_conf 84079999989999999999982859999999994307787565555799998889999998889989862185345689 Q gi|254780611|r 22 EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101 (302) Q Consensus 22 ~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~F 101 (302) T Consensus 5 ~~~~~~~Ls~eee~~L~~~~~-~Gd~~Ar~~Li~~nlrLV~siA~ry~~~g~~~~DLiQeG~iGLi~A~ekFDp~~G~rF 83 (251) T PRK05572 5 NEVKKEQLKDEENKELIKKAQ-DGDKEARDKLVEKNLRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKAVDKFDLSYDVKF 83 (251) T ss_pred CCCCCCCCCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCH T ss_conf 124689999999999999998-0799999999998599999999877589999889999999999999622598989840 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 99757789999998532024600110230035899999999788786624478882467788861898321100000012 Q gi|254780611|r 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181 (302) Q Consensus 102 sTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~ 181 (302) T Consensus 84 sTYA~~wIr~~I~~~ir~~~-~irvp~~~~-----~~~~ki~~~~~~l~~~~~r~ps~~eia~~lg~~~~~v~~~~~~~~ 157 (251) T PRK05572 84 STYAVPMIIGEIQRFLRDDG-IIKVSRSLK-----ELANKIRKDKEELSKELGRAPTIEELAEYLGVTPEEVVLAQEASR 157 (251) T ss_pred HHHHHHHHHHHHHHHHHHCC-CCCCCHHHH-----HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHC T ss_conf 22009999999999998578-766868899-----999889999999999878899899999997939999999998817 Q ss_pred CCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHH Q ss_conf 23433552023234532000001235687056556666666777999999621999999999998278888898999999 Q gi|254780611|r 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261 (302) Q Consensus 182 ~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~ 261 (302) T Consensus 158 ~~~sl~~~~~~~d~~~~~l~d~~~~~~--~~~~~-------~~~~~L~~~l~~L~~rEr~Vi~~ry~~~--~tl~EIa~~ 226 (251) T PRK05572 158 SPQSIHETVHENDGDPITLLDQIADQS--EEDDW-------FDKIALKEAIRELDERERLIIYLRYFKD--KTQSEVAKR 226 (251) T ss_pred CCCCCCCCCCCCCCCHHHHHHHCCCCC--HHHHH-------HHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCHHHHHHH T ss_conf 987534666678997156654126873--46899-------9999999999728999999999981789--889999999 Q ss_pred HCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 7789999999999999999999997 Q gi|254780611|r 262 FEVSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 262 lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 227 lgiS~eRVrQI~~~Al~kLR~~L~e 251 (251) T PRK05572 227 LGISQVQVSRLEKKILKQMKEKLDE 251 (251) T ss_pred HCCCHHHHHHHHHHHHHHHHHHHCC T ss_conf 7979999999999999999998529 |
|
| >PRK06288 RNA polymerase sigma factor WhiG; Reviewed | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=435.77 Aligned_cols=250 Identities=23% Similarity=0.313 Sum_probs=213.0 Q ss_pred CCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHC---CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCH Q ss_conf 799999899999999999828599999999943077875655557---99998889999998889989862185345689 Q gi|254780611|r 25 KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101 (302) Q Consensus 25 ~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~---~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~F 101 (302) T Consensus 4 ~~~~~s~eee~eL~~~~~~~gd~~ar~~LI~~nlrLV~~iA~~~~~~~~~~~~~~DLiQeG~iGLi~AvekFDp~rG~rF 83 (261) T PRK06288 4 KNRKYAQQDETELWKSYKETGDAKIREYLILKYSPLVKYVAGRVAVGMPQNVEFDDLVSYGVFGLLDAIEKFDPEREIKF 83 (261) T ss_pred CCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC T ss_conf 62223869999999999881999999999998599999999998457999999999999999999999996599878883 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC Q ss_conf 99757789999998532024600110230035899999999788786624478882467788861898321100000012 Q gi|254780611|r 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181 (302) Q Consensus 102 sTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~ 181 (302) T Consensus 84 sTYA~~wIr~aI~~~lR~~~---~~pr~-----~~~~~~ki~~~~~~l~~~~gr~pt~~eia~~lg~~~~~v~~~~~~~~ 155 (261) T PRK06288 84 ETYAITRIRGAIFDELRSID---WIPRS-----VRQKARQVERAIAMLEAKLGRTPTDDEIAKELGISLEEYHSLLSKVS 155 (261) T ss_pred HHHHHHHHHHHHHHHHHHHH---HCCHH-----HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHH T ss_conf 98799999999999999860---03199-----99999999999999999868999878888781999999999999972 Q ss_pred --CCCCHHHHCCCC-CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHH Q ss_conf --234335520232-34532000001235687056556666666777999999621999999999998278888898999 Q gi|254780611|r 182 --GDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258 (302) Q Consensus 182 --~~~SLd~~i~~~-d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EI 258 (302) T Consensus 156 ~~~~~SLd~~~~~~~~~~~~~~~d~l~d~~~~~p~~~~---e~~~~~~~l~~~l~~L~erEr~Il~lry~e~--~Tl~eI 230 (261) T PRK06288 156 GTSVVSLNDLLFLGDENDEVSLMDTLEDPAAMNPDEII---EKEEIKRVIVEAINTLPEREKKVITLYYYED--LTLKEI 230 (261) T ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCCHHHHH---HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC--CCHHHH T ss_conf 69974767776579998643087870588989999999---9999999999998708999999999980799--889999 Q ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99977899999999999999999999974 Q gi|254780611|r 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 259 a~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 231 a~~lgiS~eRVrQie~~AL~kLR~~L~~~ 259 (261) T PRK06288 231 GEVLGVTESRISQIHTKAVLQLRAKLAKV 259 (261) T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99979789999999999999999999861 |
|
| >PRK07122 RNA polymerase sigma factor SigF; Reviewed | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=431.58 Aligned_cols=249 Identities=20% Similarity=0.261 Sum_probs=206.7 Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHH--HHCC---HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH Q ss_conf 05999999840799999899999999999--8285---999999999430778756555579999888999999888998 Q gi|254780611|r 14 IGLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGD---LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88 (302) Q Consensus 14 ~~~~~yl~~i~~~~~Lt~eee~~l~~~~~--~~gd---~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~ 88 (302) T Consensus 8 ~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~aR~~lI~~nLrLV~~iA~ry~~rGl~~~DLiQeG~iGLi~ 79 (263) T PRK07122 8 GGSARRPDEYADVPE--------MFRELAGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRGEPRDDLVQVARVGLVN 79 (263) T ss_pred CCCCCCCCCHHHHHH--------HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH T ss_conf 999998430335999--------999998568999899999999999909999999987216898888999999999999 Q ss_pred HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCC Q ss_conf 98621853456899975778999999853202460011023003589999999978878662447888246778886189 Q gi|254780611|r 89 AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168 (302) Q Consensus 89 Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgi 168 (302) T Consensus 80 A~ekFDp~rG~rFsTYA~~wIrgaI~r~lr~~~~~IRlP~~~~-----~~~~ki~~~~~~l~~~~gr~Pt~~EiA~~lg~ 154 (263) T PRK07122 80 AVNRFDVEAGSDFVSFAVPTIMGEVRRHFRDNSWSVKVPRRLK-----ELHLRLGRATAELSQRLGRAPTASELAAELGM 154 (263) T ss_pred HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH-----HHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCC T ss_conf 9997198779985999999999999999998287546579999-----99899999999999986889999999989693 Q ss_pred CCCCCCCCCCC--CCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH Q ss_conf 83211000000--1223433552023234532000001235687056556666666777999999621999999999998 Q gi|254780611|r 169 SESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246 (302) Q Consensus 169 s~~~v~~l~~~--~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~r 246 (302) T Consensus 155 ~~~~v~~~l~~~~~~~~~SlD~~~~~~~~~~~~l~d~~~d~~~----~~----e~~~~~~~L~~~l~~L~eREr~Vi~lr 226 (263) T PRK07122 155 DREEVVEGLVAGSSYNTLSIDSGGGSGDDDARAIADTLGDVDA----GL----DHIENREALRPLLAALPERERTVLVLR 226 (263) T ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCH----HH----HHHHHHHHHHHHHHCCCHHHHHHHHHH T ss_conf 9999999998733589877878888888652035464169764----28----999999999999975999999999999 Q ss_pred HCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 278888898999999778999999999999999999999 Q gi|254780611|r 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302) Q Consensus 247 y~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302) T Consensus 227 y~--e~~Tl~EIa~~lGiSreRVrQIe~~AL~KLR~~Le 263 (263) T PRK07122 227 FF--ESMTQTQIAERVGISQMHVSRLLAKSLARLRDQLE 263 (263) T ss_pred HC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC T ss_conf 56--99989999999897999999999999999999749 |
|
| >PRK05911 RNA polymerase sigma factor sigma-28; Reviewed | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=415.83 Aligned_cols=244 Identities=20% Similarity=0.270 Sum_probs=202.6 Q ss_pred CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH Q ss_conf 98999999999998285999999999430778756555579---999888999999888998986218534568999757 Q gi|254780611|r 30 EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302) Q Consensus 30 t~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~---~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302) T Consensus 5 ~~~~~~~lw~~y~~~~d~~ar~~LI~~nLrLV~~iA~r~~~~~p~~v~~~DLiQeG~iGLi~AiekFDp~kG~rFsTYA~ 84 (257) T PRK05911 5 KTQNIAETWQLYWETQEIEYRDVLIEFYLPLVKNVAHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPEKSRRFEGYAL 84 (257) T ss_pred CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH T ss_conf 06789999999988399999999999839999999999864699999889999999999999998329866999488769 Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC--CCC Q ss_conf 789999998532024600110230035899999999788786624478882467788861898321100000012--234 Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDE 184 (302) Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~--~~~ 184 (302) T Consensus 85 ~wIr~aI~~~lr~~~~---lpr~~-----~~~~~ki~~~~~~l~~~~gr~pt~~eiA~~l~i~~~~v~~~~~~~~~~~~~ 156 (257) T PRK05911 85 FLIKAAIIDDLRKQDW---VPRSV-----HQKANKLADAMDSLRQSLGKEPTDGELCEYLNISQQELSGWFSSARPALIL 156 (257) T ss_pred HHHHHHHHHHHHHCCC---CCHHH-----HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCEE T ss_conf 9989999999987162---55799-----999999999999999986889999999988397999999999853552223 Q ss_pred CHHHHCCCC--CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHH Q ss_conf 335520232--345320000012356870565566666667779999996219999999999982788888989999997 Q gi|254780611|r 185 SLNALINSS--DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262 (302) Q Consensus 185 SLd~~i~~~--d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~l 262 (302) T Consensus 157 sl~~~~~~~~d~~~~~~l~d~i~d~~~~~~~~---~~~~~~~~~~L~~al~~L~erEr~Ii~lry~e~--~Tl~EIg~~l 231 (257) T PRK05911 157 SLNEEFPSQSDDEAGLALEERIADERAETGYD---VVDKKEFSSILANAILALEEKERKVMALYYYEE--LVLKEIGKIL 231 (257) T ss_pred CCCCCCCCCCCCCCCCCHHHHCCCCCCCCHHH---HHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC--CCHHHHHHHH T ss_conf 05788887888876530777467988899899---999999999999998658999999999874898--7899999897 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 789999999999999999999997 Q gi|254780611|r 263 EVSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 263 giS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 232 gvS~eRVrQi~~~AL~kLR~~L~a 255 (257) T PRK05911 232 GVSESRVSQIHSKALLKLRAALSA 255 (257) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 988999999999999999999986 |
|
| >PRK07670 RNA polymerase sigma factor SigD; Validated | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=416.72 Aligned_cols=241 Identities=21% Similarity=0.303 Sum_probs=203.2 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH Q ss_conf 999999999998285999999999430778756555579---99988899999988899898621853456899975778 Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108 (302) Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~---~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~w 108 (302) T Consensus 2 ~ee~~l~~~~~~~gD~~Ar~~LV~~nl~LV~~ia~r~~~~~~~~v~~eDLiQeG~iGLi~AiekFDp~~G~rFsTYA~~w 81 (250) T PRK07670 2 YEDQKLWDRWKEERDPEAADDLIRRYMPLVTYHVQRISAGLPKSVSKDDLKSLGMLGLYDALEKFDPSRDLKFDTYASFR 81 (250) T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH T ss_conf 78999999998859999999999981999999999997048999988899999999999999960986699907721999 Q ss_pred HHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC--CCCCCCH Q ss_conf 99999985320246001102300358999999997887866244788824677888618983211000000--1223433 Q gi|254780611|r 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESL 186 (302) Q Consensus 109 Ir~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~--~~~~~SL 186 (302) T Consensus 82 Ir~aI~~~lr~~~~---lpr~-----~~~~~~ki~~~~~~l~~~~gr~ps~~eia~~lg~s~~~v~~~~~~~~~~~~~Sl 153 (250) T PRK07670 82 IRGAIIDGLRKEDW---LPRS-----SREKTKKVEAAIEKLEQRYMRNVTPSEVAAELGMSEEEVVTTMNEGFFANLLSI 153 (250) T ss_pred HHHHHHHHHHHCCC---CHHH-----HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHCCCCCCC T ss_conf 99999999874254---0099-----999999999999999998389998889987719999999999998754798036 Q ss_pred HHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCH Q ss_conf 55202323453200000123568705655666666677799999962199999999999827888889899999977899 Q gi|254780611|r 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266 (302) Q Consensus 187 d~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~ 266 (302) T Consensus 154 d~~~~~~~~~~-~~~~~~~d~~~~~pe---~~~~~~~~~~~L~~~l~~L~~rEr~Vl~l~y~--e~~Tl~eIa~~lgvS~ 227 (250) T PRK07670 154 DEKLHDQDDGE-NVQVMIRDDKAVTPE---EKLVKEELIEQLAEKIKELNEKEQLVISLFYK--EELTLTEIGQVLNLST 227 (250) T ss_pred CCCCCCCCCCC-HHHHHHHCCCCCCHH---HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCC--CCCCHHHHHHHHCCCH T ss_conf 77777888850-477888524679999---99999999999999985589999999999748--9868999999989799 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999997 Q gi|254780611|r 267 ERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 267 eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 228 erVrQi~~~AL~kLr~~l~k 247 (250) T PRK07670 228 SRISQIHSKALFKLKKLLEK 247 (250) T ss_pred HHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999998 |
|
| >PRK05803 sporulation sigma factor SigK; Reviewed | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=417.95 Aligned_cols=211 Identities=26% Similarity=0.385 Sum_probs=172.7 Q ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHC Q ss_conf 05999999840799999899999999999828599999999943077875655557999988899999988899898621 Q gi|254780611|r 14 IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93 (302) Q Consensus 14 ~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kF 93 (302) T Consensus 15 ~~l~syl~~i~~~~~Ls~eEE~~La~~~~~-GD~~Ar~~LI~~NLRLVvsIAkky~~~g~~l~DLIQEGniGLi~AvekF 93 (228) T PRK05803 15 LFLVSYVKNNSFPQPLSEEEERKYLELMKQ-GDEEARNILIERNLRLVAHIVKKFENTGEDVDDLISIGTIGLIKAIDSF 93 (228) T ss_pred HHHHHHHHCCCCCCCCCHHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH T ss_conf 999999974788999999999999999984-6899999999987799999996277999898999999999999999984 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCC Q ss_conf 85345689997577899999985320246001102300358999999997887866244788824677888618983211 Q gi|254780611|r 94 DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173 (302) Q Consensus 94 Dp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v 173 (302) T Consensus 94 Dp~rG~rFSTYA~~wIr~~I~~~lr~~kk-------------------~~~----------------------------- 125 (228) T PRK05803 94 DAGKGTKLATYAARCIENEILMHLRNLKK-------------------TKG----------------------------- 125 (228) T ss_pred CCCCCCCCHHCCHHHHHHHHHHHHHHHHH-------------------HCC----------------------------- T ss_conf 89989970520099999999999999887-------------------535----------------------------- Q ss_pred CCCCCCCCCCCCHHHHCCCC-CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCC--C Q ss_conf 00000012234335520232-34532000001235687056556666666777999999621999999999998278--8 Q gi|254780611|r 174 ISMNCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--E 250 (302) Q Consensus 174 ~~l~~~~~~~~SLd~~i~~~-d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~--~ 250 (302) T Consensus 126 ---------~~sl~~~i~~d~e~~e~~l~d~l~~~~~~~~e~~----~~~~~~~~l~~~l~~L~~REr~II~~RfGL~~~ 192 (228) T PRK05803 126 ---------EVSLQDPIGVDKEGNEISLIDILKSESDDVIEMV----ELSMEVEKLYKKIDILDPREKEVIEMRYGLGDG 192 (228) T ss_pred ---------CCCCCCCCCCCCCCCCCHHHHHCCCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCC T ss_conf ---------5012374466878983224343168899879999----999989999999851898899999998647899 Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 888989999997789999999999999999999997 Q gi|254780611|r 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 251 ~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 193 ~~~Tl~eIg~~lgiSrERVRQIe~~Al~KLrk~L~r 228 (228) T PRK05803 193 KEKTQREIAKALGISRSYVSRIEKKALKKLFKELVR 228 (228) T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCC T ss_conf 971599999998979999999999999999998559 |
|
| >PRK08301 sporulation sigma factor SigE; Reviewed | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=397.79 Aligned_cols=206 Identities=30% Similarity=0.449 Sum_probs=160.6 Q ss_pred HHHHHHCC-CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 99984079-99998999999999998285999999999430778756555579999888999999888998986218534 Q gi|254780611|r 19 YIHEIRKI-PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97 (302) Q Consensus 19 yl~~i~~~-~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~k 97 (302) T Consensus 28 ~~~~~~~~pp~Ls~eeE~~l~~~~~-~GD~~Ar~~LI~~NLRLVv~IAkky~~~G~~l~DLIqEGniGLikAvekFDp~k 106 (239) T PRK08301 28 YIGGSEALPPPLSKEEEEVLLNKLP-KGDEAVRSILIERNLRLVVYIARKFENTGINIEDLISIGTIGLIKAVNTFNPEK 106 (239) T ss_pred EECCCCCCCCCCCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC T ss_conf 7478987999989999999999998-346999999999878999999975768997989999985899999999649888 Q ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCC Q ss_conf 56899975778999999853202460011023003589999999978878662447888246778886189832110000 Q gi|254780611|r 98 GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177 (302) Q Consensus 98 G~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~ 177 (302) T Consensus 107 G~rFSTYA~~~I~~eI~~~lr~~~~~-r~e-------------------------------------------------- 135 (239) T PRK08301 107 KIKLATYASRCIENEILMYLRRNNKV-RSE-------------------------------------------------- 135 (239) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHH-HCC-------------------------------------------------- T ss_conf 99716301999999999999970424-224-------------------------------------------------- Q ss_pred CCCCCCCCHHHHCCC-CCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCC--CCCCC Q ss_conf 001223433552023-234532000001235687056556666666777999999621999999999998278--88889 Q gi|254780611|r 178 CRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVT 254 (302) Q Consensus 178 ~~~~~~~SLd~~i~~-~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~--~~~~T 254 (302) T Consensus 136 ------vsl~epl~~d~d~~e~~l~D~l~~d~d~~~~----~~e~~~~~~~L~~al~~L~eREr~Ii~lRfGL~~~~~~T 205 (239) T PRK08301 136 ------VSFDEPLNIDWDGNELLLSDVLGTDNDIIYK----DIEDEVDKKLLLKALKKLNDREKQIMELRFGLAGGEEKT 205 (239) T ss_pred ------CHHCCCCCCCCCCCHHHHHHCCCCCCCHHHH----HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCC T ss_conf ------0001536877665622430114898750667----899999999999999648999999999995788998406 Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 89999997789999999999999999999997 Q gi|254780611|r 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 255 l~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 206 l~EIa~~lgISrerVrQIe~~AL~KLR~~l~k 237 (239) T PRK08301 206 QKEVADMLGISQSYISRLEKRIIKRLKKEINK 237 (239) T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999998978999999999999999999985 |
|
| >TIGR02885 spore_sigF RNA polymerase sigma-F factor; InterPro: IPR014236 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=384.40 Aligned_cols=231 Identities=23% Similarity=0.358 Sum_probs=202.8 Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 99999982859999999994307787565555799998889999998889989862185345689997577899999985 Q gi|254780611|r 37 LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116 (302) Q Consensus 37 l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~ 116 (302) T Consensus 1 Li~~a~-~GDk~A~dkLi~~N~~LV~siv~rF~nRGYe~eDlFQIGciGLvKAidkFD~~y~VKFSTYAVPmI~GEIkRF 79 (231) T TIGR02885 1 LIKLAK-EGDKEARDKLIEENLRLVSSIVKRFLNRGYEYEDLFQIGCIGLVKAIDKFDLSYDVKFSTYAVPMIMGEIKRF 79 (231) T ss_pred CCHHHH-HHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHH T ss_conf 904567-4048999999872334689999985206887000022211556665542176777015521222022122231 Q ss_pred HHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC Q ss_conf 32024600110230035899999999788786624478882467788861898321100000012234335520232345 Q gi|254780611|r 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196 (302) Q Consensus 117 i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~ 196 (302) T Consensus 80 LRDDG-~ikVSRSl--K~la~---k~~~~kE~L~~~l~R~PTi~Elae~lg~~~EEiv~A~Es~~~~~sly~tvh~dDGd 153 (231) T TIGR02885 80 LRDDG-IIKVSRSL--KELAR---KIRYEKEELTKKLGREPTINELAEALGVSPEEIVMALESARSLQSLYDTVHEDDGD 153 (231) T ss_pred HCCCC-CEEEEHHH--HHHHH---HHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCCCCCHHCCEEECCCCC T ss_conf 02688-55751527--89999---99877999999838998889998875878878664420257610110011417946 Q ss_pred CCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 32000001235687056556666666777999999621999999999998278888898999999778999999999999 Q gi|254780611|r 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276 (302) Q Consensus 197 ~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~A 276 (302) T Consensus 154 Pi~LlD~i~d~~~~~-~~~~~-------ki~Lke~i~~Ld~rer~ii~LRYFKD--kTQ~eVA~~LGISQVQVSRlEkk~ 223 (231) T TIGR02885 154 PILLLDQIADKGSED-SDLLE-------KIALKEAISKLDERERQIIMLRYFKD--KTQTEVAKMLGISQVQVSRLEKKV 223 (231) T ss_pred HHHHHHHHCCCCCCH-HHHHH-------HHHHHHHHHHCCCCCCEEEEEECCCC--CHHHHHHHHCCCCCCHHHHHHHHH T ss_conf 446766521257713-68999-------89999998612522678977410140--017999977185700122789999 Q ss_pred HHHHHHHH Q ss_conf 99999999 Q gi|254780611|r 277 FKKVQESI 284 (302) Q Consensus 277 L~kLR~~l 284 (302) T Consensus 224 L~~~k~~l 231 (231) T TIGR02885 224 LKKMKEKL 231 (231) T ss_pred HHHHHHHC T ss_conf 99987409 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry represent RNA polymerase sigma factor F. Within the Firmicutes, Sigma-F is specifically, and universally, a component of the endospore formation program, and is expressed in the forespore to turn on the expression of dozens of genes. It is closely related to sigma-G, which is also expressed in the forespore.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription] | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=350.50 Aligned_cols=241 Identities=24% Similarity=0.378 Sum_probs=204.8 Q ss_pred CCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCC-CHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH Q ss_conf 999998999999999998285999999999430778756555579999-8889999998889989862185345689997 Q gi|254780611|r 26 IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATY 104 (302) Q Consensus 26 ~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~-~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTY 104 (302) T Consensus 3 ~~~~~~~e~~~~~~~~~-~g~~~~~-~Li~~ylpLV~~ia~k~~~r~~~~~dDLiqiG~iGLi~Aieryd~~kg~kF~ty 80 (247) T COG1191 3 PQPLSKEEEEKLLEYYA-EGDEEAR-RLIERYLPLVKSIARKFENRGPSEYDDLIQIGMIGLIKAIERYDPSKGTKFSTY 80 (247) T ss_pred CCCCCHHHHHHHHHHHH-HCCHHHH-HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH T ss_conf 76224689999999998-4589999-999997899999999998059985438999789999999997493128614888 Q ss_pred HHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC--C Q ss_conf 57789999998532024600110230035899999999788786624478882467788861898321100000012--2 Q gi|254780611|r 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--G 182 (302) Q Consensus 105 A~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~--~ 182 (302) T Consensus 81 A~~~I~Gei~d~LR~~~-~v~vp-----R~~~~~~~~i~~~~~~l~~el~r~pt~~EIA~~L~i~~ee~~~~~~~~~~~~ 154 (247) T COG1191 81 AVRRIRGEILDYLRKND-SVKVP-----RSLRELGRRIEEAIDELEQELGREPTDEEIAEELGIDKEEYIEALLAINGSQ 154 (247) T ss_pred HHHHHHHHHHHHHHHCC-CCCCC-----HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCC T ss_conf 99999999999998478-74676-----8998887788999999999847998689999896989999999998730124 Q ss_pred CCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHH Q ss_conf 34335520232345320000012356870565566666667779999996219999999999982788888989999997 Q gi|254780611|r 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262 (302) Q Consensus 183 ~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~l 262 (302) T Consensus 155 ~~sld~~~~~~~d~~-------~~~~~~~~~---~~~~~~~~~~~l~~~i~~L~EREk~Vl~l~y~ee--lt~kEI~~~L 222 (247) T COG1191 155 LLSLDEDVLKDDDDD-------VDDQIENPD---DGVEKEELLEILKEAIEPLPEREKLVLVLRYKEE--LTQKEIAEVL 222 (247) T ss_pred CCCCCCCCCCCCCCC-------HHHCCCCCH---HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHC--CCHHHHHHHH T ss_conf 541100001356520-------220235603---5778899999999998766899999999999701--5799999994 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 789999999999999999999997 Q gi|254780611|r 263 EVSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 263 giS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 223 gISes~VSql~kkai~kLr~~l~~ 246 (247) T COG1191 223 GISESRVSRLHKKAIKKLRKELNK 246 (247) T ss_pred CCCHHHHHHHHHHHHHHHHHHHCC T ss_conf 914989999999999999998604 |
|
| >TIGR02941 Sigma_B RNA polymerase sigma-B factor; InterPro: IPR014288 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=329.61 Aligned_cols=243 Identities=23% Similarity=0.327 Sum_probs=216.6 Q ss_pred CCCHHHHHHHHHHHHHH-CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH Q ss_conf 99989999999999982-85999999999430778756555579999888999999888998986218534568999757 Q gi|254780611|r 28 MLEKQEEYVLAKRYREH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302) Q Consensus 28 ~Lt~eee~~l~~~~~~~-gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302) T Consensus 9 n~~~e~v~~wI~e~Q~nP~n~eaQeklV~hY~~Lv~SiAykYSKg~~~HEDlvQVGM~GLlgAirRyD~s~g~~FE~Fai 88 (256) T TIGR02941 9 NLTKEDVIQWIKEFQKNPKNEEAQEKLVKHYQDLVESIAYKYSKGSAIHEDLVQVGMVGLLGAIRRYDYSYGKAFEAFAI 88 (256) T ss_pred CCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCC T ss_conf 57887899999996369983257899999998999988754048788333045676899999986511000456566236 Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC--CCCCC Q ss_conf 7899999985320246001102300358999999997887866244788824677888618983211000000--12234 Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDE 184 (302) Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~--~~~~~ 184 (302) T Consensus 89 PTiiGEIKrylRDKTWsvHVPR-----RIKelGpkIkk~~dELT~~lqrSP~i~EIA~~lg~SEEEVLE~Me~g~sY~al 163 (256) T TIGR02941 89 PTIIGEIKRYLRDKTWSVHVPR-----RIKELGPKIKKAVDELTDELQRSPKIAEIADRLGVSEEEVLEIMEMGQSYKAL 163 (256) T ss_pred CCHHHHHHHHHCCCCCCCCCCC-----CHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHCCCCCCEE T ss_conf 6100101121115643001574-----11003772014556644442148706546412177488898776147774333 Q ss_pred CHHHHCCCC-CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHC Q ss_conf 335520232-3453200000123568705655666666677799999962199999999999827888889899999977 Q gi|254780611|r 185 SLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263 (302) Q Consensus 185 SLd~~i~~~-d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lg 263 (302) T Consensus 164 SvD~~iEadsDGStVa~ld~vG~~edgYd~t-----E---~Rm~LekIlpiLserE~~ii~c~f~en--lsQKeTGErlG 233 (256) T TIGR02941 164 SVDDKIEADSDGSTVALLDLVGEVEDGYDQT-----E---KRMVLEKILPILSEREKEIIECTFIEN--LSQKETGERLG 233 (256) T ss_pred ECCCCCCCCCCCCCCHHHHHHCCCCCCHHHH-----H---HHHHHHHHHHHCCHHHHHHHHHHHHCC--CCCCHHHHHCC T ss_conf 2253000368885111111216766654578-----8---888888741000544567666553147--87300232224 Q ss_pred CCHHHHHHHHHHHHHHHHHHHH Q ss_conf 8999999999999999999999 Q gi|254780611|r 264 VSRERVRQIEARAFKKVQESIQ 285 (302) Q Consensus 264 iS~eRVrQI~~~AL~kLR~~l~ 285 (302) T Consensus 234 iSQMHVSRl~R~ai~KL~eAa~ 255 (256) T TIGR02941 234 ISQMHVSRLQRRAIKKLKEAAF 255 (256) T ss_pred HHHHHHHHHHHHHHHHHHHHHC T ss_conf 0355677888999999999722 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the sigma factor, sigmaB. It is restricted to certain species within the order Bacillales including Staphylococcus aureus , Listeria monocytogenes and Bacillus cereus (strain ATCC 14579 / DSM 31) .. |
| >TIGR02846 spore_sigmaK RNA polymerase sigma-K factor; InterPro: IPR014209 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=100.00 E-value=8.8e-44 Score=312.14 Aligned_cols=212 Identities=29% Similarity=0.411 Sum_probs=183.9 Q ss_pred CCCHHHHHHHHHHHCCC-CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH Q ss_conf 87405999999840799-99989999999999982859999999994307787565555799998889999998889989 Q gi|254780611|r 11 NGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89 (302) Q Consensus 11 ~~~~~~~~yl~~i~~~~-~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~A 89 (302) T Consensus 11 ~~~lfL~gY~~n~~~FP~PLs~~eE~~YL~~l~-~GD~~Ar~~LiErNLRLVAHiVKKf~~~G~~~dDLISIGTiGLIKA 89 (228) T TIGR02846 11 KSLLFLVGYVTNNASFPQPLSEEEEKKYLERLK-EGDEEARNVLIERNLRLVAHIVKKFSNTGEDVDDLISIGTIGLIKA 89 (228) T ss_pred HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCHHCCCCHHEECC T ss_conf 999998777506888978898668999999987-3159999997763330002156511788741000010022010001 Q ss_pred HHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCC Q ss_conf 86218534568999757789999998532024600110230035899999999788786624478882467788861898 Q gi|254780611|r 90 VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169 (302) Q Consensus 90 i~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis 169 (302) T Consensus 90 idsf~~~KGt~LATYAArCiENEILM~lR~~K------------------------------------------------ 121 (228) T TIGR02846 90 IDSFDPEKGTRLATYAARCIENEILMHLRALK------------------------------------------------ 121 (228) T ss_pred EECCCCCCCCHHHHHHHHHHHHHHHHHHHHCC------------------------------------------------ T ss_conf 10224787731566786653478999997436------------------------------------------------ Q ss_pred CCCCCCCCCCCCCCCCHHHHCCCC-CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH-HCCCHHHHHHHHHHH Q ss_conf 321100000012234335520232-345320000012356870565566666667779999996-219999999999982 Q gi|254780611|r 170 ESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARR 247 (302) Q Consensus 170 ~~~v~~l~~~~~~~~SLd~~i~~~-d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l-~~L~~rEr~II~~ry 247 (302) T Consensus 122 ---------K~k~eV~L~DPIG~DKEGNEIsL~DiL~~~~d~v~e~v~~~~----~~~~l~~~~~~~L~~rE~~vi~~Ry 188 (228) T TIGR02846 122 ---------KTKGEVSLQDPIGVDKEGNEISLIDILGSDEDSVIEQVEKKL----EIKKLYKKLNSVLKGREREVIEMRY 188 (228) T ss_pred ---------CCCCCEEECCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHC T ss_conf ---------747833210788867676423000001688731688888644----5999999999874088899998743 Q ss_pred CCC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 788--8889899999977899999999999999999999 Q gi|254780611|r 248 LQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302) Q Consensus 248 ~~~--~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302) T Consensus 189 GL~~~~~~tQREIA~~LgISRSYVSRIEK~Al~Kl~~~~ 227 (228) T TIGR02846 189 GLKDGREKTQREIAKILGISRSYVSRIEKKALKKLYKEL 227 (228) T ss_pred CCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHC T ss_conf 668889541789987708650045488899999998633 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homologue sigma-E (sigma-29, see IPR014200 from INTERPRO), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note: that in Bacillus subtilis (and apparently also in Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >TIGR02850 spore_sigG RNA polymerase sigma-G factor; InterPro: IPR014212 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=100.00 E-value=1e-40 Score=291.63 Aligned_cols=252 Identities=23% Similarity=0.329 Sum_probs=219.2 Q ss_pred CCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHH Q ss_conf 55745587405999999840799999899999999999828599999999943077875655557999988899999988 Q gi|254780611|r 5 NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84 (302) Q Consensus 5 ~~~~~~~~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~i 84 (302) T Consensus 2 kvei~Gv~t~----------klPvl~~~~~~~l~~~~~-~G~~~ar~~l~~~nlrlvlsviqrf~nrGe~~ddlfqvGCi 70 (254) T TIGR02850 2 KVEICGVNTS----------KLPVLKNEEMRELFVRMK-SGDKSAREKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 70 (254) T ss_pred CEEECCCCCC----------CCCCCCHHHHHHHHHHHH-CCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH T ss_conf 2241265500----------055435478999999985-12078999987522688888888751145403456763257 Q ss_pred HHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH Q ss_conf 89989862185345689997577899999985320246001102300358999999997887866244788824677888 Q gi|254780611|r 85 GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164 (302) Q Consensus 85 GLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~ 164 (302) T Consensus 71 Gl~k~idnfdl~~nv~fstyavPmiiGeirrylrdn~-~irvsrs-----lrd~ay~alqvr~~l~~~~~~eP~~~~ia~ 144 (254) T TIGR02850 71 GLIKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRS-----LRDIAYKALQVRDKLVSKNSKEPTVSEIAK 144 (254) T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCC-CEEEHHH-----HHHHHHHHHHHHHHHHHHHCCCCCHHHHHH T ss_conf 7777655310111320011346678898899852487-4130355-----889999999999999853125875889998 Q ss_pred HCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH Q ss_conf 61898321100000012234335520232345320000012356870565566666667779999996219999999999 Q gi|254780611|r 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244 (302) Q Consensus 165 ~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~ 244 (302) T Consensus 145 ~l~~~~~~~v~aldaiq~PvslfeP~y~d~Gd~i~vmdq~~d~~~~d~~W~~--------~~~l~~~~~~l~~re~~il~ 216 (254) T TIGR02850 145 ELDVPKEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDEKNKDEQWLE--------EIALKEALKRLNEREKLILK 216 (254) T ss_pred HHCCCHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHH--------HHHHHHHHHHHHHHHHHHHH T ss_conf 7347557877656642164234310013799748874010020345699998--------88999999987667887777 Q ss_pred HHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 982788888989999997789999999999999999999 Q gi|254780611|r 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302) Q Consensus 245 ~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302) T Consensus 217 ~rff~G--~tqmeva~eiGisqaqvsrlek~a~~~~~k~ 253 (254) T TIGR02850 217 LRFFEG--KTQMEVAEEIGISQAQVSRLEKAALKHMRKY 253 (254) T ss_pred HHHHCC--CHHHHHHHHHCCHHHHHHHHHHHHHHHHHHC T ss_conf 553146--3133456540301688888889999997512 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also designated stage III sporulation protein G (SpoIIIG). Members of this entry are closely related to sigma-F (SpoIIAC), another sporulation sigma factor.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >TIGR02835 spore_sigmaE RNA polymerase sigma-E factor; InterPro: IPR014200 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=99.97 E-value=8.5e-31 Score=225.36 Aligned_cols=198 Identities=31% Similarity=0.469 Sum_probs=165.0 Q ss_pred CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH Q ss_conf 99998999999999998285999999999430778756555579999888999999888998986218534568999757 Q gi|254780611|r 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302) Q Consensus 27 ~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302) T Consensus 32 PPl~~eee~~l~~~l~-~Gd~~~~~~liernlrlvvyia~kf~ntG~~~edl~s~GtiGlikav~tf~P~k~iklatyas 110 (234) T TIGR02835 32 PPLTKEEEEALLEKLE-KGDEAAKSILIERNLRLVVYIARKFENTGINIEDLVSIGTIGLIKAVNTFNPEKKIKLATYAS 110 (234) T ss_pred CCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH T ss_conf 9887157999999987-547999999886222431121012202562110222221478887765227301103556776 Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH Q ss_conf 78999999853202460011023003589999999978878662447888246778886189832110000001223433 Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186 (302) Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SL 186 (302) T Consensus 111 ~Cieneilmylrr~~~~---------------------------------------------------------~~evsf 133 (234) T TIGR02835 111 RCIENEILMYLRRNNKI---------------------------------------------------------RSEVSF 133 (234) T ss_pred HHHHHHHHHHHHHHCCC---------------------------------------------------------CCEEEE T ss_conf 76788899988751121---------------------------------------------------------000000 Q ss_pred HHHCCC-CCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCCHHHHHHHHC Q ss_conf 552023-2345320000012356870565566666667779999996219999999999982788--8889899999977 Q gi|254780611|r 187 NALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFE 263 (302) Q Consensus 187 d~~i~~-~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~--~~~Tl~EIa~~lg 263 (302) T Consensus 134 ~ePln~dW~Gnelllsd~lGt~~~~----~~~~~e~~v~~~ll~~al~~l~~re~~i~~lrfGl~~~~e~tqk~vad~lG 209 (234) T TIGR02835 134 DEPLNVDWDGNELLLSDVLGTDSDI----VYKVLEEEVDRELLKKALKKLNDREKKIMELRFGLAGGTEKTQKEVADLLG 209 (234) T ss_pred CCCCCCCCCCCHHHHHHHHCCCHHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHH T ss_conf 2554656676211434441474268----899999999999999999987676787667630436772146788898862 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 89999999999999999999997 Q gi|254780611|r 264 VSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 264 iS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 210 isqsyisrlek~i~krl~ke~~~ 232 (234) T TIGR02835 210 ISQSYISRLEKRILKRLKKEINR 232 (234) T ss_pred HHHHHHHHHHHHHHHHHHHHHHH T ss_conf 46899999999999999999873 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry represent the endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. In Bacillus subtilis, sigma-29 is synthesized as a precursor (P31), specifically in the mother cell compartment, and is activated by a cleavage that removes the N-terminal 29 amino acids .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >PRK08295 RNA polymerase factor sigma-70; Validated | Back alignment and domain information |
|---|
Probab=99.97 E-value=3.5e-28 Score=207.92 Aligned_cols=201 Identities=19% Similarity=0.265 Sum_probs=152.2 Q ss_pred CCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH Q ss_conf 99999899999999999828599999999943077875655557999988899999988899898621853456899975 Q gi|254780611|r 26 IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105 (302) Q Consensus 26 ~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA 105 (302) T Consensus 4 ~~-~~~~~d~~Li~~~~-~GD~~Af~~L~~~y~~~v~~~~~~~~~~~~d~EDlvQe~~i~l~kai~~f~~~k~~~F~t~~ 81 (209) T PRK08295 4 YN-LRDKEDEELVELAQ-SGDTEALEYLIEKYKNFVRAKARSYFLIGAEREDIVQEGMIGLYKAIRDYDEDKLSSFKSFA 81 (209) T ss_pred CC-CCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH T ss_conf 89-87201999999999-16799999999998999999999982898779999999999999999856865487289999 Q ss_pred HHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCC Q ss_conf 77899999985320246001102300358999999997887866244788824677888618983211000000122343 Q gi|254780611|r 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185 (302) Q Consensus 106 ~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~S 185 (302) T Consensus 82 ~~~i~~~i~~~ir~~~r~k~~~----------------------------------------------------~~~~~s 109 (209) T PRK08295 82 ELCITRQIITAIKTANRQKHIP----------------------------------------------------LNSYVS 109 (209) T ss_pred HHHHHHHHHHHHHHHHCCCCCC----------------------------------------------------CCHHHC T ss_conf 9999999999999983304545----------------------------------------------------202414 Q ss_pred HHHHCCCCCCCCCCHHCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCC Q ss_conf 35520232345320000012356-87056556666666777999999621999999999998278888898999999778 Q gi|254780611|r 186 LNALINSSDKNSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264 (302) Q Consensus 186 Ld~~i~~~d~~~~~~~d~l~~~~-~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgi 264 (302) T Consensus 110 ld~~~~~~~-~~~~~~~~~~~~~~~~pe~~~~~~e~~---~~i~~~i~~~l~~~e~~V~~~~-~--eg~s~~EIA~~l~i 182 (209) T PRK08295 110 LDKPIYDEE-SDRTLLDVISGAKVTDPEELIISKEEL---EIIEEKILELLSDLEKEVLELY-L--DGKSYQEIAEELNR 182 (209) T ss_pred CCCCCCCCC-CHHHHHHHCCCCCCCCHHHHHHHHHHH---HHHHHHHHHCCCHHHHHHHHHH-H--CCCCHHHHHHHHCC T ss_conf 566645554-203565430467789999999999999---9999999846918999999999-8--69999999999892 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999999974 Q gi|254780611|r 265 SRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 265 S~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 183 s~~tV~~~l~RarkkLr~~L~~~ 205 (209) T PRK08295 183 HVKSIDNALQRVKRKLEKYLEIR 205 (209) T ss_pred CHHHHHHHHHHHHHHHHHHHHHC T ss_conf 99999999999999999998744 |
|
| >PRK11922 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.80 E-value=1.5e-17 Score=136.87 Aligned_cols=193 Identities=19% Similarity=0.246 Sum_probs=139.3 Q ss_pred CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH Q ss_conf 99998999999999998285999999999430778756555579999888999999888998986218534568999757 Q gi|254780611|r 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302) Q Consensus 27 ~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302) T Consensus 10 ~~~~~~~D~eLi~~~~-~GD~~Af~~L~~ry~~~ly~~a~~~~~~~~dAEDlvQevFlk~~~~l~~f~~~~--~f~tWL~ 86 (231) T PRK11922 10 TPLSAADDAELVARVL-AGDEAAFEQLMRRHNRRLYRLARAILRDDAEAEDVVQEAYLRAFRALARFRGDA--SLSTWLS 86 (231) T ss_pred CCCCCCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCC--CHHHHHH T ss_conf 9999975999999999-565999999999999999999999929999999999999999998753057756--5999999 Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH Q ss_conf 78999999853202460011023003589999999978878662447888246778886189832110000001223433 Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186 (302) Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SL 186 (302) T Consensus 87 ~Ia~N~~ld~lRk~~~----------------------~~~~~-~~~-----------------------------~~~~ 114 (231) T PRK11922 87 RIVLNEALGRLRRRRR----------------------DVIEL-RLA-----------------------------TESE 114 (231) T ss_pred HHHHHHHHHHHHHHHC----------------------CCCCC-CCC-----------------------------CCCC T ss_conf 9999999999998741----------------------22311-000-----------------------------1233 Q ss_pred HHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCH Q ss_conf 55202323453200000123568705655666666677799999962199999999999827888889899999977899 Q gi|254780611|r 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266 (302) Q Consensus 187 d~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~ 266 (302) T Consensus 115 -------~~~--~~~~~~~~~~~~pe~----~~~~~E~~~~l~~al~~Lp~~~R~v~~L~~~eg--lS~~EIA~~Lgis~ 179 (231) T PRK11922 115 -------EGE--EIEFPDADPAEDPED----AAARREIRALLERAIDALPDAFRAVFVLRVVEE--LSVEETAQALGLPE 179 (231) T ss_pred -------CCH--HHCCCCCCCCCCHHH----HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCH T ss_conf -------210--100233567899999----999999999999999809999999999999939--99999999989399 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 99999999999999999997401 Q gi|254780611|r 267 ERVRQIEARAFKKVQESIQKQVE 289 (302) Q Consensus 267 eRVrQI~~~AL~kLR~~l~~~~~ 289 (302) T Consensus 180 ~TVKsrL~RArk~LRe~La~~~~ 202 (231) T PRK11922 180 ETVKTRLHRARRLLRESLAREIG 202 (231) T ss_pred HHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999999999999999999872 |
|
| >PRK12531 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.80 E-value=2.5e-17 Score=135.33 Aligned_cols=184 Identities=18% Similarity=0.209 Sum_probs=134.5 Q ss_pred CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH Q ss_conf 99899999999999828599999999943077875655557999988899999988899898621853456899975778 Q gi|254780611|r 29 LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108 (302) Q Consensus 29 Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~w 108 (302) T Consensus 9 ~~~~~~~eLi~r~~-~GD~~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDlvQe~Flk~~~~~~~~~~~~s-~f~tWl~~I 86 (194) T PRK12531 9 FGRQEWLECMEKVK-SRDKQAFALVFSYYAPKLKQFAMKHVGNEQVAMEMVQETMSTVWQKAHLFDGQKS-ALSTWIYTI 86 (194) T ss_pred CCCHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHH T ss_conf 35166999999999-5889999999999999999999999399999999999999999998886676536-099999999 Q ss_pred HHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHH Q ss_conf 99999985320246001102300358999999997887866244788824677888618983211000000122343355 Q gi|254780611|r 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188 (302) Q Consensus 109 Ir~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~ 188 (302) T Consensus 87 a~N~~~d~lRk~~~----------------------~~~-------------------~~~~----------------~~ 109 (194) T PRK12531 87 IRNLCFDLLRKQKG----------------------KDL-------------------HIHA----------------DD 109 (194) T ss_pred HHHHHHHHHHHHCC----------------------CCC-------------------CCCH----------------HH T ss_conf 99999999997404----------------------343-------------------4321----------------11 Q ss_pred HCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHH Q ss_conf 20232345320000012356870565566666667779999996219999999999982788888989999997789999 Q gi|254780611|r 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268 (302) Q Consensus 189 ~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eR 268 (302) T Consensus 110 ~~~-~~~~~~---~~-~-~~~~~e--------~~~~~~~~~~~l~~Lp~~~R~vi~L~~~e~--~s~~EIAe~l~is~~T 173 (194) T PRK12531 110 IWP-SDYYPP---DL-V-DHYSPE--------QDMLKEQVMKFLDRLPKAQRDVLQAVYLEE--LPHQQVAEMFDIPLGT 173 (194) T ss_pred CCC-CCCCCC---CC-C-CCCCHH--------HHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHH T ss_conf 142-224783---00-0-125879--------999999999999869999999999998869--9999999998929999 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999974 Q gi|254780611|r 269 VRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 269 VrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 174 VKsrl~rA~k~LR~~Le~e 192 (194) T PRK12531 174 VKSRLRLAVEKLRHSMDAE 192 (194) T ss_pred HHHHHHHHHHHHHHHHHHC T ss_conf 9999999999999998657 |
|
| >PRK12534 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.79 E-value=6.6e-17 Score=132.53 Aligned_cols=186 Identities=16% Similarity=0.204 Sum_probs=138.0 Q ss_pred HCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHH Q ss_conf 07999998999999999998285999999999430778756555579999888999999888998986218534568999 Q gi|254780611|r 24 RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103 (302) Q Consensus 24 ~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsT 103 (302) T Consensus 2 ~~~p~~~~de~~~Li~~~~-~GD~~Af~~Ly~~y~~~l~~~~~~~~~~~~~AeDv~Qe~Fl~vw~~~~~~~~~~~-~~~t 79 (187) T PRK12534 2 SAIPGHDDDETGRLLTATA-GGDRHAFEALYRQTSPKLFGVCLRMIPQRAEAEEVLQDVFTLIWHKAGQFDPSRA-RGLT 79 (187) T ss_pred CCCCCCCCHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCC-CHHH T ss_conf 9999999628999999999-3689999999999999999999998699999999999999999987533687522-1899 Q ss_pred HHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCC Q ss_conf 75778999999853202460011023003589999999978878662447888246778886189832110000001223 Q gi|254780611|r 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183 (302) Q Consensus 104 YA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~ 183 (302) T Consensus 80 Wl~~IarN~~~d~lR~~~~~------------------------------~~---------------------------~ 102 (187) T PRK12534 80 WLAMIARNKAIDHLRANAPQ------------------------------RR---------------------------N 102 (187) T ss_pred HHHHHHHHHHHHHHHHCCCC------------------------------CC---------------------------C T ss_conf 99999999999999962441------------------------------35---------------------------7 Q ss_pred CCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHC Q ss_conf 43355202323453200000123568705655666666677799999962199999999999827888889899999977 Q gi|254780611|r 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263 (302) Q Consensus 184 ~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lg 263 (302) T Consensus 103 ~~~~~------~~~------~~~~~~~~~----e~~~~~~~~~~l~~al~~L~~~~r~vi~l~~~eg--~s~~EIA~~l~ 164 (187) T PRK12534 103 VALDD------AGE------LRAADASPL----ERTERASTRRRIDHCLAELEPPRSELIRTAFFEG--ITYEELAARTD 164 (187) T ss_pred CCCCC------CCC------CCCCCCCHH----HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHC T ss_conf 77341------100------135689827----7899999999999999868998999999999849--99999999989 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 89999999999999999999997 Q gi|254780611|r 264 VSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 264 iS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 165 i~~gTVksrl~ra~~~Lr~~Lek 187 (187) T PRK12534 165 TPIGTVKSWIRRGLAKLKACLER 187 (187) T ss_pred CCHHHHHHHHHHHHHHHHHHHCC T ss_conf 19999999999999999998667 |
|
| >PRK12519 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.78 E-value=5.5e-17 Score=133.07 Aligned_cols=185 Identities=16% Similarity=0.233 Sum_probs=134.6 Q ss_pred CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH Q ss_conf 99989999999999982859999999994307787565555799998889999998889989862185345689997577 Q gi|254780611|r 28 MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107 (302) Q Consensus 28 ~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~ 107 (302) T Consensus 10 ~m~~~tD~eLi~~~~-~GD~~Af~~L~~ry~~~l~~~a~~~~~~~~~AeDlvQe~fl~~~~~~~-~~~~~~-~~~~wL~~ 86 (194) T PRK12519 10 SLSSRSDAELFSALK-AGQSAALGVLYDRHAGLVYGLALKILGNSQEAEDLTQEIFLSLWRKSS-YDPKRG-SLSSYLLT 86 (194) T ss_pred CCCCCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH-CCCCCC-CHHHHHHH T ss_conf 999960999999999-385999999999999999999999939999999999999999998633-166624-29999999 Q ss_pred HHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH Q ss_conf 89999998532024600110230035899999999788786624478882467788861898321100000012234335 Q gi|254780611|r 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187 (302) Q Consensus 108 wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd 187 (302) T Consensus 87 ia~n~~~d~~R~~~~~~----------------------~~----------~~~~~------------------------ 110 (194) T PRK12519 87 LTRSRAIDRLRSRRSRQ----------------------RL----------LERWQ------------------------ 110 (194) T ss_pred HHHHHHHHHHHHHHCCC----------------------CH----------HHHHH------------------------ T ss_conf 99999999999863201----------------------22----------44444------------------------ Q ss_pred HHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH Q ss_conf 52023234532000001235687056556666666777999999621999999999998278888898999999778999 Q gi|254780611|r 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267 (302) Q Consensus 188 ~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~e 267 (302) T Consensus 111 ~~~~~--~----------~~~~~~~~----~~~~~e~~~~l~~al~~Lp~~~R~v~~L~~~eg--~s~~EIA~~lgis~~ 172 (194) T PRK12519 111 QELLG--E----------ASEDTPLE----QASLAERSQRVQTALAQLPESQRQVLELAYYEG--LSQSEIAKRLGIPLG 172 (194) T ss_pred HHHCC--C----------CCCCCHHH----HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHH T ss_conf 54114--6----------77898588----998999999999999819988756889999819--999999999894999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHC Q ss_conf 9999999999999999997401 Q gi|254780611|r 268 RVRQIEARAFKKVQESIQKQVE 289 (302) Q Consensus 268 RVrQI~~~AL~kLR~~l~~~~~ 289 (302) T Consensus 173 tVk~rl~rA~~~Lr~~L~e~le 194 (194) T PRK12519 173 TVKARARQGLLKLRELLQDLLE 194 (194) T ss_pred HHHHHHHHHHHHHHHHHHHHHC T ss_conf 9999999999999999898739 |
|
| >PRK09652 RNA polymerase sigma factor RpoE; Provisional | Back alignment and domain information |
|---|
Probab=99.78 E-value=5.7e-17 Score=132.95 Aligned_cols=184 Identities=15% Similarity=0.110 Sum_probs=130.6 Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 99999999828599999999943077875655557999988899999988899898621853456899975778999999 Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114 (302) Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~ 114 (302) T Consensus 7 ~~Li~~~~-~Gd~~A~~~L~~~y~~~l~~~~~~~~~~~~~aeDv~Qe~fl~l~~~~~~~~~~--~~~~~wL~~iarn~~~ 83 (192) T PRK09652 7 QELVERVQ-QGDRAAFELLVRKYQPRLYRLLSRLVRDPADAEDLAQETFIKAYRALPSFRGG--AAFYTWLYRIAVNTAI 83 (192) T ss_pred HHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCC--HHHHHHHHHHHHHHHH T ss_conf 99999998-38899999999999999999999996999999998759999988711345771--1799999999999999 Q ss_pred HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC Q ss_conf 85320246001102300358999999997887866244788824677888618983211000000122343355202323 Q gi|254780611|r 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194 (302) Q Consensus 115 ~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d 194 (302) T Consensus 84 d~~r~~~r~----------------------~~~--------~---------------------------~~~~~~~~-- 104 (192) T PRK09652 84 NYLRKQGRR----------------------PPE--------S---------------------------DLDAEDAE-- 104 (192) T ss_pred HHHHHHHCC----------------------CCC--------C---------------------------CCCHHHHH-- T ss_conf 999997165----------------------665--------5---------------------------40023454-- Q ss_pred CCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 45320000012356870565566666667779999996219999999999982788888989999997789999999999 Q gi|254780611|r 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302) Q Consensus 195 ~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302) T Consensus 105 ---~~~~~~~~~~~~~~e~~~----~~~e~~~~l~~~l~~L~~~~r~v~~l~~~~~--~s~~EIA~~lgis~~tVk~~l~ 175 (192) T PRK09652 105 ---YFEDADALREISSPEEEL----LSQELEQRVRRAIESLPEELRTAITLREIEG--LSYEEIAEIMGCPIGTVRSRIF 175 (192) T ss_pred ---HHCCCCCCCCCCCHHHHH----HHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHH T ss_conf ---300000355557679999----9999999999999839999998888999729--9999999998939999999999 Q ss_pred HHHHHHHHHHHHHHC Q ss_conf 999999999997401 Q gi|254780611|r 275 RAFKKVQESIQKQVE 289 (302) Q Consensus 275 ~AL~kLR~~l~~~~~ 289 (302) T Consensus 176 Ra~~~Lr~~L~~~~~ 190 (192) T PRK09652 176 RAREALRAKLQPLLD 190 (192) T ss_pred HHHHHHHHHHHHHHH T ss_conf 999999999898771 |
|
| >PRK11923 algU RNA polymerase sigma factor AlgU; Provisional | Back alignment and domain information |
|---|
Probab=99.78 E-value=6.8e-17 Score=132.43 Aligned_cols=191 Identities=19% Similarity=0.241 Sum_probs=135.5 Q ss_pred CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH Q ss_conf 99989999999999982859999999994307787565555799998889999998889989862185345689997577 Q gi|254780611|r 28 MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107 (302) Q Consensus 28 ~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~ 107 (302) T Consensus 1 m~t~~~D~~Li~~~~-~GD~~Af~~L~~~y~~~l~~~~~~~~~d~~~AeDi~Qe~f~~~~~~~~~~~~~--~~f~~WL~~ 77 (193) T PRK11923 1 MLTQEEDQQLVERVQ-RGDKRAFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFIKAYRALGNFRGD--SAFYTWLYR 77 (193) T ss_pred CCCCCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCC--HHHHHHHHH T ss_conf 998710999999999-48699999999999999999999990999999999999999998613212650--468999999 Q ss_pred HHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH Q ss_conf 89999998532024600110230035899999999788786624478882467788861898321100000012234335 Q gi|254780611|r 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187 (302) Q Consensus 108 wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd 187 (302) T Consensus 78 Ia~n~~~~~~~~~~r--------------------------------r~~~-~------~~~~---------------~~ 103 (193) T PRK11923 78 IAINTAKNHLVSRGR--------------------------------RPPD-S------DVSS---------------ED 103 (193) T ss_pred HHHHHHHHHHHHHHC--------------------------------CCCC-C------CCCH---------------HH T ss_conf 999999999999865--------------------------------5753-3------3453---------------46 Q ss_pred HHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH Q ss_conf 52023234532000001235687056556666666777999999621999999999998278888898999999778999 Q gi|254780611|r 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267 (302) Q Consensus 188 ~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~e 267 (302) T Consensus 104 ~~~~~~~-------~~-~~~~~~~e~~~----~~~e~~~~i~~~l~~Lp~~~R~v~~L~~~eg--ls~~EIA~~l~is~~ 169 (193) T PRK11923 104 AEFYDGD-------HA-LKDIESPERAL----LRDEIEATVHRTIQQLPEDLRTALTLREFDG--LSYEDIASVMQCPVG 169 (193) T ss_pred HHHCCCC-------CC-CCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHH T ss_conf 6522554-------32-23448888999----9999999999999817898999999999949--999999999892999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHC Q ss_conf 9999999999999999997401 Q gi|254780611|r 268 RVRQIEARAFKKVQESIQKQVE 289 (302) Q Consensus 268 RVrQI~~~AL~kLR~~l~~~~~ 289 (302) T Consensus 170 tVk~rl~RAr~~Lr~~L~~ll~ 191 (193) T PRK11923 170 TVRSRIFRAREAIDKALQPLLQ 191 (193) T ss_pred HHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999999999999999899873 |
|
| >PRK09641 RNA polymerase sigma factor SigW; Provisional | Back alignment and domain information |
|---|
Probab=99.78 E-value=7.8e-17 Score=132.02 Aligned_cols=182 Identities=13% Similarity=0.158 Sum_probs=130.7 Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH Q ss_conf 99999999982859999999994307787565555799998889999998889989862185345689997577899999 Q gi|254780611|r 34 EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113 (302) Q Consensus 34 e~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I 113 (302) T Consensus 5 i~~Li~~~~-~GD~~Af~~L~~~y~~~l~~~~~~~~~~~~~AeD~vQe~flk~~~~~~~~~~~~--~~~~WL~~Ia~N~~ 81 (187) T PRK09641 5 IKKRIKQVK-KGDQNAFADIVDLYKDKIYQLCYRMLGNRHEAEDIAQEAFIRAYVNIDSFDINR--KFSTWLYRIATNLT 81 (187) T ss_pred HHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCC--CHHHHHHHHHHHHH T ss_conf 999999999-388999999999999999999999909999999999999999998461257413--49999999999999 Q ss_pred HHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCC Q ss_conf 98532024600110230035899999999788786624478882467788861898321100000012234335520232 Q gi|254780611|r 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193 (302) Q Consensus 114 ~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~ 193 (302) T Consensus 82 ~d~~Rk~~~~~~------------------------------------------------------------~~~~~~~~ 101 (187) T PRK09641 82 IDRLRKKKPDYY------------------------------------------------------------LDAEVAGT 101 (187) T ss_pred HHHHHHHCCCCC------------------------------------------------------------HHHHHCCC T ss_conf 999997265343------------------------------------------------------------12654031 Q ss_pred CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 34532000001235687056556666666777999999621999999999998278888898999999778999999999 Q gi|254780611|r 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273 (302) Q Consensus 194 d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302) T Consensus 102 --~~~~~~~~~~~~~~~~~~~~~----~~e~~~~l~~al~~Lp~~~r~v~~L~~~~~--~s~~EIA~~l~is~~tVk~~l 173 (187) T PRK09641 102 --EGLTMYSQLAADEALPEDQVE----SLELQETIQEEILQLPDKYRTVIVLKYIEE--LSLKEISEILDLPVGTVKTRI 173 (187) T ss_pred --CCCHHHHHCCCCCCCHHHHHH----HHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHH T ss_conf --000044303566798478999----999999999999828988889999999829--989999999893999999999 Q ss_pred HHHHHHHHHHHHH Q ss_conf 9999999999997 Q gi|254780611|r 274 ARAFKKVQESIQK 286 (302) Q Consensus 274 ~~AL~kLR~~l~~ 286 (302) T Consensus 174 ~RAr~~Lr~~Lk~ 186 (187) T PRK09641 174 HRGREALRKQLRH 186 (187) T ss_pred HHHHHHHHHHHHC T ss_conf 9999999998666 |
|
| >PRK12513 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.77 E-value=1.5e-16 Score=130.23 Aligned_cols=180 Identities=19% Similarity=0.240 Sum_probs=131.3 Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 99999999828599999999943077875655557999988899999988899898621853456899975778999999 Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114 (302) Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~ 114 (302) T Consensus 14 ~eL~~~~~-~GD~~Af~~L~~~y~~~l~~~~~~~~~d~~~AeDl~Qevfl~~~~~~~~~~~~--~~~~~wL~~ia~n~~~ 90 (194) T PRK12513 14 EALMLRYR-AGDAAAFEALYARHRTGLYRFLLRLARDPALADDIFQETWLRVIRARSQWQPR--ARFRTWLYQIARNRLI 90 (194) T ss_pred HHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHH T ss_conf 99999999-46299999999999999999999996999999999989999999887616975--4599999999999999 Q ss_pred HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC Q ss_conf 85320246001102300358999999997887866244788824677888618983211000000122343355202323 Q gi|254780611|r 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194 (302) Q Consensus 115 ~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d 194 (302) T Consensus 91 ~~~R~~~~----------------------~~-------~~~---------------------------~~~~~------ 108 (194) T PRK12513 91 DHWRKHGA----------------------RQ-------APS---------------------------LDADE------ 108 (194) T ss_pred HHHHHHHC----------------------CC-------CCC---------------------------CCHHH------ T ss_conf 99998744----------------------37-------753---------------------------11036------ Q ss_pred CCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 45320000012356870565566666667779999996219999999999982788888989999997789999999999 Q gi|254780611|r 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302) Q Consensus 195 ~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302) T Consensus 109 -----~~~~~~~~~~~~e~~~----~~~e~~~~l~~~l~~Lp~~~r~il~L~~~~g--~s~~EIA~~l~is~~tVk~~l~ 177 (194) T PRK12513 109 -----LAHALADDGAGPEQQL----SLFRDRRRLQAALETLPDEQREVFLLREHGD--LSLEEIAQLTGVPLETVKSRLR 177 (194) T ss_pred -----HHHCCCCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHH T ss_conf -----6503677889999999----9999999999999729989999999999849--9999999998949999999999 Q ss_pred HHHHHHHHHHHHHHCC Q ss_conf 9999999999974012 Q gi|254780611|r 275 RAFKKVQESIQKQVEL 290 (302) Q Consensus 275 ~AL~kLR~~l~~~~~~ 290 (302) T Consensus 178 rA~~~Lr~~L~~e~~~ 193 (194) T PRK12513 178 YALQKLRELLAEEVAV 193 (194) T ss_pred HHHHHHHHHHHHHHCC T ss_conf 9999999999885355 |
|
| >PRK09646 RNA polymerase sigma factor SigK; Reviewed | Back alignment and domain information |
|---|
Probab=99.77 E-value=5.9e-17 Score=132.86 Aligned_cols=182 Identities=16% Similarity=0.209 Sum_probs=126.6 Q ss_pred CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH Q ss_conf 99998999999999998285999999999430778756555579999888999999888998986218534568999757 Q gi|254780611|r 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302) Q Consensus 27 ~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302) T Consensus 10 ~~~~~~d~~~Li~~~~-~GD~~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDivQevFl~~~~~~~~~~~~~~-~~~~WL~ 87 (194) T PRK09646 10 PPAPSPDLDALLRRVA-RGDQDAFAELYDRTASRVYGLVRRVLRDPGYSEETTQEVYLEVWRTASRFDPARG-SALAWLL 87 (194) T ss_pred CCCCCCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHH T ss_conf 6437966999999999-3679999999999999999999999299999999999999999997521475426-5999999 Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH Q ss_conf 78999999853202460011023003589999999978878662447888246778886189832110000001223433 Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186 (302) Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SL 186 (302) T Consensus 88 ~Ia~n~~~d----------------------~~R~~~~~~~~--------~~--------------------~~-~~~~~ 116 (194) T PRK09646 88 TLAHRRAVD----------------------RVRSEQAASQR--------EV--------------------RY-GARNV 116 (194) T ss_pred HHHHHHHHH----------------------HHHHHHHHHHH--------HH--------------------HH-CCCCC T ss_conf 999999999----------------------99998741324--------43--------------------20-00236 Q ss_pred HHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCH Q ss_conf 55202323453200000123568705655666666677799999962199999999999827888889899999977899 Q gi|254780611|r 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266 (302) Q Consensus 187 d~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~ 266 (302) T Consensus 117 ~-------~---------~--~~~~~----e~~~~~~~~~~l~~~l~~Lp~~~R~vi~L~~~~g--~s~~EIA~~Lgis~ 172 (194) T PRK09646 117 D-------P---------A--FDQVA----EEVEARLERERVRGCLDALTDTQREAITLAYYGG--LTYREVAERLAVPL 172 (194) T ss_pred C-------C---------C--CCCCH----HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCH T ss_conf 8-------8---------7--55314----7899899999999999867815789999999939--99999999989199 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999 Q gi|254780611|r 267 ERVRQIEARAFKKVQESIQ 285 (302) Q Consensus 267 eRVrQI~~~AL~kLR~~l~ 285 (302) T Consensus 173 ~TVk~rl~rA~~~LR~~LG 191 (194) T PRK09646 173 GTVKTRMRDGLRRLRDCLG 191 (194) T ss_pred HHHHHHHHHHHHHHHHHHC T ss_conf 9999999999999999837 |
|
| >PRK13919 putative RNA polymerase sigma E protein; Provisional | Back alignment and domain information |
|---|
Probab=99.77 E-value=9.2e-17 Score=131.57 Aligned_cols=176 Identities=22% Similarity=0.237 Sum_probs=125.8 Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 99999999828599999999943077875655557999988899999988899898621853456899975778999999 Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114 (302) Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~ 114 (302) T Consensus 11 ~eLi~~~~-~GD~~Af~~L~~ry~~~l~~~~~~~~~d~~~AEDivQe~flki~~~~~~~~~~~~-~~~~wL~~ia~n~~~ 88 (187) T PRK13919 11 EALLALVA-RGDEEAFRALFRRYAGSFLALARRMGLDGAAAEDVVQEAMIRVWQKAKEFDPRRG-SARAFLLTLGHHAAV 88 (187) T ss_pred HHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHH T ss_conf 99999999-4779999999999999999999999099999999999999999999987687646-499999999999999 Q ss_pred HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC Q ss_conf 85320246001102300358999999997887866244788824677888618983211000000122343355202323 Q gi|254780611|r 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194 (302) Q Consensus 115 ~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d 194 (302) T Consensus 89 d~~Rk~~~~---~---------------------~-~~~-~~~~~----------------------~~~~~~------- 113 (187) T PRK13919 89 DEVRRRAAR---P---------------------L-PLE-PDPER----------------------EEEAFD------- 113 (187) T ss_pred HHHHHHHCC---C---------------------C-CCC-CCCHH----------------------HHHHCC------- T ss_conf 999976267---7---------------------8-777-66101----------------------133204------- Q ss_pred CCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 45320000012356870565566666667779999996219999999999982788888989999997789999999999 Q gi|254780611|r 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302) Q Consensus 195 ~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302) T Consensus 114 ---------~~~~~~~~e--------~~~~~~~l~~al~~L~~~~r~vi~L~~~~g--~s~~EIA~~L~is~~TVk~~l~ 174 (187) T PRK13919 114 ---------LPGPGLDEE--------GHLDRTRLGRALKALSPEERRVIEVLYYQG--YTHREAARLLGLPLGTLKTWAR 174 (187) T ss_pred ---------CCCCCCCHH--------HHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHH T ss_conf ---------688640278--------789999999999849999999999999859--9999999998939999999999 Q ss_pred HHHHHHHHHHHH Q ss_conf 999999999997 Q gi|254780611|r 275 RAFKKVQESIQK 286 (302) Q Consensus 275 ~AL~kLR~~l~~ 286 (302) T Consensus 175 rA~k~Lr~~Lke 186 (187) T PRK13919 175 RALSKLKEVLRE 186 (187) T ss_pred HHHHHHHHHHCC T ss_conf 999999998459 |
|
| >PRK06811 RNA polymerase factor sigma-70; Validated | Back alignment and domain information |
|---|
Probab=99.76 E-value=3.7e-16 Score=127.52 Aligned_cols=174 Identities=18% Similarity=0.253 Sum_probs=125.2 Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCC---CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH Q ss_conf 999999999828599999999943077875655557999---98889999998889989862185345689997577899 Q gi|254780611|r 34 EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG---LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110 (302) Q Consensus 34 e~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g---~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr 110 (302) T Consensus 3 d~~Li~~~~-~GD~~Af~~l~~~y~~~v~~~~~~~l~~~~~~~~aeD~vQevFi~~~~~~~~~~~~~~-~f~~WL~~Ia~ 80 (185) T PRK06811 3 EDNFIKELK-KKNEKALEFIIDTYGNLIKKIVHKVLGTDQYKQLIEECVNDIFLSIWNNIDKFDEEKG-SFKNWIAAISK 80 (185) T ss_pred HHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHCHHCCCCCC-CHHHHHHHHHH T ss_conf 999999998-2789999999999999999999999677688989999999999999983700388645-29999999999 Q ss_pred HHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHC Q ss_conf 99998532024600110230035899999999788786624478882467788861898321100000012234335520 Q gi|254780611|r 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190 (302) Q Consensus 111 ~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i 190 (302) T Consensus 81 n~~~d~~Rk~~r----------------------~~~------------------------------------~~~~~~~ 102 (185) T PRK06811 81 YKAIDYKRKLTK----------------------NNN------------------------------------IDSDEFI 102 (185) T ss_pred HHHHHHHHHHCC----------------------CCC------------------------------------CCHHHHC T ss_conf 999999997426----------------------566------------------------------------6456521 Q ss_pred CCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHH Q ss_conf 23234532000001235687056556666666777999999621999999999998278888898999999778999999 Q gi|254780611|r 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270 (302) Q Consensus 191 ~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVr 270 (302) T Consensus 103 --------------~~~~~~~e~~~~----~~e~~~~l~~~l~~L~~~~r~v~~l~~~~~--~s~~EIA~~l~is~~tVk 162 (185) T PRK06811 103 --------------LISEESIENEII----LKENKEEIIKLINDLKKLDREIFIKRYLLG--ESIEEIAKKLGLTRSAID 162 (185) T ss_pred --------------CCCCCCHHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHH T ss_conf --------------355588788999----999999999998489999999999999949--999999999892999999 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 99999999999999974 Q gi|254780611|r 271 QIEARAFKKVQESIQKQ 287 (302) Q Consensus 271 QI~~~AL~kLR~~l~~~ 287 (302) T Consensus 163 ~rl~Rar~~Lr~~L~~~ 179 (185) T PRK06811 163 NRLSRGRKKLKNKLNIL 179 (185) T ss_pred HHHHHHHHHHHHHHHHH T ss_conf 99999999999998898 |
|
| >PRK09648 RNA polymerase sigma factor SigD; Reviewed | Back alignment and domain information |
|---|
Probab=99.76 E-value=3.8e-16 Score=127.42 Aligned_cols=179 Identities=17% Similarity=0.238 Sum_probs=127.0 Q ss_pred CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC----CCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH Q ss_conf 989999999999982859999999994307787565555799----9988899999988899898621853456899975 Q gi|254780611|r 30 EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY----GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105 (302) Q Consensus 30 t~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~----g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA 105 (302) T Consensus 5 ~~~~l~~Li~~a~-~GD~~Af~~L~~~~~~~v~r~~~~~l~~~~~~~~dAeDl~Qe~fl~~~~~l~~f~~-~~~~f~~Wl 82 (187) T PRK09648 5 AGEELDALVAEAV-AGDRRALREVLETIHPLVVRYCRARLGTVERSGLSADDVAQEVCLAVITALPRYRD-QGRPFLAFV 82 (187) T ss_pred CHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC-CCCCHHHHH T ss_conf 2178999999998-45899999999999999999999997144587643999999999999983766266-778499999 Q ss_pred HHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCC Q ss_conf 77899999985320246001102300358999999997887866244788824677888618983211000000122343 Q gi|254780611|r 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185 (302) Q Consensus 106 ~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~S 185 (302) T Consensus 83 ~~Ia~n~~~d~~----------------------R~~~r~--------~~~~~--------------------------- 105 (187) T PRK09648 83 YGIAAHKVADAH----------------------RAAGRD--------KAYPT--------------------------- 105 (187) T ss_pred HHHHHHHHHHHH----------------------HHHHCC--------CCCCC--------------------------- T ss_conf 999999999999----------------------987467--------64321--------------------------- Q ss_pred HHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCC Q ss_conf 35520232345320000012356870565566666667779999996219999999999982788888989999997789 Q gi|254780611|r 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265 (302) Q Consensus 186 Ld~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS 265 (302) T Consensus 106 -~~-~~----------~-~~~~~~~pe~~~~~~----e~~~~l~~~l~~Lp~~~R~vl~L~~~~g--~s~~EIA~~lg~s 166 (187) T PRK09648 106 -EE-VP----------E-RPSDEAGPEQRALEA----ESSARMRELLEILPEKQREILILRVVVG--LSAEETAEAVGST 166 (187) T ss_pred -CC-CC----------C-CCCCCCCHHHHHHHH----HHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCC T ss_conf -12-33----------3-478778858999989----9999999999839999999999999849--9999999998939 Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999997 Q gi|254780611|r 266 RERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 266 ~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 167 ~~tVk~~l~RA~~~Lr~~lE~ 187 (187) T PRK09648 167 PGAVRVAQHRALSRLRAEIEQ 187 (187) T ss_pred HHHHHHHHHHHHHHHHHHHCC T ss_conf 999999999999999998659 |
|
| >PRK05602 RNA polymerase sigma factor; Reviewed | Back alignment and domain information |
|---|
Probab=99.75 E-value=4.5e-16 Score=126.92 Aligned_cols=177 Identities=18% Similarity=0.228 Sum_probs=127.5 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH Q ss_conf 99999999999828599999999943077875655557999988899999988899898621853456899975778999 Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111 (302) Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~ 111 (302) T Consensus 5 ~sD~eLi~~~~-~Gd~~Af~~L~~~y~~~l~~~~~~~~~d~~~AeDivQe~fl~~~~~~~~~~~~~~-~~~~wL~~ia~n 82 (186) T PRK05602 5 DPDAELMARVG-AGDASAFRVLVARKLPRLLALATRMLGDPAEAEDVAQETFLRIWNQAPSWRPGEA-RFDTWLHRVVLN 82 (186) T ss_pred CCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCH-HHHHHHHHHHHH T ss_conf 42999999999-2889999999999999999999999299999999999999999987222588620-399999999999 Q ss_pred HHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC Q ss_conf 99985320246001102300358999999997887866244788824677888618983211000000122343355202 Q gi|254780611|r 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191 (302) Q Consensus 112 ~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~ 191 (302) T Consensus 83 ~~~d~----------------------~Rk~~-~~----------~------------~~~-------------~~~--- 101 (186) T PRK05602 83 LCYDR----------------------LRRRR-EV----------P------------VED-------------APE--- 101 (186) T ss_pred HHHHH----------------------HHHHH-CC----------C------------CCC-------------CCC--- T ss_conf 99999----------------------98714-15----------7------------322-------------200--- Q ss_pred CCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH Q ss_conf 32345320000012356870565566666667779999996219999999999982788888989999997789999999 Q gi|254780611|r 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271 (302) Q Consensus 192 ~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ 271 (302) T Consensus 102 ------------~~~~~~~~~~~~----~~~e~~~~l~~al~~Lp~~~R~v~~L~~~~g--~s~~EIA~~l~is~~tVk~ 163 (186) T PRK05602 102 ------------VPDPAPGPDERL----EARQRARRVEQALAALPERQREAIVLQYYQG--LSNIEAARVMGLSVDALES 163 (186) T ss_pred ------------CCCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHH T ss_conf ------------034689877899----9999999999999759987889999998638--9999999998939999999 Q ss_pred HHHHHHHHHHHHHHHHHC Q ss_conf 999999999999997401 Q gi|254780611|r 272 IEARAFKKVQESIQKQVE 289 (302) Q Consensus 272 I~~~AL~kLR~~l~~~~~ 289 (302) T Consensus 164 ~l~RAr~~Lr~~L~e~~~ 181 (186) T PRK05602 164 LLARARRALRAQLAELPP 181 (186) T ss_pred HHHHHHHHHHHHHHCCCC T ss_conf 999999999999766797 |
|
| >PRK12543 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.73 E-value=1.5e-15 Score=123.53 Aligned_cols=176 Identities=17% Similarity=0.189 Sum_probs=125.5 Q ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH Q ss_conf 99999999998285999999999430778756555579999888999999888998986218534568999757789999 Q gi|254780611|r 33 EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112 (302) Q Consensus 33 ee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~ 112 (302) T Consensus 5 d~~~Li~~~~-~Gd~~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeD~vQe~Flk~~~~~~~~~~~~--~~~~WL~~ia~n~ 81 (190) T PRK12543 5 DYKHLIQLTL-SGNKEAYSELYDVTIQEVYKTVHFLIEDKTDVDDVVQEVYIQLYESLRKYDSEK--PFRPWLIGLVIKQ 81 (190) T ss_pred CHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHH T ss_conf 8999999999-566999999999999999999999909999999999999999999998718888--6899999999999 Q ss_pred HHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCC Q ss_conf 99853202460011023003589999999978878662447888246778886189832110000001223433552023 Q gi|254780611|r 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192 (302) Q Consensus 113 I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~ 192 (302) T Consensus 82 ~~~~~r~~~----------------------~~~~~~-------------------------------~~~~~~~----- 103 (190) T PRK12543 82 IHSYRRKRW----------------------MRLRIF-------------------------------KKAEEQR----- 103 (190) T ss_pred HHHHHHHHH----------------------HHCCCC-------------------------------CCHHHHC----- T ss_conf 999999875----------------------003412-------------------------------2001001----- Q ss_pred CCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHH Q ss_conf 23453200000123568705655666666677799999962199999999999827888889899999977899999999 Q gi|254780611|r 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272 (302) Q Consensus 193 ~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI 272 (302) T Consensus 104 ------------~~~~~~~~~~~~~~----~~~~~l~~~l~~Lp~~~R~vi~L~~~~g--~s~~EIA~~l~is~~tVk~r 165 (190) T PRK12543 104 ------------KPVQIDFSNDLLSK----ISNQKLIELIHKLPYKLKQVIILRYLHD--YSQEEVAQILHIPIGTVKSR 165 (190) T ss_pred ------------CCCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHH T ss_conf ------------55568826899999----9999999999849999999999999859--99999999989399999999 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 999999999999974 Q gi|254780611|r 273 EARAFKKVQESIQKQ 287 (302) Q Consensus 273 ~~~AL~kLR~~l~~~ 287 (302) T Consensus 166 l~rA~k~LR~kle~~ 180 (190) T PRK12543 166 IHAALKKLRQKEQIE 180 (190) T ss_pred HHHHHHHHHHHHHHH T ss_conf 999999999999999 |
|
| >PRK11924 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.73 E-value=9.8e-16 Score=124.69 Aligned_cols=178 Identities=17% Similarity=0.194 Sum_probs=130.3 Q ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 99999998285999999999430778756555579999888999999888998986218534568999757789999998 Q gi|254780611|r 36 VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115 (302) Q Consensus 36 ~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~ 115 (302) T Consensus 2 ~l~~~a~-~Gd~~Af~~ly~~y~~~l~~~~~~~~~d~~~AeDi~Qe~fi~l~~~~~~~~~~~--~~~~wL~~iarn~~~d 78 (180) T PRK11924 2 QLPAVAA-SGDKEAFSELFLPHAPDLLRYARRQLGNRALAEDAVQEAFLRAWRKADLFNGKG--SARTWLLTIARNKCYD 78 (180) T ss_pred HHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCC--CHHHHHHHHHHHHHHH T ss_conf 8889999-559999999999999999999999929999999999999999988632235434--7999999999999999 Q ss_pred HHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCC Q ss_conf 53202460011023003589999999978878662447888246778886189832110000001223433552023234 Q gi|254780611|r 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195 (302) Q Consensus 116 ~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~ 195 (302) T Consensus 79 ~~rk~~~~~~--------------------------~---~~---------------------------~~~~~~----- 97 (180) T PRK11924 79 MLRRRRRERK--------------------------E---AA---------------------------EDEDLA----- 97 (180) T ss_pred HHHHHHHHCC--------------------------C---CC---------------------------CHHHCC----- T ss_conf 9999720102--------------------------2---33---------------------------110013----- Q ss_pred CCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 53200000123568705655666666677799999962199999999999827888889899999977899999999999 Q gi|254780611|r 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275 (302) Q Consensus 196 ~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302) T Consensus 98 -------~~~~~~~~~e~~~----~~~~~~~~l~~~l~~L~~~~r~il~l~~~~g--~s~~eIA~~lgis~~tv~~~l~R 164 (180) T PRK11924 98 -------PLSAEFETPEAAL----LAKDDLARIDRCLDALPEKQREVFLLRYVEG--LSYQEIADQLGVPLGTVKSRLRR 164 (180) T ss_pred -------CCCCCCCCHHHHH----HHHHHHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHH T ss_conf -------3344669858999----9999999999999859999999999999968--59999999989499999999999 Q ss_pred HHHHHHHHHHHHHCC Q ss_conf 999999999974012 Q gi|254780611|r 276 AFKKVQESIQKQVEL 290 (302) Q Consensus 276 AL~kLR~~l~~~~~~ 290 (302) T Consensus 165 a~~~Lr~~Le~~~~~ 179 (180) T PRK11924 165 ARQKLRECLEAQWSA 179 (180) T ss_pred HHHHHHHHHHHHHCC T ss_conf 999999999986546 |
|
| >PRK12514 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.73 E-value=1.4e-15 Score=123.65 Aligned_cols=178 Identities=14% Similarity=0.169 Sum_probs=127.9 Q ss_pred CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH Q ss_conf 98999999999998285999999999430778756555579999888999999888998986218534568999757789 Q gi|254780611|r 30 EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109 (302) Q Consensus 30 t~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wI 109 (302) T Consensus 2 ~p~d~~~Li~~~~-~GD~~Af~~L~~~y~~~l~~~a~~~~~d~~~AeDi~Qe~fl~~~~~~~~~~~~~-~~~~~wL~~ia 79 (179) T PRK12514 2 QPDDIEKLIVRVS-LGDRDAFSSLYDATSAKLFGICLRVLKDRSEAEEALQDVYVKIWTKADRFAVSG-LSPMTWLITIA 79 (179) T ss_pred CCCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC-CCHHHHHHHHH T ss_conf 9710999999999-658999999999999999999999909999999999999999998875157665-53999999999 Q ss_pred HHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHH Q ss_conf 99999853202460011023003589999999978878662447888246778886189832110000001223433552 Q gi|254780611|r 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189 (302) Q Consensus 110 r~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~ 189 (302) T Consensus 80 rN~~id~~----------------------R~~~----------~~~---------------------------~~~~~~ 100 (179) T PRK12514 80 RNHAIDRL----------------------RARK----------AVA---------------------------VDIDEA 100 (179) T ss_pred HHHHHHHH----------------------HHCC----------CCC---------------------------CCHHHH T ss_conf 99999999----------------------8637----------777---------------------------874567 Q ss_pred CCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH Q ss_conf 02323453200000123568705655666666677799999962199999999999827888889899999977899999 Q gi|254780611|r 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269 (302) Q Consensus 190 i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV 269 (302) T Consensus 101 ~-----------~-~~~~~~~~e~~~~~~~----~~~~l~~~l~~Lp~~~r~~~~l~~~eg--~s~~EIA~~l~is~~tV 162 (179) T PRK12514 101 H-----------D-LADPSPGPEAEVIAGD----EGQRIDACLEELEKDRAAAVRRAYLEG--LSYKELAERHDVPLNTM 162 (179) T ss_pred H-----------H-HCCCCCCHHHHHHHHH----HHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHH T ss_conf 6-----------5-1246898699999889----999999999875599999999996069--98999999889099999 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 99999999999999997 Q gi|254780611|r 270 RQIEARAFKKVQESIQK 286 (302) Q Consensus 270 rQI~~~AL~kLR~~l~~ 286 (302) T Consensus 163 k~~l~rA~~~Lr~~L~k 179 (179) T PRK12514 163 RTWLRRSLLKLRECLSR 179 (179) T ss_pred HHHHHHHHHHHHHHHCC T ss_conf 99999999999998576 |
|
| >PRK12526 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.73 E-value=2.3e-15 Score=122.25 Aligned_cols=186 Identities=13% Similarity=0.157 Sum_probs=130.1 Q ss_pred CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH Q ss_conf 99989999999999982859999999994307787565555799998889999998889989862185345689997577 Q gi|254780611|r 28 MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107 (302) Q Consensus 28 ~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~ 107 (302) T Consensus 19 ~~p~~~~~~Lv~~A~-~GD~~AF~~Ly~~y~~~l~~~~~r~l~d~~~AEDvvQetFlkvw~~~~~~~~~~~-~f~tWL~~ 96 (206) T PRK12526 19 QVPTELSQWLILVAI-SRDKQAFTHLFQFFAPKIKRFGIKQLGNEAQANELVQETMSNVWRKAHLYNGDKG-AATTWVYT 96 (206) T ss_pred CCCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHH T ss_conf 673689999999999-6589999999999999999999999199999999999999999983876586425-29999999 Q ss_pred HHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH Q ss_conf 89999998532024600110230035899999999788786624478882467788861898321100000012234335 Q gi|254780611|r 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187 (302) Q Consensus 108 wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd 187 (302) T Consensus 97 IarN~~~d~lRk~----------------------~~~~~~------------------~~~-~d~----------~~~~ 125 (206) T PRK12526 97 VMRNAAFDMLRKI----------------------KAKKEQ------------------NLG-DDI----------WPIE 125 (206) T ss_pred HHHHHHHHHHHHH----------------------HCCCCC------------------CCC-CHH----------CHHH T ss_conf 9999999999865----------------------312222------------------321-000----------0044 Q ss_pred HHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH Q ss_conf 52023234532000001235687056556666666777999999621999999999998278888898999999778999 Q gi|254780611|r 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267 (302) Q Consensus 188 ~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~e 267 (302) T Consensus 126 --------------~~~~~-~~~~~~~~~~~----~~~~~l~~~l~~LP~~~R~vi~L~~~eg--ls~~EIA~~l~is~~ 184 (206) T PRK12526 126 --------------QALAE-SQSESEEFSDH----LMDKQILSYIEKLPEAQQTVVKGVYFQE--LSQEQLAQQLNVPLG 184 (206) T ss_pred --------------HCCCC-CCCCHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHH T ss_conf --------------30145-78835789989----9999999999868999888989999859--999999999893999 Q ss_pred HHHHHHHHHHHHHHHHHHHH Q ss_conf 99999999999999999974 Q gi|254780611|r 268 RVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 268 RVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 185 TVksrl~rAlk~LR~~L~e~ 204 (206) T PRK12526 185 TVKSRLRLALAKLKVQMGEQ 204 (206) T ss_pred HHHHHHHHHHHHHHHHHHCC T ss_conf 99999999999999987303 |
|
| >PRK12524 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.72 E-value=2.4e-15 Score=122.06 Aligned_cols=179 Identities=17% Similarity=0.231 Sum_probs=127.9 Q ss_pred CCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH Q ss_conf 99989999999999982859999999994307787565555799998889999998889989862185345689997577 Q gi|254780611|r 28 MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107 (302) Q Consensus 28 ~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~ 107 (302) T Consensus 10 ~~sD~---~Lv~~~~-~GD~~Af~~L~~ry~~~l~~~a~~~l~d~~~AEDlvQe~Fl~~~~~~~~~~~~~~-~~~tWL~~ 84 (196) T PRK12524 10 DVSDE---ALLVLFA-NGDPAAARALTLRLAPRALAVATRVLGNRAEAEDVTQEAMLRLWRIAPDWRQGEA-RVSTWLYR 84 (196) T ss_pred CCCHH---HHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHH T ss_conf 89999---9999999-2889999999999999999999999199999999999999999997466156520-79999999 Q ss_pred HHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHH Q ss_conf 89999998532024600110230035899999999788786624478882467788861898321100000012234335 Q gi|254780611|r 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187 (302) Q Consensus 108 wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd 187 (302) T Consensus 85 Ia~N~~~d~----------------------~R~~~~~---------~----------------------------~~~~ 105 (196) T PRK12524 85 VVCNLCTDR----------------------LRRQRRA---------S----------------------------VDLD 105 (196) T ss_pred HHHHHHHHH----------------------HHHHHCC---------C----------------------------CCCC T ss_conf 999999999----------------------9985056---------7----------------------------7611 Q ss_pred HHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHH Q ss_conf 52023234532000001235687056556666666777999999621999999999998278888898999999778999 Q gi|254780611|r 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267 (302) Q Consensus 188 ~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~e 267 (302) T Consensus 106 ~------~--~----~~~~~~~~~e~~~~----~~~~~~~l~~al~~Lp~~~R~vi~L~~~eg--~s~~EIA~~lgis~~ 167 (196) T PRK12524 106 D------A--P----EPADAAPGAEEALQ----EGDRMRALDAALAALPERQRQAVVLRHIEG--LSNPEIAEVMQIGVE 167 (196) T ss_pred C------C--C----CCCCCCCCHHHHHH----HHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHH T ss_conf 2------4--3----32456898879999----899999999999859999999989999808--999999999892999 Q ss_pred HHHHHHHHHHHHHHHHHHHHH Q ss_conf 999999999999999999740 Q gi|254780611|r 268 RVRQIEARAFKKVQESIQKQV 288 (302) Q Consensus 268 RVrQI~~~AL~kLR~~l~~~~ 288 (302) T Consensus 168 tVk~~l~Rark~Lr~~L~~~r 188 (196) T PRK12524 168 AVESLTARGKRALAALLAGQR 188 (196) T ss_pred HHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999999987179 |
|
| >PRK12515 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.72 E-value=2.5e-15 Score=121.98 Aligned_cols=175 Identities=19% Similarity=0.247 Sum_probs=125.9 Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH Q ss_conf 99999999982859999999994307787565555799998889999998889989862185345689997577899999 Q gi|254780611|r 34 EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113 (302) Q Consensus 34 e~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I 113 (302) T Consensus 9 D~~Lv~~~~-~gd~~Af~~L~~ry~~~l~~~~~~~~~~~~~AeDivQe~Fl~~~~~~~~~~~~--~~~~~WL~~Iarn~~ 85 (189) T PRK12515 9 DEMLLARIA-QGDRTAMHTLYGRHHVRVYRFGLRLVRDEQTAEDLVSEVFLDVWRQAGQFEGR--SQVSTWLLSIARFKA 85 (189) T ss_pred HHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHH T ss_conf 999999999-37799999999999999999999992999999999999999999865102530--229999999999999 Q ss_pred HHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCC Q ss_conf 98532024600110230035899999999788786624478882467788861898321100000012234335520232 Q gi|254780611|r 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193 (302) Q Consensus 114 ~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~ 193 (302) T Consensus 86 ~~~----------------------~r~~~~-------~~~~--------------~~~-----------------~--- 102 (189) T PRK12515 86 LSA----------------------LRQRKD-------EEID--------------DEA-----------------A--- 102 (189) T ss_pred HHH----------------------HHHCCC-------CCCC--------------HHH-----------------H--- T ss_conf 999----------------------985133-------6665--------------456-----------------7--- Q ss_pred CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 34532000001235687056556666666777999999621999999999998278888898999999778999999999 Q gi|254780611|r 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273 (302) Q Consensus 194 d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302) T Consensus 103 ----~----~~~~~~~~~e~~~----~~~~~~~~l~~~l~~L~~~~R~vi~l~~~e~--~s~~EIA~~lgis~~tV~~~l 168 (189) T PRK12515 103 ----A----AIEDGSDTPEVAL----QKKDTSAILRACIAKLSPAHREIIDLVYYHE--KSVEEVGEIVGIPESTVKTRM 168 (189) T ss_pred ----H----HCCCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHH T ss_conf ----6----3367789988999----8999999999998759999999999999849--999999999892999999999 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 999999999999740 Q gi|254780611|r 274 ARAFKKVQESIQKQV 288 (302) Q Consensus 274 ~~AL~kLR~~l~~~~ 288 (302) T Consensus 169 ~RAr~~Lr~~L~~~g 183 (189) T PRK12515 169 FYARKKLAELLKAAG 183 (189) T ss_pred HHHHHHHHHHHHHHC T ss_conf 999999999999728 |
|
| >PRK12537 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.71 E-value=1.5e-15 Score=123.53 Aligned_cols=177 Identities=11% Similarity=0.116 Sum_probs=122.8 Q ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH Q ss_conf 89999999999982859999999994307787565555799998889999998889989862185345689997577899 Q gi|254780611|r 31 KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110 (302) Q Consensus 31 ~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr 110 (302) T Consensus 7 p~d~e~ll~~~~-~GD~~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDivQe~Fl~~~~~~~~~~~~~~-~~~~WL~~Iar 84 (184) T PRK12537 7 PFDYEACLQACA-RGERRALQRLYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTKAASFDAARG-SARGWIYSVTR 84 (184) T ss_pred CCCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCC-CHHHHHHHHHH T ss_conf 999999999999-5889999999999999999999999299999999999999999986041684426-39999999999 Q ss_pred HHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHC Q ss_conf 99998532024600110230035899999999788786624478882467788861898321100000012234335520 Q gi|254780611|r 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190 (302) Q Consensus 111 ~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i 190 (302) T Consensus 85 n~~~~~lR~~~r~~-----------------------------~~~~~--------------------------~~~~-~ 108 (184) T PRK12537 85 HLALNTLRDTRREV-----------------------------VLDDD--------------------------ASEQ-A 108 (184) T ss_pred HHHHHHHHHHCCCC-----------------------------CCCCH--------------------------HHHH-C T ss_conf 99999999850656-----------------------------66510--------------------------0210-1 Q ss_pred CCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHH Q ss_conf 23234532000001235687056556666666777999999621999999999998278888898999999778999999 Q gi|254780611|r 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270 (302) Q Consensus 191 ~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVr 270 (302) T Consensus 109 ~---~~----------~~~~~~~----~~~~~~~~~~l~~~l~~L~~~~r~~i~l~~~eg--~s~~EIA~~l~is~~TVk 169 (184) T PRK12537 109 T---AQ----------GWQEIID----DFDLWVNSGKIHRCLEQLEPARRNCILHAYVDG--CSHAEIAQRLGAPLGTVK 169 (184) T ss_pred C---CC----------CCCCCCC----HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHH T ss_conf 3---46----------7777556----798999999999999809998999999988439--999999999892999999 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 99999999999999 Q gi|254780611|r 271 QIEARAFKKVQESI 284 (302) Q Consensus 271 QI~~~AL~kLR~~l 284 (302) T Consensus 170 ~rl~rA~~~LR~~L 183 (184) T PRK12537 170 AWIKRSLKALRECM 183 (184) T ss_pred HHHHHHHHHHHHHC T ss_conf 99999999999872 |
|
| >PRK12538 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.71 E-value=3.3e-15 Score=121.14 Aligned_cols=175 Identities=15% Similarity=0.232 Sum_probs=128.0 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH Q ss_conf 99999999999828599999999943077875655557999988899999988899898621853456899975778999 Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111 (302) Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~ 111 (302) T Consensus 48 d~D~eLv~R~~-~GD~~AF~~Ly~ry~~~l~~~a~r~l~d~~dAEDvvQEvFlk~w~~~~~f~~g~s-~f~tWL~~IA~N 125 (233) T PRK12538 48 DEDEELLDRLA-TDDEAAFRLLVERHIDRAYAIALRIVGNRADAEDVVQDTMLKVWTHRGRWQHGRA-KFSTWLYRVVSN 125 (233) T ss_pred CCHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCC-HHHHHHHHHHHH T ss_conf 97899999999-6029999999999999999999999599999999999999999998844777867-399999999999 Q ss_pred HHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC Q ss_conf 99985320246001102300358999999997887866244788824677888618983211000000122343355202 Q gi|254780611|r 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191 (302) Q Consensus 112 ~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~ 191 (302) T Consensus 126 ~~id~----------------------~Rk~r------------~~~~------------------------d~~~e--- 144 (233) T PRK12538 126 RCIDL----------------------RRKPR------------TENV------------------------DAVPE--- 144 (233) T ss_pred HHHHH----------------------HHHHC------------CCCC------------------------CCCCC--- T ss_conf 99999----------------------97414------------5652------------------------23444--- Q ss_pred CCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH Q ss_conf 32345320000012356870565566666667779999996219999999999982788888989999997789999999 Q gi|254780611|r 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271 (302) Q Consensus 192 ~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ 271 (302) T Consensus 145 ------------~~d~~~~~~~~----l~~~e~~~~L~~aL~~Lp~~~R~vl~L~~~eg--ls~~EIA~~Lgis~~TVKs 206 (233) T PRK12538 145 ------------VADGKPDAVSV----IERNELSDLLEAAMQRLPEQQRIAVILSYHEN--MSNGEIAEVMDTTVAAVES 206 (233) T ss_pred ------------CCCCCCCHHHH----HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHH T ss_conf ------------45689888789----99999999999999759999999999999849--9999999998929999999 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 9999999999999974 Q gi|254780611|r 272 IEARAFKKVQESIQKQ 287 (302) Q Consensus 272 I~~~AL~kLR~~l~~~ 287 (302) T Consensus 207 rL~RAr~~LR~~L~r~ 222 (233) T PRK12538 207 LLKRGRQQLRDLLRRH 222 (233) T ss_pred HHHHHHHHHHHHHHHH T ss_conf 9999999999999987 |
|
| >PRK09643 RNA polymerase sigma factor SigM; Reviewed | Back alignment and domain information |
|---|
Probab=99.71 E-value=4.7e-15 Score=120.13 Aligned_cols=177 Identities=15% Similarity=0.142 Sum_probs=128.6 Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 99999999828599999999943077875655557999988899999988899898621853456899975778999999 Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114 (302) Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~ 114 (302) T Consensus 15 ~eLi~~~~-~GD~~Af~~L~~ry~~~l~~~a~~~~~~~~~AeDvvQe~flk~~~~~~~~~~~--~~f~~WL~~Ia~N~~~ 91 (197) T PRK09643 15 AELLAAHV-AGDRYAFGELFRRHHRQLWRLARRTSGTREDAADALQDAMLSAHRGAGSFRGD--AAVSSWLHRIVVNACL 91 (197) T ss_pred HHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC--CHHHHHHHHHHHHHHH T ss_conf 99999999-27799999999999999999999991999999999999999999988633886--3499999999999999 Q ss_pred HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC Q ss_conf 85320246001102300358999999997887866244788824677888618983211000000122343355202323 Q gi|254780611|r 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194 (302) Q Consensus 115 ~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d 194 (302) T Consensus 92 d~----------------------~Rk~~~~-----------~-------------------------~~~~~~~~---- 109 (197) T PRK09643 92 DR----------------------LRRAKAR-----------P-------------------------TVPLEDVY---- 109 (197) T ss_pred HH----------------------HHHHCCC-----------C-------------------------CCCCCCCC---- T ss_conf 99----------------------9985146-----------7-------------------------78866567---- Q ss_pred CCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 45320000012356870565566666667779999996219999999999982788888989999997789999999999 Q gi|254780611|r 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302) Q Consensus 195 ~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302) T Consensus 110 --------------~~~~~~~~~----~e~~~~l~~al~~Lp~~~R~vl~L~~~eg--~s~~EIA~~lgis~~tVKsrl~ 169 (197) T PRK09643 110 --------------PVADRETAR----VETAIAVQRALMRLPVEQRAALVAVDMQG--YSVADTARMLGVAEGTVKSRCA 169 (197) T ss_pred --------------CCCCCHHHH----HHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHH T ss_conf --------------786520313----89999999999769998879999999819--9999999998939999999999 Q ss_pred HHHHHHHHHHHHHHCCCCCCCC Q ss_conf 9999999999974012246776 Q gi|254780611|r 275 RAFKKVQESIQKQVELSSSPPL 296 (302) Q Consensus 275 ~AL~kLR~~l~~~~~~~~~~~~ 296 (302) T Consensus 170 RAr~~Lr~~L~~l~~~g~~~~~ 191 (197) T PRK09643 170 RGRARLAELLGYLRAGGNASPG 191 (197) T ss_pred HHHHHHHHHHHHHHCCCCCCCC T ss_conf 9999999999988457899998 |
|
| >PRK09638 RNA polymerase sigma factor SigY; Reviewed | Back alignment and domain information |
|---|
Probab=99.70 E-value=2.4e-15 Score=122.12 Aligned_cols=174 Identities=14% Similarity=0.186 Sum_probs=122.5 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH Q ss_conf 99999999999828599999999943077875655557999988899999988899898621853456899975778999 Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111 (302) Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~ 111 (302) T Consensus 4 ~~d~~Li~~~~-~GD~~Af~~L~~~y~~~l~~~~~~~~~~~~~AeDivQe~fl~~~~~~~~~~~~--~~~~~wL~~ia~n 80 (177) T PRK09638 4 MEEKELIRRAK-KGNDAALTKLLQQHYNFLYGYVLKLTLNPDLAEDLVQETMLKAIENIHQFQGR--SKFSTWLISIASR 80 (177) T ss_pred CCHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--HHHHHHHHHHHHH T ss_conf 77999999999-47799999999999999999999991999999999999999999988770650--0799999999999 Q ss_pred HHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC Q ss_conf 99985320246001102300358999999997887866244788824677888618983211000000122343355202 Q gi|254780611|r 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191 (302) Q Consensus 112 ~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~ 191 (302) T Consensus 81 ~~~d~~Rk~~----------------------r~~-------~----~~~----------------------~~~~~~~~ 105 (177) T PRK09638 81 LYLDHLRKRK----------------------REE-------L----REE----------------------AATEETLR 105 (177) T ss_pred HHHHHHHHHC----------------------CCC-------C----CCC----------------------CCCCCCCC T ss_conf 9999999860----------------------301-------1----000----------------------23333556 Q ss_pred CCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH Q ss_conf 32345320000012356870565566666667779999996219999999999982788888989999997789999999 Q gi|254780611|r 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271 (302) Q Consensus 192 ~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ 271 (302) T Consensus 106 ----------------~-~~~~~~~~~~~----~~~l~~~l~~Lp~~~r~v~~L~~~eg--~s~~EIA~~l~is~~tVk~ 162 (177) T PRK09638 106 ----------------K-EKWETAISGHE----WSELLDLLMKLPPELRAPFILKHYYG--YTYEEIAKMLGIPEGTVKS 162 (177) T ss_pred ----------------C-CCCCHHHHHHH----HHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHH T ss_conf ----------------6-76114653799----99999999759998989999999919--9999999998939999999 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 999999999999997 Q gi|254780611|r 272 IEARAFKKVQESIQK 286 (302) Q Consensus 272 I~~~AL~kLR~~l~~ 286 (302) T Consensus 163 ~l~rA~~~Lr~~L~~ 177 (177) T PRK09638 163 RVHHGLKKIRKELGQ 177 (177) T ss_pred HHHHHHHHHHHHHCC T ss_conf 999999999998582 |
|
| >PRK12512 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.70 E-value=6e-15 Score=119.44 Aligned_cols=174 Identities=16% Similarity=0.203 Sum_probs=124.2 Q ss_pred CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC-C---CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH Q ss_conf 989999999999982859999999994307787565555799-9---988899999988899898621853456899975 Q gi|254780611|r 30 EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY-G---LPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105 (302) Q Consensus 30 t~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~-g---~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA 105 (302) T Consensus 5 ~~~e~~~Li~~~~-~GD~~Af~~L~~~~~~~l~~~~~~~l~~~~~~~~dAeDlvQevfl~~~~~~~~~~~~--~~f~~WL 81 (184) T PRK12512 5 REDEWTDLMRSAN-AGDAAAYRRLLKAVTPVLRAAARRGLARAGQPADQAEDIVQEILLAVHLKRHTWDPG--APFAPWL 81 (184) T ss_pred CHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCCCCCC--CCHHHHH T ss_conf 5287999999998-278999999999999999999999988468998899999999999999872314888--8589999 Q ss_pred HHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCC Q ss_conf 77899999985320246001102300358999999997887866244788824677888618983211000000122343 Q gi|254780611|r 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185 (302) Q Consensus 106 ~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~S 185 (302) T Consensus 82 ~~Iarn~~~d~~Rk~~~~~~----------------------------------------------------------~~ 103 (184) T PRK12512 82 FAIARNKLIDALRRRGRRVF----------------------------------------------------------VD 103 (184) T ss_pred HHHHHHHHHHHHHHHCCCCC----------------------------------------------------------CC T ss_conf 99999999999997437778----------------------------------------------------------98 Q ss_pred HHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCC Q ss_conf 35520232345320000012356870565566666667779999996219999999999982788888989999997789 Q gi|254780611|r 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265 (302) Q Consensus 186 Ld~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS 265 (302) T Consensus 104 ~~~~~-----------~~~~~-~~~~-~~~--------~~~~l~~~L~~Lp~~~R~vi~L~~~~g--~s~~EIA~~lgis 160 (184) T PRK12512 104 IDDFA-----------ETLPS-EPAA-ETL--------PAGDVGRHLETLPPRQRDVVQSIAVEG--ASIKETAAKLSMS 160 (184) T ss_pred HHHHH-----------HCCCC-CCCC-CHH--------HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCC T ss_conf 34442-----------21678-8876-426--------899999999689999999999998559--7999999998919 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999974 Q gi|254780611|r 266 RERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 266 ~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 161 ~~tVk~~l~RA~~~Lr~~l~~e 182 (184) T PRK12512 161 EGAVRVALHRGLAALAAKFRSE 182 (184) T ss_pred HHHHHHHHHHHHHHHHHHHHHC T ss_conf 9999999999999999998608 |
|
| >PRK09647 RNA polymerase sigma factor SigE; Reviewed | Back alignment and domain information |
|---|
Probab=99.68 E-value=1.5e-14 Score=116.72 Aligned_cols=184 Identities=14% Similarity=0.206 Sum_probs=129.4 Q ss_pred CCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH Q ss_conf 99998999999999998285999999999430778756555579999888999999888998986218534568999757 Q gi|254780611|r 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302) Q Consensus 27 ~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302) T Consensus 26 ~~~~~~~~~~~~~~~~~~~d~~AF~eLv~rh~~~vy~~a~r~~gn~~dAEDlvQEtFlka~r~l~~f~~~---sf~tWL~ 102 (222) T PRK09647 26 EPSDELTGTAVFDATGDKATMPSWEELVRQHADRVYRLAYRLSGNQHDAEDLTQETFIRVFRSLQNYQPG---TFEGWLH 102 (222) T ss_pred CCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC---CHHHHHH T ss_conf 9865444448887414524589999999999999999999985999899999999999999862224773---0899999 Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH Q ss_conf 78999999853202460011023003589999999978878662447888246778886189832110000001223433 Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186 (302) Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SL 186 (302) T Consensus 103 rIA~N~~iD~----------------------~Rr~~r-~--------~~---------------------------~~~ 124 (222) T PRK09647 103 RITTNLFLDM----------------------VRRRQR-I--------RM---------------------------EAL 124 (222) T ss_pred HHHHHHHHHH----------------------HHHCCC-C--------CC---------------------------CCC T ss_conf 9999999999----------------------981124-6--------65---------------------------556 Q ss_pred HHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCH Q ss_conf 55202323453200000123568705655666666677799999962199999999999827888889899999977899 Q gi|254780611|r 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266 (302) Q Consensus 187 d~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~ 266 (302) T Consensus 125 ~e------~-----~e~~~~~~~~pe~~~~~----~~~~~~L~~al~~Lp~~qR~vl~Lr~~eg--lS~~EIAe~Lgis~ 187 (222) T PRK09647 125 PE------D-----YDRVPADEPNPEQIYHD----ARLDPDLQAALDSLPPEFRAAVVLCDIEG--LSYEEIAATLGVKL 187 (222) T ss_pred CC------H-----HHHCCCCCCCHHHHHHH----HHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCH T ss_conf 11------3-----44256678997899999----99999999999829999988998799639--99999999989399 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999740 Q gi|254780611|r 267 ERVRQIEARAFKKVQESIQKQV 288 (302) Q Consensus 267 eRVrQI~~~AL~kLR~~l~~~~ 288 (302) T Consensus 188 gTVKsrl~RAr~~LR~~Lea~~ 209 (222) T PRK09647 188 GTVRSRIHRGRQALRAYLAAHA 209 (222) T ss_pred HHHHHHHHHHHHHHHHHHHHCC T ss_conf 9999999999999999987109 |
|
| >PRK12539 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.64 E-value=7.3e-14 Score=112.19 Aligned_cols=176 Identities=17% Similarity=0.224 Sum_probs=120.9 Q ss_pred CCHHHH-HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHC----CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHH Q ss_conf 998999-99999999828599999999943077875655557----9999888999999888998986218534568999 Q gi|254780611|r 29 LEKQEE-YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR----GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103 (302) Q Consensus 29 Lt~eee-~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~----~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsT 103 (302) T Consensus 2 ~~~~~~~~~Lv~~~~-~GD~~Af~~L~~r~~~~l~~~~~~~l~r~~~~~~dAeDlvQe~fl~~~~~~~~~~~~~--~~~~ 78 (184) T PRK12539 2 MSKENELKALMLASL-DGDAAAHRALLERLSGHLRAYYKGKLARIGRGAEEAEDLVQEALMAIHTRRHTYDPEQ--PLTP 78 (184) T ss_pred CCCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHH T ss_conf 997799999999998-0889999999999899999999999998439998999999999999998377559998--5799 Q ss_pred HHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCC Q ss_conf 75778999999853202460011023003589999999978878662447888246778886189832110000001223 Q gi|254780611|r 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183 (302) Q Consensus 104 YA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~ 183 (302) T Consensus 79 WL~~Ia~n~~~d~~R----------------------~~~~~~~-------------------~---------------- 101 (184) T PRK12539 79 WVYAIARYKLIDHLR----------------------RTRASLA-------------------D---------------- 101 (184) T ss_pred HHHHHHHHHHHHHHH----------------------HCCCCCC-------------------C---------------- T ss_conf 999999999999998----------------------5145534-------------------4---------------- Q ss_pred CCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHC Q ss_conf 43355202323453200000123568705655666666677799999962199999999999827888889899999977 Q gi|254780611|r 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263 (302) Q Consensus 184 ~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lg 263 (302) T Consensus 102 ~~~~~----~~~-------~~~~~~--~-~~~----e---~~~~l~~~l~~Lp~~~r~v~~L~~~eg--~s~~EIA~~lg 158 (184) T PRK12539 102 VPIDD----ADE-------LVAHDD--A-AAV----E---STLDLGRLLARLPEKMRLAIQAVKLDG--LSVAEAATRSG 158 (184) T ss_pred CCCCC----CCC-------CCCCCC--H-HHH----H---HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHC T ss_conf 88443----444-------567851--3-318----8---999999999849999999999999949--99999999989 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 899999999999999999999974 Q gi|254780611|r 264 VSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 264 iS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 159 is~~tVks~l~Rark~Lr~~L~~e 182 (184) T PRK12539 159 MSESAVKVSVHRGLKALAALIGRE 182 (184) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 199999999999999999998650 |
|
| >PRK09415 RNA polymerase factor sigma C; Reviewed | Back alignment and domain information |
|---|
Probab=99.64 E-value=4.8e-14 Score=113.39 Aligned_cols=174 Identities=7% Similarity=0.133 Sum_probs=124.4 Q ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 99999998285999999999430778756555579999888999999888998986218534568999757789999998 Q gi|254780611|r 36 VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115 (302) Q Consensus 36 ~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~ 115 (302) T Consensus 4 ~~i~~~~~e~~e~Af~~L~~~y~~~v~~~~~~~~~d~~~AeD~~Qe~fl~~~~~~~~~~~~--~~~~~Wl~~ia~N~~~d 81 (177) T PRK09415 4 LTIEAFEIEDKEDLIDEIMNKYGQEVLQLVYSYVKNKEVAEDLTQEIFVKCYKSLHTYKGK--SNLKTWLYRIAINHCKD 81 (177) T ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHH T ss_conf 9999998769299999999999999999999990999999999999999999987455885--54999999999999999 Q ss_pred HHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCC Q ss_conf 53202460011023003589999999978878662447888246778886189832110000001223433552023234 Q gi|254780611|r 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195 (302) Q Consensus 116 ~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~ 195 (302) T Consensus 82 ~~R~----------------------~~~~~-----~~---~~----------------------------~~~~----- 98 (177) T PRK09415 82 YLKS----------------------WHNKK-----VI---VT----------------------------EDIF----- 98 (177) T ss_pred HHHH----------------------HHCCC-----CC---CC----------------------------HHHH----- T ss_conf 9999----------------------87135-----56---30----------------------------3566----- Q ss_pred CCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 53200000123568705655666666677799999962199999999999827888889899999977899999999999 Q gi|254780611|r 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275 (302) Q Consensus 196 ~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302) T Consensus 99 ------~~~~~~~~~~~~~~----~~~~~~~~l~~~l~~L~~~~r~ii~l~~~~~--~s~~EIA~~l~is~~tV~~rl~R 166 (177) T PRK09415 99 ------TYMESQKESVEEEV----IQNAEDERLASAVMSLPIKYREVIYLFYYEE--LSIKEIATVTGVNENTIKTRLKK 166 (177) T ss_pred ------HHCCCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHH T ss_conf ------40255579989999----9999999999999769999999999999809--98999999889299999999999 Q ss_pred HHHHHHHHHHH Q ss_conf 99999999997 Q gi|254780611|r 276 AFKKVQESIQK 286 (302) Q Consensus 276 AL~kLR~~l~~ 286 (302) T Consensus 167 ark~Lr~~Lee 177 (177) T PRK09415 167 AKELLKKGLEE 177 (177) T ss_pred HHHHHHHHHCC T ss_conf 99999988368 |
|
| >PRK12518 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.64 E-value=3.9e-14 Score=113.98 Aligned_cols=171 Identities=14% Similarity=0.192 Sum_probs=119.6 Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 99999982859999999994307787565555799998889999998889989862185345689997577899999985 Q gi|254780611|r 37 LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116 (302) Q Consensus 37 l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~ 116 (302) T Consensus 1 Li~~~~-~Gd~~Af~~ly~~y~~~l~~~~~~~~~~-~~AEDi~Qd~fik~~~~~~~~~~~-~-~~~~wl~~ia~N~~~d~ 76 (175) T PRK12518 1 LIQRCQ-RGDRQAFRQLYRRYQQKVRSTLYQLCGR-ELLDDLVQEVFLRVWKGLPKLRNP-A-YFSTWLYRITWNVATDA 76 (175) T ss_pred CHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHCCCCCCCC-C-HHHHHHHHHHHHHHHHH T ss_conf 989898-6589999999999999999999997799-889999999999998711127982-3-59999999999999999 Q ss_pred HHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC Q ss_conf 32024600110230035899999999788786624478882467788861898321100000012234335520232345 Q gi|254780611|r 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196 (302) Q Consensus 117 i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~ 196 (302) T Consensus 77 ~Rk~----------------------~r~~~-------~~~~------------------------~~~~~-------~- 95 (175) T PRK12518 77 RRQF----------------------AKRPS-------RIQQ------------------------DSSLD-------Q- 95 (175) T ss_pred HHHH----------------------HCCCC-------CCCC------------------------CCCCC-------C- T ss_conf 9998----------------------70243-------2332------------------------10002-------4- Q ss_pred CCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 32000001235687056556666666777999999621999999999998278888898999999778999999999999 Q gi|254780611|r 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276 (302) Q Consensus 197 ~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~A 276 (302) T Consensus 96 --------~~~~~~~~~-~~~----~~~~~~l~~~l~~Lp~~~r~vi~l~~~~~--~s~~EIA~~l~is~~tVk~~l~Ra 160 (175) T PRK12518 96 --------PSRPSDEPD-LMQ----LHYQDLVQQGLATLSLEHRAVLVLHDLED--LPQKEIAEILNIPVGTVKSRLFYA 160 (175) T ss_pred --------CCCCCCCHH-HHH----HHHHHHHHHHHHCCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHH T ss_conf --------567889769-999----99999999999769999999999999929--999999999895999999999999 Q ss_pred HHHHHHHHHHH Q ss_conf 99999999974 Q gi|254780611|r 277 FKKVQESIQKQ 287 (302) Q Consensus 277 L~kLR~~l~~~ 287 (302) T Consensus 161 ~k~Lr~~L~~e 171 (175) T PRK12518 161 RRQLRKFLQQQ 171 (175) T ss_pred HHHHHHHHHHC T ss_conf 99999999986 |
|
| >PRK09640 RNA polymerase sigma factor SigX; Reviewed | Back alignment and domain information |
|---|
Probab=99.63 E-value=5.9e-14 Score=112.81 Aligned_cols=177 Identities=16% Similarity=0.229 Sum_probs=123.6 Q ss_pred CCHHHHHHHHHHHHH--HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH Q ss_conf 998999999999998--285999999999430778756555579999888999999888998986218534568999757 Q gi|254780611|r 29 LEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106 (302) Q Consensus 29 Lt~eee~~l~~~~~~--~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~ 106 (302) T Consensus 8 l~D~e---Lv~~~~~g~~gD~~AF~~L~~~y~~~v~~~~~~~~~~~~dAEDl~Qe~flk~~~~l~~~~~~--~~f~~WL~ 82 (188) T PRK09640 8 LNDEE---LVARVHVELFHVTRAYEELMRRYQRTLFNVCARYLGNDRDADDVCQEVMLKVLYGLKNFEGK--SKFKTWLY 82 (188) T ss_pred CCHHH---HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHH T ss_conf 99999---99999827963899999999999999999999990999999999999999999988765898--87899999 Q ss_pred HHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCH Q ss_conf 78999999853202460011023003589999999978878662447888246778886189832110000001223433 Q gi|254780611|r 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186 (302) Q Consensus 107 ~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SL 186 (302) T Consensus 83 ~Ia~N~~~d~~Rk~----------------------~r~~--------~~------------------------~~~~~~ 108 (188) T PRK09640 83 SITYNECITQYRKE----------------------RRKR--------RL------------------------MDALSL 108 (188) T ss_pred HHHHHHHHHHHHHH----------------------CCCC--------CC------------------------CCCCCC T ss_conf 99999999999986----------------------1545--------55------------------------430002 Q ss_pred HHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCH Q ss_conf 55202323453200000123568705655666666677799999962199999999999827888889899999977899 Q gi|254780611|r 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266 (302) Q Consensus 187 d~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~ 266 (302) T Consensus 109 ~~-~~---~---------~~~~~~---------~~~e~~~~l~~~l~~L~~~~R~vl~L~~~~~--ls~~EIA~~l~is~ 164 (188) T PRK09640 109 DP-LE---E---------ASEEKA---------PKPEERGGLDRWLVHVNPIDREILVLRFVAE--LEFQEIADIMHMGL 164 (188) T ss_pred CC-CC---C---------CCCCCC---------HHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCH T ss_conf 44-45---6---------863100---------2489999999999848999999999999929--99999999989299 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999999740 Q gi|254780611|r 267 ERVRQIEARAFKKVQESIQKQV 288 (302) Q Consensus 267 eRVrQI~~~AL~kLR~~l~~~~ 288 (302) T Consensus 165 ~tVksrl~RAr~~Lr~~L~~~~ 186 (188) T PRK09640 165 SATKMRYKRALDKLREKFAGLA 186 (188) T ss_pred HHHHHHHHHHHHHHHHHHHCCC T ss_conf 9999999999999999864514 |
|
| >PRK12536 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.62 E-value=1.5e-13 Score=110.07 Aligned_cols=173 Identities=16% Similarity=0.175 Sum_probs=119.5 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH Q ss_conf 99999999999828599999999943077875655557999-98889999998889989862185345689997577899 Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110 (302) Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g-~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr 110 (302) T Consensus 3 ~~l~~Ll~~~~-~GD~~Af~~l~~~y~~~l~~~~~~~l~~~~~~AEDl~Qe~fl~~~~~~~~~~~~~--~~~~WL~~Ia~ 79 (178) T PRK12536 3 SRLKALLLRGL-AGDAAAYRQFLTELARHLRAFLRRRLPQLPDEVEDLVQEILLAVHNARHTYRPDQ--PLTAWVQAIAR 79 (178) T ss_pred HHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHH T ss_conf 88999999998-1569999999999999999999999099876899999999999999787669999--68999999999 Q ss_pred HHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHC Q ss_conf 99998532024600110230035899999999788786624478882467788861898321100000012234335520 Q gi|254780611|r 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190 (302) Q Consensus 111 ~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i 190 (302) T Consensus 80 n~~~d~~R~~~----------------------r~~------~~~----------------------------~~~~~~~ 103 (178) T PRK12536 80 YKLADFLRRRA----------------------RRE------ALH----------------------------DPLDDEA 103 (178) T ss_pred HHHHHHHHHHH----------------------CCC------CCC----------------------------CCCHHHH T ss_conf 99999999874----------------------645------445----------------------------7511232 Q ss_pred CCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHH Q ss_conf 23234532000001235687056556666666777999999621999999999998278888898999999778999999 Q gi|254780611|r 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270 (302) Q Consensus 191 ~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVr 270 (302) T Consensus 104 -----------~~~~~~~~~~~----------~~~~~l~~~l~~Lp~~~R~~~~l~~~eg--~s~~EIA~~lgis~~tVk 160 (178) T PRK12536 104 -----------ELFATSDDEAA----------EARRDLGKLLEQLPDRQRLPIVHVKLEG--LSVEETAQLTGLSESAVK 160 (178) T ss_pred -----------HCCCCCCCCHH----------HHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHH T ss_conf -----------02478863589----------9999999999869998999999998859--999999999892999999 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 9999999999999997 Q gi|254780611|r 271 QIEARAFKKVQESIQK 286 (302) Q Consensus 271 QI~~~AL~kLR~~l~~ 286 (302) T Consensus 161 ~rl~Ra~k~Lr~~L~g 176 (178) T PRK12536 161 VGIHRGLKALAAKIRG 176 (178) T ss_pred HHHHHHHHHHHHHHCC T ss_conf 9999999999998079 |
|
| >TIGR02859 spore_sigH RNA polymerase sigma-H factor; InterPro: IPR014218 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=99.59 E-value=9.8e-14 Score=111.32 Aligned_cols=190 Identities=18% Similarity=0.255 Sum_probs=142.1 Q ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH Q ss_conf 99999998285999999999430778756555579999888999999888998986218534568999757789999998 Q gi|254780611|r 36 VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115 (302) Q Consensus 36 ~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~ 115 (302) T Consensus 8 ~~~~~~~-~G~~~a~~~~i~~y~~fv~ak~~~yfl~Gad~edi~qeGmiGlyka~rd~~~~~l~sf~afaelC~trqiit 86 (198) T TIGR02859 8 EIVELAR-EGDEKALEYLIEKYKNFVKAKARSYFLVGADKEDIIQEGMIGLYKAIRDYKEDKLSSFKAFAELCVTRQIIT 86 (198) T ss_pred HHHHHHH-CCHHHHHHHHHHHHHHHHHHHHHHHEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9999997-011889999999999998775311013206456566611689999997531567899999999999999999 Q ss_pred HHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCC Q ss_conf 53202460011023003589999999978878662447888246778886189832110000001223433552023234 Q gi|254780611|r 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195 (302) Q Consensus 116 ~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~ 195 (302) T Consensus 87 aiktatrqkhiP----------------------------------------------------ln~y~sl~kPiy~~-~ 113 (198) T TIGR02859 87 AIKTATRQKHIP----------------------------------------------------LNSYVSLNKPIYDE-E 113 (198) T ss_pred HHHHHHHHCCCC----------------------------------------------------CHHHEECCCCCCCC-C T ss_conf 988765202465----------------------------------------------------20000025652545-2 Q ss_pred CCCCHHCCCCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 5320000012356-870565566666667779999996219999999999982788888989999997789999999999 Q gi|254780611|r 196 NSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302) Q Consensus 196 ~~~~~~d~l~~~~-~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302) T Consensus 114 sdrtl~d~~~~~~~~dP~~l~i~~e~~~~~~~~~~~~---ls~le~~vl~~yl---~G~~yqei~~~l~r~~ksi----d 183 (198) T TIGR02859 114 SDRTLLDVVSEAKVADPEELIISKEEYEKIESKLEEL---LSDLELKVLVLYL---DGKSYQEIAEDLNRHVKSI----D 183 (198) T ss_pred CHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH---CCCHHHHHHHHHHHHHHHH----H T ss_conf 0147999885443225277763168899999999999---9999999999984---5740788998864566789----9 Q ss_pred HHHHHHHHHHHHHHC Q ss_conf 999999999997401 Q gi|254780611|r 275 RAFKKVQESIQKQVE 289 (302) Q Consensus 275 ~AL~kLR~~l~~~~~ 289 (302) T Consensus 184 nalqrvkrkle~~l~ 198 (198) T TIGR02859 184 NALQRVKRKLEKYLE 198 (198) T ss_pred HHHHHHHHHHHHHCC T ss_conf 999999999976309 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Members of this entry represent the RNA polymerase sigma-H factor required for sporulation in endospore-forming bacteria. These proteins are also called Sigma-30 and SigH. Related sequences exist in Listeria, but as Listeria does not form spores the role of these related sigma factors in that genus is in doubt.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >PRK12535 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.56 E-value=2.5e-12 Score=101.88 Aligned_cols=178 Identities=16% Similarity=0.144 Sum_probs=118.6 Q ss_pred HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH Q ss_conf 99999999999828599999999943077875655557999988899999988899898621853456899975778999 Q gi|254780611|r 32 QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111 (302) Q Consensus 32 eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~ 111 (302) T Consensus 11 a~~~~Lv~~a~-~GD~~Af~~L~~r~~~~v~r~~~~l~~~-~~AeDl~QEtflk~~~~l~~f~~~--~~f~tWL~~Ia~n 86 (195) T PRK12535 11 AHVTELALAAG-RGDRAALTEFIRATQDDVWRLLAHLGGH-DIADDLTQETYLRVMSALPRFAAR--SSARTWLLSLARR 86 (195) T ss_pred HHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHH T ss_conf 88999999998-2209999999999999999999893799-779999999999999988770788--8799999999999 Q ss_pred HHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC Q ss_conf 99985320246001102300358999999997887866244788824677888618983211000000122343355202 Q gi|254780611|r 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191 (302) Q Consensus 112 ~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~ 191 (302) T Consensus 87 ~~~d----------------------~~R~~~~----------~~~~----------~~-------------~~~~---- 107 (195) T PRK12535 87 VWVD----------------------NIRHDMA----------RPRK----------SA-------------VEYE---- 107 (195) T ss_pred HHHH----------------------HHHHHHC----------CCCC----------CC-------------CCCC---- T ss_conf 9999----------------------9998851----------6665----------53-------------3322---- Q ss_pred CCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH Q ss_conf 32345320000012356870565566666667779999996219999999999982788888989999997789999999 Q gi|254780611|r 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271 (302) Q Consensus 192 ~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ 271 (302) T Consensus 108 ---~~-------~~~d~-~~~~~~~~-------~~~l~~~l~~Lp~~~R~~l~L~~~~g--~s~~EIA~ilgi~~gTVKs 167 (195) T PRK12535 108 ---DT-------GATDA-TNAGIWSE-------WIDVRTLIDALPPERREALILTQVLG--YTYEEAAKIADVRVGTIRS 167 (195) T ss_pred ---CC-------CCCCC-CCCHHHHH-------HHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHH T ss_conf ---35-------66777-64035777-------99999999849998879999999829--9899999998939999999 Q ss_pred HHHHHHHHHHHHHHHHHCCCC Q ss_conf 999999999999997401224 Q gi|254780611|r 272 IEARAFKKVQESIQKQVELSS 292 (302) Q Consensus 272 I~~~AL~kLR~~l~~~~~~~~ 292 (302) T Consensus 168 Rl~RAr~~Lr~~L~~~~~~~~ 188 (195) T PRK12535 168 RVARARADLVAATATGDSSAE 188 (195) T ss_pred HHHHHHHHHHHHHHCCCCCCC T ss_conf 999999999999756897655 |
|
| >PRK09649 RNA polymerase sigma factor SigC; Reviewed | Back alignment and domain information |
|---|
Probab=99.55 E-value=1.2e-12 Score=104.07 Aligned_cols=176 Identities=12% Similarity=0.147 Sum_probs=117.4 Q ss_pred CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHH Q ss_conf 99899999999999828599999999943077875655557999988899999988899898621853456899975778 Q gi|254780611|r 29 LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108 (302) Q Consensus 29 Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~w 108 (302) T Consensus 6 ~dd~~l~aLv~~a~-~GD~~Af~~L~~~~~~~v~r~~~-~l~d~~~AeDl~QEtFlka~~~l~~f~~~--s~f~tWL~~I 81 (185) T PRK09649 6 SDDEAVTALALSAA-KGNGRALEAFIKATQQDVWRFVA-YLSDVGSADDLTQETFLRAIGAIPRFSAR--SSARTWLLAI 81 (185) T ss_pred CCHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHH-HHCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHH T ss_conf 46099999999999-44799999999999999999999-93899899999999999999988762887--6189999999 Q ss_pred HHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHH Q ss_conf 99999985320246001102300358999999997887866244788824677888618983211000000122343355 Q gi|254780611|r 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188 (302) Q Consensus 109 Ir~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~ 188 (302) T Consensus 82 A~N~~~d----------------------~~Rk~~~~----------~~~~------~~~~~e~---------------- 107 (185) T PRK09649 82 ARHVVAD----------------------HIRHVRSR----------PRTT------RGARPEH---------------- 107 (185) T ss_pred HHHHHHH----------------------HHHHHHCC----------CCCC------CCCCHHH---------------- T ss_conf 9999999----------------------99987437----------7643------4457231---------------- Q ss_pred HCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHH Q ss_conf 20232345320000012356870565566666667779999996219999999999982788888989999997789999 Q gi|254780611|r 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268 (302) Q Consensus 189 ~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eR 268 (302) T Consensus 108 ---------------~~~~~~-~~~~~e-------~~~~l~~al~~Lp~~~R~vl~L~~~eg--ls~~EIA~~lg~~~gT 162 (185) T PRK09649 108 ---------------LIDGDR-HARGFE-------DLVEVTTMIADLTTDQREALLLTQLLG--LSYADAAAVCGCPVGT 162 (185) T ss_pred ---------------CCCCCC-CCCCHH-------HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHH T ss_conf ---------------158431-102378-------899999999849999999999899729--9999999998939999 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999999999974 Q gi|254780611|r 269 VRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 269 VrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 163 VKsRl~RAR~~L~a~le~~ 181 (185) T PRK09649 163 IRSRVARARDALLADAEPD 181 (185) T ss_pred HHHHHHHHHHHHHHHCCCC T ss_conf 9999999999999766855 |
|
| >pfam07638 Sigma70_ECF ECF sigma factor | Back alignment and domain information |
|---|
Probab=99.54 E-value=1.1e-12 Score=104.29 Aligned_cols=175 Identities=14% Similarity=0.142 Sum_probs=115.0 Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCC-----CHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH Q ss_conf 999999998285999999999430778756555579999-----888999999888998986218534568999757789 Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-----PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109 (302) Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~-----~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wI 109 (302) T Consensus 5 teLi~~~k-~GD~~Af~~L~~~y~~~l~r~a~~~l~~~~~~ed~~~~~lvqe~Flrl~~~~~~~~~~~~~~f~~~l~~i~ 83 (185) T pfam07638 5 TQLLQQVK-DGDAAATEQLLPLVYDELRRLAGSKLQNERRGHTLQPTALVHEAFVRLVDTEDFPDWSGRGHFFAAAAEAM 83 (185) T ss_pred HHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHH T ss_conf 99999998-67799999999999999999999996353210167789999999999984020236775689999999999 Q ss_pred HHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHH Q ss_conf 99999853202460011023003589999999978878662447888246778886189832110000001223433552 Q gi|254780611|r 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189 (302) Q Consensus 110 r~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~ 189 (302) T Consensus 84 ~~~~id~~R~~~~----------------------~-~----~~~~~~-------------------------~~~~~~~ 111 (185) T pfam07638 84 RRILIDHARRRQR----------------------Q-K----RGGDVQ-------------------------RRELDEV 111 (185) T ss_pred HHHHHHHHHHHHH----------------------H-H----CCCCCH-------------------------HCCHHHH T ss_conf 9999999998886----------------------6-1----266410-------------------------1010110 Q ss_pred CCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH Q ss_conf 02323453200000123568705655666666677799999962199999999999827888889899999977899999 Q gi|254780611|r 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269 (302) Q Consensus 190 i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV 269 (302) T Consensus 112 ~~~-------------~~~~~~-~~~~------~l~-~~~~~l~~Lpp~~r~v~~L~~~eg--lS~~EIAe~Lgis~~TV 168 (185) T pfam07638 112 VDN-------------GDSPNP-DLLL------DLD-EALEQLFSLSPRQARLVELRFFAG--LSNDEIAERLGVSERTV 168 (185) T ss_pred CCC-------------CCCCCH-HHHH------HHH-HHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHH T ss_conf 014-------------568987-8899------999-999998648998888988899759--99999999979699899 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 9999999999999999 Q gi|254780611|r 270 RQIEARAFKKVQESIQ 285 (302) Q Consensus 270 rQI~~~AL~kLR~~l~ 285 (302) T Consensus 169 k~rl~~Ar~~Lr~~l~ 184 (185) T pfam07638 169 ERNWALARAWLHRELR 184 (185) T ss_pred HHHHHHHHHHHHHHHC T ss_conf 9999999999998824 |
These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to pfam04542 and pfam04545. |
| >TIGR02948 SigW_bacill RNA polymerase sigma-W factor; InterPro: IPR014294 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=99.32 E-value=2.1e-11 Score=95.74 Aligned_cols=179 Identities=18% Similarity=0.277 Sum_probs=131.6 Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 99999999828599999999943077875655557999988899999988899898621853456899975778999999 Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114 (302) Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~ 114 (302) T Consensus 6 Kk~ik~v~-~GD~~AfAdlVdlYKDKiY~l~YRMlGN~HEA~D~AQEAF~RAY~~IDtyd~~~--KFSTWLy-------- 74 (187) T TIGR02948 6 KKRIKEVK-KGDENAFADLVDLYKDKIYQLCYRMLGNVHEAEDVAQEAFIRAYVNIDTYDIER--KFSTWLY-------- 74 (187) T ss_pred HHHHHHHH-HCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCC--CHHHHHH-------- T ss_conf 88999986-021788899999964247777776506743055688888888654114316664--3147899-------- Q ss_pred HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC Q ss_conf 85320246001102300358999999997887866244788824677888618983211000000122343355202323 Q gi|254780611|r 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194 (302) Q Consensus 115 ~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d 194 (302) T Consensus 75 ----------RIATNl~----IDrlRK----------rKP----------------------------D~yLd~~V~G~d 102 (187) T TIGR02948 75 ----------RIATNLT----IDRLRK----------RKP----------------------------DFYLDDEVAGTD 102 (187) T ss_pred ----------HHHHHHH----HHHHHC----------CCC----------------------------CCCCCCCCCCCC T ss_conf ----------9998778----865413----------488----------------------------864367557867 Q ss_pred CCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHH Q ss_conf 45320000012356870565566666667779999996219999999999982788888989999997789999999999 Q gi|254780611|r 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274 (302) Q Consensus 195 ~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~ 274 (302) T Consensus 103 G--LT~~sQlaa~~~~~~d~V~~l----E~~~~iQ~~I~~LP~KYR~~ivLKY~ed--LSL~EIS~IL~lPVgTVK---- 170 (187) T TIGR02948 103 G--LTMESQLAADEASPEDEVVSL----ELRDTIQEEIEALPEKYRSVIVLKYMED--LSLKEISEILDLPVGTVK---- 170 (187) T ss_pred C--CHHHHCCCCCCCCCHHHHHHH----HHHHHHHHHHHHCCHHHCEEHHHHHHHH--HHHHHHHHHHCCCCCCEE---- T ss_conf 7--400100110124621465553----5678999999743433512224544444--218889998578943100---- Q ss_pred HHHHHHHHHHHHHH Q ss_conf 99999999999740 Q gi|254780611|r 275 RAFKKVQESIQKQV 288 (302) Q Consensus 275 ~AL~kLR~~l~~~~ 288 (302) T Consensus 171 TRiHRGREALRk~l 184 (187) T TIGR02948 171 TRIHRGREALRKQL 184 (187) T ss_pred CCCCCCHHHHHHHH T ss_conf 24302458999873 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents sigmaW, which is restricted to certain lineages of the order Bacillales.. |
| >TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family; InterPro: IPR014298 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=99.25 E-value=2.7e-10 Score=88.38 Aligned_cols=169 Identities=15% Similarity=0.217 Sum_probs=120.0 Q ss_pred HHHHHHHCCHHHHHHHHHHHHHHH-HHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH Q ss_conf 999998285999999999430778-7565555799998889999998889989862185345689997577899999985 Q gi|254780611|r 38 AKRYREHGDLSAAHRLVTSHLRLV-VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116 (302) Q Consensus 38 ~~~~~~~gd~~Ar~~Li~~nlrlV-~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~ 116 (302) T Consensus 2 l~~a~-~~e~~Afa~lye~Y~~~vYrYI~yrv-g~~~tAEDL~s~vF~~~L~~i~~f~~~~~t~f~~WLf~iA~N~v~Dy 79 (171) T TIGR02952 2 LERAQ-EKEEDAFARLYETYSDKVYRYIYYRV-GDKYTAEDLTSEVFLRVLRKIDSFKEQKNTDFEAWLFTIARNVVADY 79 (171) T ss_pred CHHHH-HHHHHHHHHHHHHHHHHHHHHHEEEE-CCEEEHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH T ss_conf 03577-67699999998987256662101312-88531146478999999731221012578772247899999999988 Q ss_pred HHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCC Q ss_conf 32024600110230035899999999788786624478882467788861898321100000012234335520232345 Q gi|254780611|r 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196 (302) Q Consensus 117 i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~ 196 (302) T Consensus 80 fr~~~r~---------------------------------~-------------------------~~~~~~~~------ 95 (171) T TIGR02952 80 FRKSKRR---------------------------------P-------------------------LLSLDVVK------ 95 (171) T ss_pred HHCCCCC---------------------------------C-------------------------CCCHHHHH------ T ss_conf 5113455---------------------------------2-------------------------10099989------ Q ss_pred CCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHH Q ss_conf 32000001235687056556666666777999999621999999999998278888898999999778999999999999 Q gi|254780611|r 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276 (302) Q Consensus 197 ~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~A 276 (302) T Consensus 96 ------~l~~~e~~P~e~~----~~~~~n~~L~~a~~~L~p~qq~viaLrF~~~--L~~~EvA~ilGk~~gavk~Lq~rA 163 (171) T TIGR02952 96 ------ELLSAEPSPEEAV----LKELANEKLLEAVKKLTPKQQEVIALRFAQN--LPIAEVARILGKTEGAVKALQFRA 163 (171) T ss_pred ------HHHHCCCCHHHHH----HHHHHHHHHHHHHHHCCHHHHHHHHHHHCCC--CCHHHHHHHHCCCCCHHHHHHHHH T ss_conf ------8873489817899----9888899999999610832312033321168--838789987268974689999999 Q ss_pred HHHHHHHH Q ss_conf 99999999 Q gi|254780611|r 277 FKKVQESI 284 (302) Q Consensus 277 L~kLR~~l 284 (302) T Consensus 164 v~~L~r~l 171 (171) T TIGR02952 164 VKKLARQL 171 (171) T ss_pred HHHHHHHC T ss_conf 99987309 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >PRK08241 RNA polymerase factor sigma-70; Validated | Back alignment and domain information |
|---|
Probab=99.13 E-value=5.6e-09 Score=79.53 Aligned_cols=191 Identities=15% Similarity=0.150 Sum_probs=120.1 Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH Q ss_conf 99999999828599999999943077875655557999988899999988899898621853456899975778999999 Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114 (302) Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~ 114 (302) T Consensus 10 ~~~~a~a~-~GD~~Af~~Lv~~~r~~L~~~cyRmlGs~~dAED~vQEt~lrawr~~~~f~~~--~~~rtWL~rIatn~cL 86 (341) T PRK08241 10 VAGLAAAA-DGDRDAFLALAEPHRRELLAHCYRMLGSLHDAEDLVQETLLRAWRSYDRFEGR--SSLRTWLYRIATNVCL 86 (341) T ss_pred HHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCC--CCCCEEEHHHHHHHHH T ss_conf 99999997-47999999999999999999999980999899999999999998513222655--6641310198999999 Q ss_pred HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCC Q ss_conf 85320246001102300358999999997887866244788824677888618983211000000122343355202323 Q gi|254780611|r 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194 (302) Q Consensus 115 ~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d 194 (302) T Consensus 87 d~Lr~r~R---------------------R~--~~~~-l~-~~~------------~~------------~~~~~-~--~ 114 (341) T PRK08241 87 DALEGRAR---------------------RP--LPTG-LG-PPS------------AD------------PSAAL-V--E 114 (341) T ss_pred HHHHHHHC---------------------CC--CCCC-CC-CCC------------CC------------CCCCC-C--C T ss_conf 99987424---------------------46--7444-56-665------------66------------54455-5--5 Q ss_pred CCCCCHHC-----CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH Q ss_conf 45320000-----0123568705655666666677799999962199999999999827888889899999977899999 Q gi|254780611|r 195 KNSSQWQD-----WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269 (302) Q Consensus 195 ~~~~~~~d-----~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV 269 (302) T Consensus 115 ~~~~~WleP~Pd~~~~~~~~dP~~~~~~r---Esv~lA~laaLq~Lpp~QRavlvLRdV~g--~s~~EiAe~Lg~S~aAV 189 (341) T PRK08241 115 RPEVPWLEPLPDALLDPAAADPAAIVVAR---ESVRLAFVAALQHLPPRQRAVLLLRDVLG--WSAAEVAEALGTSTAAV 189 (341) T ss_pred CCCCCCCCCCCCCCCCCCCCCHHHHHHHH---HHHHHHHHHHHHHCCHHHHEEEEHHHHCC--CCHHHHHHHHCCCHHHH T ss_conf 55666546677534566779988998887---78999999999839997902001297529--98899999978999999 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 9999999999999999 Q gi|254780611|r 270 RQIEARAFKKVQESIQ 285 (302) Q Consensus 270 rQI~~~AL~kLR~~l~ 285 (302) T Consensus 190 ks~L~RARa~L~~~~p 205 (341) T PRK08241 190 NSALQRARATLAERRP 205 (341) T ss_pred HHHHHHHHHHHHHHCC T ss_conf 9999999999986477 |
|
| >TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family; InterPro: IPR014300 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=99.00 E-value=4.2e-08 Score=73.72 Aligned_cols=166 Identities=14% Similarity=0.207 Sum_probs=111.3 Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH Q ss_conf 99999999982859999999994307787565555799998889999998889989862185345689997577899999 Q gi|254780611|r 34 EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113 (302) Q Consensus 34 e~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I 113 (302) T Consensus 3 ~~~Lv~~a~-~Gn~~aF~~Li~~~ke~LYk~Af~Yvkne~DALd~i~EtvyKAY~sI~kLk~~-~Y-F~TW~---trILI 76 (173) T TIGR02954 3 DIELVKKAI-RGNKEAFESLIKKNKEKLYKTAFIYVKNEHDALDVIQETVYKAYLSIEKLKHP-EY-FNTWL---TRILI 76 (173) T ss_pred HHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCC-CC-CHHHH---HHHHH T ss_conf 368999987-24934789999984366857665440673405899999999999989983361-00-02567---89999 Q ss_pred H---HHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHC Q ss_conf 9---8532024600110230035899999999788786624478882467788861898321100000012234335520 Q gi|254780611|r 114 Q---EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190 (302) Q Consensus 114 ~---~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i 190 (302) T Consensus 77 n~ci~lL~K~kk~i------------------------------------------------------------~~~~~~ 96 (173) T TIGR02954 77 NECIDLLKKKKKVI------------------------------------------------------------LFDKNT 96 (173) T ss_pred HHHHHHHHCCCCEE------------------------------------------------------------ECCCCC T ss_conf 99999984389753------------------------------------------------------------068871 Q ss_pred CCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHH- Q ss_conf 2323453200000123568705655666666677799999962199999999999827888889899999977899999- Q gi|254780611|r 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV- 269 (302) Q Consensus 191 ~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRV- 269 (302) T Consensus 97 ~~~~~---------~~-~~~----~~~~lef----~dLy~Ai~~L~~~~~t~IIL~Yy~D--L~I~eIa~vM~~P~gTvK 156 (173) T TIGR02954 97 KIEKK---------EC-EVD----ADERLEF----EDLYKAIDTLNDKYKTAIILRYYHD--LKIKEIAEVMNKPEGTVK 156 (173) T ss_pred CHHHH---------HC-CCC----HHHHHCH----HHHHHHHHHHHHHHHHHHHHHHCCC--CCHHHHHHHCCCCCCCHH T ss_conf 01223---------21-668----6886258----6899999731145440264332179--984259985168985178 Q ss_pred HHHHHHHHHHHHHHHHH Q ss_conf 99999999999999997 Q gi|254780611|r 270 RQIEARAFKKVQESIQK 286 (302) Q Consensus 270 rQI~~~AL~kLR~~l~~ 286 (302) T Consensus 157 tyl-~Ra~~~lk~~l~~ 172 (173) T TIGR02954 157 TYL-RRAKKKLKKELEE 172 (173) T ss_pred HHH-HHHHHHHHHHHCC T ss_conf 999-9999998886236 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This entry is found in certain Bacillus and Clostridium species.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family; InterPro: IPR011517 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=98.72 E-value=2.4e-06 Score=62.00 Aligned_cols=159 Identities=19% Similarity=0.285 Sum_probs=98.3 Q ss_pred HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHC-----CCCCC----------HHHHHHHHHHHHH--HHHHHCCCCC Q ss_conf 99999999828599999999943077875655557-----99998----------8899999988899--8986218534 Q gi|254780611|r 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR-----GYGLP----------ISEVVSEGNIGLM--QAVKKFDPER 97 (302) Q Consensus 35 ~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~-----~~g~~----------~~DLiQeG~iGLi--~Ai~kFDp~k 97 (302) T Consensus 5 t~ll~~~~-~Gd~~A~~~L~~~~Y~~LR~~A~~~~~~~~~~~~Lq~~~~~~ci~stT~LV~EAylrL~~t~~~~~~~-~r 82 (194) T TIGR02999 5 TELLQQWQ-NGDQAARDQLFPALYQELRRIARRELRRERSGQTLQVEVLAVCIDSTTALVHEAYLRLVDTQDEQEWS-DR 82 (194) T ss_pred HHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCHHHHHHHHHHHHHCCCCHHHHC-CH T ss_conf 99999883-64588999999999999999999999851036652044677510466788998766421232023222-50 Q ss_pred CCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCC Q ss_conf 56899975778999999853202460011023003589999999978878662447888246778886189832110000 Q gi|254780611|r 98 GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177 (302) Q Consensus 98 G~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~ 177 (302) T Consensus 83 ~H-F~~~AA----~aMRrIL~D~A------------------R~~-~~--~--KRGg~~~-------------------- 114 (194) T TIGR02999 83 RH-FFAAAA----KAMRRILVDHA------------------RRR-RA--Q--KRGGGAV-------------------- 114 (194) T ss_pred HH-HHHHHH----HHHHHHHHHHH------------------HHH-HH--H--CCCCCCC-------------------- T ss_conf 88-999999----99999999999------------------999-87--4--1367763-------------------- Q ss_pred CCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHH Q ss_conf 00122343355202323453200000123568705655666666677799999962199999999999827888889899 Q gi|254780611|r 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257 (302) Q Consensus 178 ~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~E 257 (302) T Consensus 115 -----~~~l~~~~--------------~~~~~~~~~------~L~~Ld~aL~-~L~~~~Pr~a~~veLr~F~G--l~~~E 166 (194) T TIGR02999 115 -----RVSLDEVL--------------PDAEADADE------ELLDLDDALD-KLAQVDPRQAEVVELRFFAG--LTVEE 166 (194) T ss_pred -----CCCCCCCC--------------CCCCCCCHH------HHHHHHHHHH-HHHHCCHHHHHHHHHHHHCC--CCHHH T ss_conf -----35520000--------------135777403------5999999998-77400678899885311048--89899 Q ss_pred HHHHHCCCHHHHHH Q ss_conf 99997789999999 Q gi|254780611|r 258 LSSEFEVSRERVRQ 271 (302) Q Consensus 258 Ia~~lgiS~eRVrQ 271 (302) T Consensus 167 ~A~~L~~S~~Tv~R 180 (194) T TIGR02999 167 IAELLGVSVRTVER 180 (194) T ss_pred HHHHHCCCHHHHHH T ss_conf 99986888878998 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE; InterPro: IPR014286 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=98.55 E-value=5.2e-06 Score=59.67 Aligned_cols=181 Identities=21% Similarity=0.280 Sum_probs=123.5 Q ss_pred HHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH Q ss_conf 99999999982859999999994307787565555799998889999998889989862185345689997577899999 Q gi|254780611|r 34 EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113 (302) Q Consensus 34 e~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I 113 (302) T Consensus 8 D~~Lv~RVQ-rG~k~AF~lLV~KYQ~kv~~Lv~Ryv~~~~e~~DVAQe~FvkAYRAl~~FRGd--saFYTWLy------- 77 (192) T TIGR02939 8 DLELVERVQ-RGEKQAFDLLVRKYQHKVVSLVGRYVRDSEEVEDVAQEAFVKAYRALASFRGD--SAFYTWLY------- 77 (192) T ss_pred HHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHCCHHCCCCHHHHHHHHHHHHHCCCCCC--HHHHHHHH------- T ss_conf 289988873-32235677788999999999998761481003401477899999751235551--36789999------- Q ss_pred HHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCC Q ss_conf 98532024600110230035899999999788786624478882467788861898321100000012234335520232 Q gi|254780611|r 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193 (302) Q Consensus 114 ~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~ 193 (302) T Consensus 78 -----------RIa-----------vNTAKNyLV---aq~Rr~p~~d------g~~~e---------------------- 104 (192) T TIGR02939 78 -----------RIA-----------VNTAKNYLV---AQGRRPPTSD------GVEAE---------------------- 104 (192) T ss_pred -----------HHH-----------HHHHHHHHH---HCCCCCCCCC------CCCCH---------------------- T ss_conf -----------999-----------988777664---2479887445------67604---------------------- Q ss_pred CCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHH Q ss_conf 34532000001235687056556666666777999999621999999999998278888898999999778999999999 Q gi|254780611|r 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273 (302) Q Consensus 194 d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~ 273 (302) T Consensus 105 dAE~F~~a~~Lr-~~~tPE~~ll----~~el~~~v~~a~~aLPE~Lr~Ai~LREl--eGLSYe~IA~~MdCPvGTVRSRI 177 (192) T TIGR02939 105 DAEQFEEADALR-DIDTPERLLL----SRELEQTVNKALEALPEDLRTAITLREL--EGLSYEDIAEIMDCPVGTVRSRI 177 (192) T ss_pred HHHCCCCCCCCC-CCCCHHHHHH----HHHHHHHHHHHHHHCCHHHHHHHHHHHC--CCCCHHHHHHHCCCCCCCCCCHH T ss_conf 331200267665-5666167999----9999999999986172678745446512--68787888733069988621146 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 999999999999740 Q gi|254780611|r 274 ARAFKKVQESIQKQV 288 (302) Q Consensus 274 ~~AL~kLR~~l~~~~ 288 (302) T Consensus 178 FRA----REAi~~~l 188 (192) T TIGR02939 178 FRA----REAIAKRL 188 (192) T ss_pred HHH----HHHHHHHH T ss_conf 775----89999862 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the clade of sigma factors called RpoE. These proteins are variously annotated as sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family; InterPro: IPR014293 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=90.59 E-value=1.3 Score=23.51 Aligned_cols=177 Identities=15% Similarity=0.150 Sum_probs=89.8 Q ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH-H Q ss_conf 999999999982859999999994307787565555799998889999998889989862185345689997577899-9 Q gi|254780611|r 33 EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK-A 111 (302) Q Consensus 33 ee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr-~ 111 (302) T Consensus 5 ~~~~~~~rfe-rdal~~~dqly~aalrm--------~rnPadaed~vqe~y~kaf~~f~~~~~Gtn--l~aWlyriltnt 73 (193) T TIGR02947 5 TEEQRAQRFE-RDALEYLDQLYGAALRM--------TRNPADAEDLVQEAYVKAFSAFKQFKPGTN--LKAWLYRILTNT 73 (193) T ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHHH--------HCCCCCHHHHHHHHHHHHHHHHHHHCCCCH--HHHHHHHHHHHH T ss_conf 2689998776-77999999999999876--------238654788999999999998874137742--899999999999 Q ss_pred HHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCC Q ss_conf 99985320246001102300358999999997887866244788824677888618983211000000122343355202 Q gi|254780611|r 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191 (302) Q Consensus 112 ~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~ 191 (302) T Consensus 74 yin~yrk~q----r~P~~~~~----------------------~~~~dWq~a~~---------------~~h~s~--Glr 110 (193) T TIGR02947 74 YINSYRKKQ----REPAQSDS----------------------DEIEDWQLAKA---------------ASHTSS--GLR 110 (193) T ss_pred HHHHHHHHH----CCCCCCCC----------------------CHHHHHHHHHH---------------HHHHHC--CCH T ss_conf 999888752----27655652----------------------01468888765---------------311001--204 Q ss_pred CCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHH Q ss_conf 32345320000012356870565566666667779999996219999999999982788888989999997789999999 Q gi|254780611|r 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271 (302) Q Consensus 192 ~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQ 271 (302) T Consensus 111 ---sae~eald~lPd-------------------~~~~~al~~~~~efr~~v~~--adveGf~ykei~~im~tP~Gtvms 166 (193) T TIGR02947 111 ---SAEVEALDALPD-------------------DDIKAALQELPEEFRLAVYF--ADVEGFAYKEIAEIMGTPIGTVMS 166 (193) T ss_pred ---HHHHHHHHCCCH-------------------HHHHHHHHHHHHHHHHHHHH--HHHCCCCHHHHHHHHCCCHHHHHH T ss_conf ---777888752884-------------------89999998737999898887--620353157799885474779999 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 9999999999999974 Q gi|254780611|r 272 IEARAFKKVQESIQKQ 287 (302) Q Consensus 272 I~~~AL~kLR~~l~~~ 287 (302) T Consensus 167 rl~r~rk~l~~~l~d~ 182 (193) T TIGR02947 167 RLHRGRKQLRDLLADV 182 (193) T ss_pred HHHHHHHHHHHHHHHH T ss_conf 9899999999999988 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family (IPR014284 from INTERPRO). They and appear by homology, tree building, bidirectional best hits and (with one exception, a paralog in Thermobifida fusca strain YX) their one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor (see IPR014295 from INTERPRO) in an apparent operon.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD; InterPro: IPR012760 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=502.91 Aligned_cols=229 Identities=29% Similarity=0.484 Sum_probs=207.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCC Q ss_conf 99999994307787565555799998889999998889989862185345689997577899999985320246001102 Q gi|254780611|r 49 AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128 (302) Q Consensus 49 Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~ 128 (302) T Consensus 1 Ak~~l~~sNLRLVvSIAKkY~nRGL~F~DLIQEGn~GL~KAv~KFdy~kGyKFSTYATWWIRQAITRAIADQARtIRiPV 80 (240) T TIGR02393 1 AKKKLVESNLRLVVSIAKKYTNRGLSFLDLIQEGNIGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 80 (240) T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCH T ss_conf 93568873014666676663047863343676523578988776213578865511578999999998875137201103 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCC Q ss_conf 30035899999999788786624478882467788861898321100000012234335520232345320000012356 Q gi|254780611|r 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208 (302) Q Consensus 129 ~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~ 208 (302) T Consensus 81 Hm~E-----TINk~~~~~R~l~Q~~Gr~Pt~EelAe~~g~~~~Kv~~i~~~~~~PiSLe~piG~--e~dS~l~DFi~D~~ 153 (240) T TIGR02393 81 HMVE-----TINKLIKAERKLLQELGREPTDEELAERMGLPVEKVREIKKIAQEPISLETPIGE--EEDSSLGDFIEDES 153 (240) T ss_pred HHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCC--CCCCCCCCCCCCCC T ss_conf 2667-----8889999989999872889987789987089989999999862488656667788--77774426525744 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHH-CCCHHHHHHHHHHHCCC---CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 8705655666666677799999962-19999999999982788---8889899999977899999999999999999999 Q gi|254780611|r 209 DGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRLQE---NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302) Q Consensus 209 ~~~~~~~~e~~e~~~~~~~L~~~l~-~L~~rEr~II~~ry~~~---~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302) T Consensus 154 ~~~P~---~~~~~~~l~~~l~~vL~~~L~~rE~~Vl~~RyGL~d~~~~~TLEEVG~~f~VTRERIRQIE~KALRKLrhp~ 230 (240) T TIGR02393 154 IESPE---DAAAKELLREQLEEVLENTLTERERKVLRMRYGLLDGEKPKTLEEVGKEFNVTRERIRQIESKALRKLRHPS 230 (240) T ss_pred CCCHH---HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCHH T ss_conf 46858---999999999999999860178889999987438998876533788876517871145688899988502843 Q ss_pred HHH Q ss_conf 974 Q gi|254780611|r 285 QKQ 287 (302) Q Consensus 285 ~~~ 287 (302) T Consensus 231 r~~ 233 (240) T TIGR02393 231 RSK 233 (240) T ss_pred HHH T ss_conf 667 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents the C-terminal region of sigma 70 (RpoD) which contains the well-conserved regions 2, 3 and 4. Region 2 of sigma-70 is the most conserved region of the entire protein. 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 thought to mediate strand separation, thereby allowing transcription initiation , . 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 in 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 .Region 4 is involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily; InterPro: IPR014322 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=422.92 Aligned_cols=224 Identities=28% Similarity=0.380 Sum_probs=203.1 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH Q ss_conf 59999999994307787565555799998-88999999888998986218534568999757789999998532024600 Q gi|254780611|r 46 DLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124 (302) Q Consensus 46 d~~Ar~~Li~~nlrlV~~iA~~y~~~g~~-~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~I 124 (302) T Consensus 1 ~~~~R~~Lv~~nlpLv~~~A~RF~~RGe~~~EDL~QVG~iGL~kAidrFD~~~g~~F~tyAVPtI~GEIkR~fRD~~W~v 80 (229) T TIGR02980 1 DKEAREKLVELNLPLVESIARRFRSRGEPHLEDLVQVGTIGLVKAIDRFDPSYGVKFSTYAVPTIMGEIKRFFRDDTWAV 80 (229) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCHHCCCCCCCCCCCCEEEEEEEEEECCCCEE T ss_conf 96788999996127999999985137887431157888888887775301111698664104602332313342487326 Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCC--CCCHHHHCC-CCCCCCCCHH Q ss_conf 1102300358999999997887866244788824677888618983211000000122--343355202-3234532000 Q gi|254780611|r 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALIN-SSDKNSSQWQ 201 (302) Q Consensus 125 RiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~--~~SLd~~i~-~~d~~~~~~~ 201 (302) T Consensus 81 rVPRrl-----kEl~~~~~~a~eeL~~~lgR~Pt~~EiAe~L~~s~EEv~~aleA~~~Y~~~Sld~~~~a~~dg~~~~L~ 155 (229) T TIGR02980 81 RVPRRL-----KELRLKINKATEELTQRLGRSPTVAEIAEELGVSEEEVVEALEAGNSYSALSLDATIEADDDGDPIALL 155 (229) T ss_pred ECCHHH-----HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHH T ss_conf 605138-----988999999999999982889887899988588999999999865417861120004558888424566 Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH Q ss_conf 00123568705655666666677799999962199999999999827888889899999977899999999999999999 Q gi|254780611|r 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302) Q Consensus 202 d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302) T Consensus 156 D~lG~~D~~~e~~--------~~~~aLk~~l~~LpeRER~il~lRFf~~--~TQ~eiA~~lGiSQMhVSRl~~~~L~~LR 225 (229) T TIGR02980 156 DTLGDEDDALETV--------EDRLALKPLLAALPERERRILLLRFFED--KTQSEIAERLGISQMHVSRLLRRALKRLR 225 (229) T ss_pred HHHCCCCCHHHHH--------HHHHHHHHHHHHCCHHHCEEEEEEEECC--CCHHHHHHHCCCCHHHHHHHHHHHHHHHH T ss_conf 4440224326789--------9999999998507902707610001069--77899997818436788999999999999 Q ss_pred HHH Q ss_conf 999 Q gi|254780611|r 282 ESI 284 (302) Q Consensus 282 ~~l 284 (302) T Consensus 226 ~~l 228 (229) T TIGR02980 226 EQL 228 (229) T ss_pred HHC T ss_conf 860 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:IPR014236 from INTERPRO and SigG:IPR014212 from INTERPRO as well as SigB:IPR014288 from INTERPRO), and the high GC Gram-positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >PRK06986 fliA flagellar biosynthesis sigma factor; Validated | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=382.92 Aligned_cols=227 Identities=21% Similarity=0.292 Sum_probs=182.8 Q ss_pred HHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC---CCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH Q ss_conf 9982859999999994307787565555799---9988899999988899898621853456899975778999999853 Q gi|254780611|r 41 YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117 (302) Q Consensus 41 ~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~---g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i 117 (302) T Consensus 2 ~~~-~g~~Ar~~Lv~~nl~LV~~iA~r~~~r~~~~v~~~DLiQeG~iGLi~AvekFDp~~G~rFsTYA~~~Ir~aI~~~~ 80 (234) T PRK06986 2 YTA-QGKMSQDSLVEQYAPLVKRIALRLKARLPASVDLDDLIQAGMIGLLEASRRYDGEQGASFETYAGQRIRGAMLDEL 80 (234) T ss_pred CCH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH T ss_conf 617-6899999999981999999999997338999988999999999999999981886699969999999999999999 Q ss_pred HCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCC--CCCCCHHHHCCCCCC Q ss_conf 202460011023003589999999978878662447888246778886189832110000001--223433552023234 Q gi|254780611|r 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDK 195 (302) Q Consensus 118 ~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~--~~~~SLd~~i~~~d~ 195 (302) T Consensus 81 r~~~~---~~r~-----~~~~~~~i~~~~~~l~~~~~r~pt~~eia~~l~~s~e~v~~~~~~~~~~~~~sld~~~~~~~- 151 (234) T PRK06986 81 RSGDW---VPRS-----VRRNAREVADAIRELEQELGREPTDTEVAEKLGLSLEEYREMLLDTNISQLFSIDDLGESGE- 151 (234) T ss_pred HHCCC---CCHH-----HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCC- T ss_conf 85456---6499-----99999999999999999878799899999895949999999999850577868776776643- Q ss_pred CCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHH Q ss_conf 53200000123568705655666666677799999962199999999999827888889899999977899999999999 Q gi|254780611|r 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275 (302) Q Consensus 196 ~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~ 275 (302) T Consensus 152 ---~~~~~~~~~~~~----~~~~~~~~~~~~~l~~~l~~L~~rEr~Ii~l~y~--~~~tl~eIa~~lgiS~eRVrQie~~ 222 (234) T PRK06986 152 ---LLTDEDQSEHED----PLQQLEDEELREALVEAIEKLPEREQLVLSLYYD--EELNLKEIGAVLGVSESRVSQIHSQ 222 (234) T ss_pred ---CCCCCCCCCCCC----HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCC--CCCCHHHHHHHHCCCHHHHHHHHHH T ss_conf ---111222457899----9999999999999999998099999999998738--9989999999979789999999999 Q ss_pred HHHHHHHHHHH Q ss_conf 99999999997 Q gi|254780611|r 276 AFKKVQESIQK 286 (302) Q Consensus 276 AL~kLR~~l~~ 286 (302) T Consensus 223 AL~kLR~~L~e 233 (234) T PRK06986 223 AIKRLRARLGE 233 (234) T ss_pred HHHHHHHHHHC T ss_conf 99999998753 |
|
| >PRK12427 flagellar biosynthesis sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=346.41 Aligned_cols=216 Identities=16% Similarity=0.232 Sum_probs=176.3 Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCC---CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 28599999999943077875655557999---988899999988899898621853456899975778999999853202 Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYG---LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120 (302) Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g---~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~ 120 (302) T Consensus 9 ~~~~~~k~~lV~~~L~LV~~ia~r~~~~~~~~vd~dDLiq~G~iGLi~Ai~rFD~~~g-~F~tYA~~rIrGaI~d~lR~~ 87 (229) T PRK12427 9 TLTAAEEGKYLNAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHRIRGSILDQLREH 87 (229) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHHHHHHHH T ss_conf 6899999999999599999999999742877798888999999999999984499898-859999999999999999872 Q ss_pred CCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC--CCCCCCHHHHCCCCCCCCC Q ss_conf 46001102300358999999997887866244788824677888618983211000000--1223433552023234532 Q gi|254780611|r 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSS 198 (302) Q Consensus 121 ~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~--~~~~~SLd~~i~~~d~~~~ 198 (302) T Consensus 88 ~~~---p-----R~~r~~~~ki~~a~~~l~~~lgr~Pt~~EiA~~l~is~~~v~~~~~~~~~~~~~sld~~~~~e~~~~- 158 (229) T PRK12427 88 DWR---P-----RRLRQKTHKTNEAIRQIAKRLGHEPNFEEISAELNLTADEYQEYLLLENAGAMESLDEILALEAHND- 158 (229) T ss_pred CCC---C-----HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC- T ss_conf 137---5-----9999999999999999999858899999999891999999999999873668757233445788765- Q ss_pred CHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 00000123568705655666666677799999962199999999999827888889899999977899999999999999 Q gi|254780611|r 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278 (302) Q Consensus 199 ~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~ 278 (302) T Consensus 159 ----~~-~-~~~~~e-------~~~~~~~L~~al~~L~erEr~Vi~l~y~e--~ltlkEIa~~LgvS~~RVsQi~~kal~ 223 (229) T PRK12427 159 ----IL-Q-SRDLEE-------NIIIEDNLKQAISQLDEREQMILHLYYQQ--ELSMKEIAQVLDLTEARICQLNKKLVQ 223 (229) T ss_pred ----CC-C-CCCHHH-------HHHHHHHHHHHHHHCCHHHHHHHHHHCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf ----45-6-766467-------89999999999971999999999998058--998999999979889999999999999 Q ss_pred HHHHHH Q ss_conf 999999 Q gi|254780611|r 279 KVQESI 284 (302) Q Consensus 279 kLR~~l 284 (302) T Consensus 224 kLR~~f 229 (229) T PRK12427 224 KIKSFF 229 (229) T ss_pred HHHHHC T ss_conf 988439 |
|
| >TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family; InterPro: IPR012845 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=100.00 E-value=0 Score=347.98 Aligned_cols=220 Identities=23% Similarity=0.358 Sum_probs=191.8 Q ss_pred HHHHHHHHHHHHHHHHCC---CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC Q ss_conf 999430778756555579---99988899999988899898621853456899975778999999853202460011023 Q gi|254780611|r 53 LVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129 (302) Q Consensus 53 Li~~nlrlV~~iA~~y~~---~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302) T Consensus 1 l~~~Y~pLVk~~a~rl~~~~P~~v~~~DL~q~G~~GL~dA~~ryd~~~g~~F~TyA~~RIRGAmlDELR~~DW---~P-- 75 (227) T TIGR02479 1 LIKKYLPLVKRIAGRLVVQLPSSVELDDLIQAGMIGLLDAIERYDPSKGVKFETYAVQRIRGAMLDELRKLDW---VP-- 75 (227) T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHCCCCHHHHHHHHHHCCC---CC-- T ss_conf 9001268999988664310488234875898889999999983188888944100011130205788753066---78-- Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCC--CCCCHHHHCCCCCCC--CCCHHCCCC Q ss_conf 0035899999999788786624478882467788861898321100000012--234335520232345--320000012 Q gi|254780611|r 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKN--SSQWQDWLV 205 (302) Q Consensus 130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~--~~~SLd~~i~~~d~~--~~~~~d~l~ 205 (302) T Consensus 76 ---Rs~R~~~~~~~~a~~~Le~~LgR~P~~~EiA~~Lg~~~~e~~~~~~~~~~~~~~SLd~~~~~~~~~~~~~~~~~~~~ 152 (227) T TIGR02479 76 ---RSLRQKARKLEEAIEELEARLGREPTEEEIAEELGMDLKEVRQALNEINAESLVSLDELLESGDDGGAEGSLIDLIE 152 (227) T ss_pred ---HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHEEC T ss_conf ---36899986899999999998698988889999839999899999999889987648999841463223453231001 Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 35687056556666666777999999621999999999998278888898999999778999999999999999999999 Q gi|254780611|r 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302) Q Consensus 206 ~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302) T Consensus 153 ~~~~~~P~~~---~~~~~L~~~l~~ai~~L~eRE~LVl~LYY~eE--LnLKEIg~VL~lsESRvSQiHs~A~~~Lr~~L~ 227 (227) T TIGR02479 153 DDKSEDPEEE---LEREELREALAEAIEKLSEREKLVLSLYYYEE--LNLKEIGEVLGLSESRVSQIHSQALKKLRAKLS 227 (227) T ss_pred CCCCCCHHHH---HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCC T ss_conf 4357681358---99999999999997406855788888864127--668899988378705799999999999987539 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . 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.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0045449 regulation of transcription. |
| >PRK06759 RNA polymerase factor sigma-70; Validated | Back alignment and domain information |
|---|
Probab=99.93 E-value=2.6e-24 Score=182.01 Aligned_cols=151 Identities=21% Similarity=0.284 Sum_probs=118.0 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHC Q ss_conf 99999999430778756555579999888999999888998986218534568999757789999998532024600110 Q gi|254780611|r 48 SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127 (302) Q Consensus 48 ~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP 127 (302) T Consensus 4 ~sFee~~~~Y~pmI~~~lkkl~i~-~d~dd~~Q~g~i~Lw~a~~~yd~~kg-~fstya~~~ir~~~ld~lrKe~~~~--- 78 (154) T PRK06759 4 ATFTEAVVLYEGLIVNQIKKLGIY-QDYEEYYQCGLIGLWHAYERYDEKKG-SFPAYAVVTVRGYILERLKKEFAVQ--- 78 (154) T ss_pred CCHHHHHHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHHHHHHHCCCCC--- T ss_conf 559999999878999999993673-33899999999999999997694347-6699999999999999998631433--- Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCC Q ss_conf 23003589999999978878662447888246778886189832110000001223433552023234532000001235 Q gi|254780611|r 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207 (302) Q Consensus 128 ~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~ 207 (302) T Consensus 79 -----------------------e~~------------------------------~~----~~~~-e------d~~--- 91 (154) T PRK06759 79 -----------------------EKC------------------------------VC----VGEY-E------DHF--- 91 (154) T ss_pred -----------------------CCC------------------------------CC----CCCC-H------HHH--- T ss_conf -----------------------433------------------------------35----5652-2------555--- Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 68705655666666677799999962199999999999827888889899999977899999999999999999999 Q gi|254780611|r 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302) Q Consensus 208 ~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302) T Consensus 92 ------------~~~d~~~~l~~~l~~L~~re~~ii~~~~~~g--~t~~EIA~~~gis~~~Vk~~~r~Al~KLR~~~ 154 (154) T PRK06759 92 ------------HFEDVEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWIYRQALEKMRNSV 154 (154) T ss_pred ------------HHCHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCC T ss_conf ------------1011889999999849999999999999969--98999999989899999999999999987339 |
|
| >TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family; InterPro: IPR014284 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=99.92 E-value=5.1e-24 Score=180.06 Aligned_cols=162 Identities=24% Similarity=0.320 Sum_probs=129.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHC Q ss_conf 99999999430778756555579999888999999888998986218534568999757789999998532024600110 Q gi|254780611|r 48 SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127 (302) Q Consensus 48 ~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP 127 (302) T Consensus 1 ~a~~~l~~~~~~~~~~~a~~~~~~~~~aeDl~Qe~~~~~~~~~~~~~~~-~~~f~~wl~~~~~n~~~d~~R~~~~~~~~~ 79 (162) T TIGR02937 1 EAFEELVERYLPLLYRYARRYLGDDADAEDLVQEAFLKLLEALDRFDPE-GGSFKAWLFRIARNLILDYLRRKRRRVRRL 79 (162) T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHH T ss_conf 9788999999999999999971787579999999999999878624878-765389999999999999999866442001 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCC Q ss_conf 23003589999999978878662447888246778886189832110000001223433552023234532000001235 Q gi|254780611|r 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207 (302) Q Consensus 128 ~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~ 207 (302) T Consensus 80 ~~---------------~~~-------------------------------------~~------------~~~~~~-~- 93 (162) T TIGR02937 80 RV---------------ELD-------------------------------------ED------------DELEEL-E- 93 (162) T ss_pred HH---------------HHC-------------------------------------CH------------HHHHHH-C- T ss_conf 45---------------412-------------------------------------21------------344321-3- Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 68705655666666677799999962199999999999827888889899999977899999999999999999999 Q gi|254780611|r 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302) Q Consensus 208 ~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302) T Consensus 94 ~~~----~~~-~~-~~~~~~l~~al~~Lp~~~r~~~~l~~~~~--~s~~eIA~~lg~s~~~v~~~~~ra~~~L~~~l 162 (162) T TIGR02937 94 DPS----PEE-LE-EEEREALREALEKLPEREREVLVLRYLEG--LSYKEIAEILGISEGTVKSRLKRARKKLRELL 162 (162) T ss_pred CCC----HHH-HH-HHHHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHC T ss_conf 578----778-99-99999999998747998999999999718--99889999868999999999999999998529 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry is found in 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 (IPR000394 from INTERPRO) are included within this entry. ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >PRK12542 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.67 E-value=9.5e-15 Score=118.11 Aligned_cols=171 Identities=21% Similarity=0.216 Sum_probs=121.7 Q ss_pred HHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHC Q ss_conf 99982859999999994307787565555799998889999998889989862185345689997577899999985320 Q gi|254780611|r 40 RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119 (302) Q Consensus 40 ~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~ 119 (302) T Consensus 2 rv~-~GD~~afe~Ly~~y~~~ly~~a~~~~~d~~~AEDivQe~Flk~~~~~~~~~~~~~~~~~~wL~rIa~N~~id~~Rk 80 (185) T PRK12542 2 KVT-NNDYEKMEELYELYEQKVYYVAYSILNNIQQAEDAVQETFITLYKNLEKLHSLNTQELKRYILRVAKNKAIDSYRK 80 (185) T ss_pred CCC-CCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 641-3489999999999999999999999499999999999999999998887166552679999999999999999997 Q ss_pred CCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCC Q ss_conf 24600110230035899999999788786624478882467788861898321100000012234335520232345320 Q gi|254780611|r 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199 (302) Q Consensus 120 ~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~ 199 (302) T Consensus 81 ~k----------------------~~~--------~--~~~~~--------------~~-----~~----~~~------- 98 (185) T PRK12542 81 NK----------------------RHE--------T--FLEEY--------------ER-----ES----IEA------- 98 (185) T ss_pred HC----------------------CCC--------C--CHHHH--------------HC-----CC----CCC------- T ss_conf 32----------------------434--------4--20132--------------10-----23----356------- Q ss_pred HHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH Q ss_conf 00001235687056556666666777999999621999999999998278888898999999778999999999999999 Q gi|254780611|r 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279 (302) Q Consensus 200 ~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~k 279 (302) T Consensus 99 -----~--~~~~e~----~~~~~~~~~~l~~~l~~Lp~~~R~v~~L~~~~g--ls~~EIA~~L~is~~tVk~rl~RArk~ 165 (185) T PRK12542 99 -----V--DENIEE----WEKRKMSEVQIDTLLKELNESNRQVFKYKVFYN--LTYQEISSVMGITEANVRKQFERARKR 165 (185) T ss_pred -----C--CCCHHH----HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHH T ss_conf -----7--877437----999998999999999829998889976799839--999999999892999999999999999 Q ss_pred HHHHHHH Q ss_conf 9999997 Q gi|254780611|r 280 VQESIQK 286 (302) Q Consensus 280 LR~~l~~ 286 (302) T Consensus 166 Lr~~Lgg 172 (185) T PRK12542 166 VQNMIGG 172 (185) T ss_pred HHHHHCC T ss_conf 9998767 |
|
| >PRK12544 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.59 E-value=2.3e-13 Score=108.81 Aligned_cols=184 Identities=13% Similarity=0.148 Sum_probs=120.4 Q ss_pred CHHHHHH-----HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCC Q ss_conf 5999999-----99943077875655557999988899999988899898621853456899975778999999853202 Q gi|254780611|r 46 DLSAAHR-----LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120 (302) Q Consensus 46 d~~Ar~~-----Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~ 120 (302) T Consensus 12 ~~~~~~~~~~~~l~e~y~~~L~r~A~r~l~d~~~AEDlvQEtFlka~~~l~~F~g~--s~f~tWL~~Ia~N~~iD~lRk~ 89 (207) T PRK12544 12 SSDAVNVLQDPVFLEDLRAQMLKFAKLQLRDNHLAEDAVQEALFSAYQNADSFAGR--AAFKTWVFAILKNKIIDLLRQK 89 (207) T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHH T ss_conf 28887611589999999999999999994999999999999999999817743888--8609899999999999999985 Q ss_pred CCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCH Q ss_conf 46001102300358999999997887866244788824677888618983211000000122343355202323453200 Q gi|254780611|r 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200 (302) Q Consensus 121 ~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~ 200 (302) T Consensus 90 ~r~~~~~~--------------------~---~-~~~~~-----------------------~~~~~~~~d---~~g~~~ 119 (207) T PRK12544 90 KRHVSASQ--------------------L---E-DGDEG-----------------------EALIEALFD---ESGHWQ 119 (207) T ss_pred CCCCCCCC--------------------C---C-CCCCH-----------------------HHHHHHHHC---CCCCCC T ss_conf 16565210--------------------1---3-45410-----------------------134666511---123433 Q ss_pred HCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH Q ss_conf 00012356870565566666667779999996219999999999982788888989999997789999999999999999 Q gi|254780611|r 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280 (302) Q Consensus 201 ~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kL 280 (302) T Consensus 120 ~~e~p~~~~~p----ee~l~~~e~~~~l~~aL~~Lp~~~R~vl~Lr~~eg--lS~~EIAe~Lgis~~tVks~L~RAR~~L 193 (207) T PRK12544 120 KDERPQKWDQP----EEGVEQEQFWRIFDACLDALPAKYARVFMMREFIE--LETPEICHNEDLTVSNLNVMLYRSRLRL 193 (207) T ss_pred CCCCCCCCCCH----HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHH T ss_conf 33465333898----99999999999999999839999999999999819--9999999997979999999999999999 Q ss_pred HHHHHHH Q ss_conf 9999974 Q gi|254780611|r 281 QESIQKQ 287 (302) Q Consensus 281 R~~l~~~ 287 (302) T Consensus 194 r~~Le~~ 200 (207) T PRK12544 194 RECLENH 200 (207) T ss_pred HHHHHHH T ss_conf 9999984 |
|
| >PRK12522 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.57 E-value=6.9e-13 Score=105.67 Aligned_cols=170 Identities=11% Similarity=0.117 Sum_probs=117.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH Q ss_conf 99999999943077875655557999988899999988899898621853456899975778999999853202460011 Q gi|254780611|r 47 LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126 (302) Q Consensus 47 ~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRi 126 (302) T Consensus 2 Eeafe~L~~~y~~~l~~~~~~~~~~~~~AeDl~Qe~flk~~~~~~~~~~~~--~~~~WL~~Ia~N~~~d~~Rk~~r---- 75 (173) T PRK12522 2 EEKVEELIDIYKDQIYSLCYKLAKTKEDAEDIFQETWIKVFSSRHQLSYVE--NYKKWITTICVRTFYDFYRKKKR---- 75 (173) T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHHHHHHHHCC---- T ss_conf 799999999999999999999919999999999999999999777668854--48999999999999999998634---- Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCC Q ss_conf 02300358999999997887866244788824677888618983211000000122343355202323453200000123 Q gi|254780611|r 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206 (302) Q Consensus 127 P~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~ 206 (302) T Consensus 76 ------------------~~~~~~~---------------------------------~~~----~~~~~-----~~~~~ 95 (173) T PRK12522 76 ------------------WKDRILD---------------------------------LFH----KEDGG-----EIEFA 95 (173) T ss_pred ------------------CCCCCCC---------------------------------CCC----HHHHH-----CCCCC T ss_conf ------------------1211101---------------------------------000----10000-----12356 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 56870565566666667779999996219999999999982788888989999997789999999999999999999997 Q gi|254780611|r 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 207 ~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 96 ~~~~~~~~~~~----~~~~~~l~~~l~~L~~~~R~vi~L~~~~~--~s~~EIA~~l~is~~tVksrl~rAr~~Lr~~Le~ 169 (173) T PRK12522 96 DDVNISEEFIQ----KVEAEMIREVIQLLNEKYKTVLVLYYYEQ--YSYKEMSEILNIPIGTVKYRLNYAKKQMREHLEG 169 (173) T ss_pred CCCCCHHHHHH----HHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHC T ss_conf 77885299999----99999999999819999999999999839--9999999998939999999999999999998756 Q ss_pred HH Q ss_conf 40 Q gi|254780611|r 287 QV 288 (302) Q Consensus 287 ~~ 288 (302) T Consensus 170 ~~ 171 (173) T PRK12522 170 FV 171 (173) T ss_pred CC T ss_conf 51 |
|
| >PRK12520 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.56 E-value=6.3e-13 Score=105.94 Aligned_cols=184 Identities=15% Similarity=0.207 Sum_probs=123.4 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCH Q ss_conf 99994307787565555799998889999998889989862185345689997577899999985320246001102300 Q gi|254780611|r 52 RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131 (302) Q Consensus 52 ~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~ 131 (302) T Consensus 6 ~~le~~r~~L~r~A~~~v~d~~~AEDvvQetfl~~~~~~~~f~~~--~~~~tWL~~IarN~~id~lR~~~r~~~~~~~~- 82 (191) T PRK12520 6 AQLEALRPYLLRFARLQLRDEAWAEDAVSETLLAALEKPERFAGQ--SQLKTYLVGILKHKIIDALRSGRREVRLSLDE- 82 (191) T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC- T ss_conf 999999999999999994999999999999999999817642765--45598999999999999999836755554334- Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCC Q ss_conf 35899999999788786624478882467788861898321100000012234335520232345320000012356870 Q gi|254780611|r 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211 (302) Q Consensus 132 ~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~ 211 (302) T Consensus 83 -------------------~~~---~~~------------------------~~~~~~~~~~~~~---~~~-~p~~~~~P 112 (191) T PRK12520 83 -------------------GDE---QSD------------------------DDLFDALFTADGH---YRE-PPSDWGDP 112 (191) T ss_pred -------------------CCC---CCH------------------------HHHHHHHHCCCCC---CCC-CCCCCCCH T ss_conf -------------------565---540------------------------4677776223443---235-87665999 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH-HCC Q ss_conf 5655666666677799999962199999999999827888889899999977899999999999999999999974-012 Q gi|254780611|r 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ-VEL 290 (302) Q Consensus 212 ~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~-~~~ 290 (302) T Consensus 113 e~~----l~~~e~~~~l~~aL~~Lp~~~R~v~~Lr~~~~--ls~~EIA~~l~~s~~tVk~~l~RAR~~Lr~~Le~~~~~~ 186 (191) T PRK12520 113 EAT----LQRRQFFEVLQACVERLPARTGRVFMMREWLE--LETEEICKELQITATNLWVMLYRARLRLRECLELHWFGN 186 (191) T ss_pred HHH----HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCC T ss_conf 999----99999999999999877499999999999938--999999999894999999999999999999998862789 Q ss_pred CCCC Q ss_conf 2467 Q gi|254780611|r 291 SSSP 294 (302) Q Consensus 291 ~~~~ 294 (302) T Consensus 187 ~~~~ 190 (191) T PRK12520 187 QPAP 190 (191) T ss_pred CCCC T ss_conf 9999 |
|
| >PRK12532 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.56 E-value=1.1e-12 Score=104.25 Aligned_cols=178 Identities=13% Similarity=0.126 Sum_probs=111.4 Q ss_pred HHHHHHHHHHHHHHH-HHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCC Q ss_conf 999943077875655-5579999888999999888998986218534568999757789999998532024600110230 Q gi|254780611|r 52 RLVTSHLRLVVKIAM-GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130 (302) Q Consensus 52 ~Li~~nlrlV~~iA~-~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~ 130 (302) T Consensus 10 ~l~~~r~~L~-~fa~~~L~~~~d~AEDlvQEtflka~~~~~~f~~--~s~f~tWL~~IarN~~id~lR~~~r~~~~~~~~ 86 (195) T PRK12532 10 ELIESRKLLL-HFARLQLPDHPDLAEDLVQETLLSAYSAGDSFQG--RALVNSWLFAILKNKIIDALRQIGRQRKVFTAL 86 (195) T ss_pred HHHHHHHHHH-HHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC T ss_conf 9999899999-9999980898757999999999999986874589--887888999999999999999862766767532 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCC Q ss_conf 03589999999978878662447888246778886189832110000001223433552023234532000001235687 Q gi|254780611|r 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210 (302) Q Consensus 131 ~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~ 210 (302) T Consensus 87 ------------------------~----~e~~-------------------d~~~~~~~~~--~~~~-~~~~~p~~~~~ 116 (195) T PRK12532 87 ------------------------D----DELL-------------------DEAFESHFSQ--NGHW-TPEGQPQHWNT 116 (195) T ss_pred ------------------------C----HHHH-------------------HHHHHHHHCC--CCCC-CCCCCCCCCCC T ss_conf ------------------------0----2333-------------------2566654201--3445-75446555499 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 056556666666777999999621999999999998278888898999999778999999999999999999999740 Q gi|254780611|r 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288 (302) Q Consensus 211 ~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~ 288 (302) T Consensus 117 pe~----~~~~~e~~~~l~~~l~~Lp~~~R~vl~L~~~eg--ls~~EIA~~lgis~~tVks~l~RAR~~Lr~~Le~k~ 188 (195) T PRK12532 117 PEK----SLNNNEFQKILQSCLYNLPENTARVFTLKEILG--FSSDEIQQMCGISTSNYHTIMHRARESLRQCLQIKW 188 (195) T ss_pred HHH----HHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 999----999899999999999859999989999999819--999999999895999999999999999999998827 |
|
| >PRK12533 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.56 E-value=9.1e-13 Score=104.86 Aligned_cols=186 Identities=13% Similarity=0.136 Sum_probs=122.2 Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 28599999999943077875655557999988899999988899898621853456899975778999999853202460 Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123 (302) Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~ 123 (302) T Consensus 17 A~r~eaF~~Lv~rh~~~lyr~a~r~~gn~~dAEDlvQEtFlra~r~l~~frg~---~~~tWL~rIa~N~~~~-------- 85 (217) T PRK12533 17 AARGERFRALVLPHLDAAYNLARWLCGNASDADDVVQEACMRALRFFDSCRGD---NARPWLLAIVRHTWYS-------- 85 (217) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC---CHHHHHHHHHHHHHHH-------- T ss_conf 21899999999999999999999996999999999999999999867762344---2489999999999999-------- Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC Q ss_conf 01102300358999999997887866244788824677888618983211000000122343355202323453200000 Q gi|254780611|r 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203 (302) Q Consensus 124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~ 203 (302) T Consensus 86 --------------~~Rrr~~~~-----~~~-------------------------------~~~~~~~--~--~~~-~~ 110 (217) T PRK12533 86 --------------EWRRRANAH-----EVA-------------------------------YPDTLDD--A--DSP-DD 110 (217) T ss_pred --------------HHHHHHCCC-----CCC-------------------------------CCCCCCC--C--CCC-CC T ss_conf --------------999741123-----344-------------------------------2111344--3--234-33 Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 12356870565566666667779999996219999999999982788888989999997789999999999999999999 Q gi|254780611|r 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302) Q Consensus 204 l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302) T Consensus 111 ~~~~~~~pe~~~----~~~e~~~~l~~AL~~Lp~~~R~vl~Lr~~eg--lS~~EIAeiLgip~gTVKSRL~RAR~~Lr~~ 184 (217) T PRK12533 111 WQPAVEDPLALL----LRGEDVRLVNAALAKLPVEYREVLVLRELED--MSYREIAAIADVPVGTVMSRLARARRRLAAL 184 (217) T ss_pred CCCCCCCHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH T ss_conf 467879999999----9889999999999809998868999999809--9999999998949999999999999999997 Q ss_pred HHHHHCCCCCCCCCCCCC Q ss_conf 997401224677645899 Q gi|254780611|r 284 IQKQVELSSSPPLLQKPR 301 (302) Q Consensus 284 l~~~~~~~~~~~~~~~~~ 301 (302) T Consensus 185 L~~~~~~~~~~~~~~~~~ 202 (217) T PRK12533 185 LGGAAQAAPGPRAGGRAR 202 (217) T ss_pred CCCCCCCCCCCCCCCCCC T ss_conf 223455678999998777 |
|
| >TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1; InterPro: IPR014326 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=99.55 E-value=7.1e-13 Score=105.60 Aligned_cols=183 Identities=20% Similarity=0.303 Sum_probs=129.2 Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHH-----HCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHH Q ss_conf 285999999999430778756555-----579999888999999888998986218534568999757789999998532 Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMG-----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118 (302) Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~-----y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~ 118 (302) T Consensus 3 ~GD~eAl~~L~~~Y~~yLr~La~~~L~~~L~~r-~dpSD~VQe~~---l~A~~~~~~fRG~t~~Ef~~W-LR~IL~~~l~ 77 (190) T TIGR02984 3 AGDQEALGELLDRYRNYLRLLARVQLDRRLRRR-VDPSDVVQETL---LEAHRDFDQFRGKTEGEFAGW-LRQILANVLA 77 (190) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHH---HHHHHHHHHHCCCCHHHHHHH-HHHHHHHHHH T ss_conf 872778988999862499999999760884001-57545899999---999988875328985789999-9999999999 Q ss_pred CCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCC Q ss_conf 02460011023003589999999978878662447888246778886189832110000001223433552023234532 Q gi|254780611|r 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198 (302) Q Consensus 119 ~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~ 198 (302) T Consensus 78 ~------------------~---~~~h~~-~qkRD~--------------------------rrE~~l~~~~~~~~~Ss~ 109 (190) T TIGR02984 78 D------------------A---LRRHLG-AQKRDI--------------------------RREQSLDAGAARVDESSV 109 (190) T ss_pred H------------------H---HHHHHH-HHCCCC--------------------------HHCCCCCCCCCCHHHHHH T ss_conf 9------------------9---998866-420262--------------------------010120124576588799 Q ss_pred CHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH Q ss_conf 00000123568705655666666677799999962199999999999827888889899999977899999999999999 Q gi|254780611|r 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278 (302) Q Consensus 199 ~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~ 278 (302) T Consensus 110 ~L~~~Laa~~~sPS~~a~r~E----~~~~L~~AL~~L~e~~REvi~LR~~EG--LS~~EvA~~Md~~~~av~~l~~Ral~ 183 (190) T TIGR02984 110 RLEAQLAADGPSPSQAAARRE----SAVRLAQALAKLPEDYREVILLRHLEG--LSFAEVAERMDRSEGAVSMLWVRALA 183 (190) T ss_pred HHHHHHCCCCCCCHHHHHHHH----HHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHH T ss_conf 999975189998558999977----999999999647922589999987603--55589998707975898758999999 Q ss_pred HHHHHHH Q ss_conf 9999999 Q gi|254780611|r 279 KVQESIQ 285 (302) Q Consensus 279 kLR~~l~ 285 (302) T Consensus 184 ~Lr~~l~ 190 (190) T TIGR02984 184 RLRQILE 190 (190) T ss_pred HHHHHCC T ss_conf 9987509 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family (IPR014284 from INTERPRO) and are apparently found only in the Planctomycetaceae family including the genus s Gemmata and Pirellula, in which seven sequences are found.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >PRK12545 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.54 E-value=8.1e-13 Score=105.20 Aligned_cols=177 Identities=10% Similarity=0.153 Sum_probs=112.8 Q ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHH Q ss_conf 94307787565555799998889999998889989862185345689997577899999985320246001102300358 Q gi|254780611|r 55 TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134 (302) Q Consensus 55 ~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~ 134 (302) T Consensus 15 ~~~r~~L~r~A~~~l~d~~~AEDlvQEtflka~~~~~~F~g~--ss~~TWL~~Ia~N~~id~lRkr~r~~~~~~------ 86 (201) T PRK12545 15 AQLRHDLLRFARLQLRDADAAEDAVQEALAAAWSQAGRFAGQ--SAHKTWVFGILRNKLIDTLRARRRTINLSA------ 86 (201) T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCC--CHHHHHHHHHHHHHHHHHHHHHCCCCCCCC------ T ss_conf 999999999999990999899999999999999854045875--238999999999999999996157788553------ Q ss_pred HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHH Q ss_conf 99999999788786624478882467788861898321100000012234335520232345320000012356870565 Q gi|254780611|r 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214 (302) Q Consensus 135 l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~ 214 (302) T Consensus 87 ---------------------------~----d----------~~~d~e~~~d~~~~~--d~----g~w~~~~~p~~~~~ 119 (201) T PRK12545 87 ---------------------------L----D----------AELDGESLLDRELFK--DN----GHWAAHAKPRPWPK 119 (201) T ss_pred ---------------------------C----C----------CCCCCCCCCHHHHHC--CC----CCCCCCCCCCCCCC T ss_conf ---------------------------4----4----------454632111055403--44----54323357888999 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 56666666777999999621999999999998278888898999999778999999999999999999999740 Q gi|254780611|r 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288 (302) Q Consensus 215 ~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~ 288 (302) T Consensus 120 Pe~~l~~~e~~~~l~~aL~~LP~~~R~v~~Lr~~eg--ls~~EIA~~L~is~~tVksrL~RAR~~LR~~L~ek~ 191 (201) T PRK12545 120 PETILQQQQFWTLFETCLDHLPEQIGRVFMMREFLD--FEIDDICTELTLTANHCSVLLYRARTRLRTCLSEKG 191 (201) T ss_pred HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCC T ss_conf 899999999999999999959999988989999928--989999999896999999999999999999999818 |
|
| >PRK09645 RNA polymerase sigma factor SigL; Provisional | Back alignment and domain information |
|---|
Probab=99.51 E-value=2.2e-12 Score=102.24 Aligned_cols=165 Identities=10% Similarity=0.123 Sum_probs=115.1 Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 28599999999943077875655557999988899999988899898621853456899975778999999853202460 Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123 (302) Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~ 123 (302) T Consensus 3 ~gD~~af~~Ly~~~~~~l~~~~~~~~~d~~~AeDivQe~F~k~~~~~~~~~~~-~~~~~~wL~~Ia~n~~~d~~------ 75 (171) T PRK09645 3 DAEAALMRALYDEHAAALWRYALRLTGDRARAEDVVQETLLRAWQHPEVLADP-TRSARAWLFTVARNLVIDER------ 75 (171) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC-CCCHHHHHHHHHHHHHHHHH------ T ss_conf 63999999999999999999999990999999999999999999858870664-14199999999999999999------ Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC Q ss_conf 01102300358999999997887866244788824677888618983211000000122343355202323453200000 Q gi|254780611|r 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203 (302) Q Consensus 124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~ 203 (302) T Consensus 76 ----------------R~~~~~~-----~~~~---------------------------~~~~~~--------------- 92 (171) T PRK09645 76 ----------------RSARARP-----VEGS---------------------------PDVLGV--------------- 92 (171) T ss_pred ----------------HHHHCCC-----CCCC---------------------------CCHHHH--------------- T ss_conf ----------------9875475-----4344---------------------------423320--------------- Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 12356870565566666667779999996219999999999982788888989999997789999999999999999999 Q gi|254780611|r 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302) Q Consensus 204 l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302) T Consensus 93 -~--~~~~~~~~~~----~~~~~~l~~ai~~L~~~~r~v~~l~~~~g--~s~~EIA~~l~is~~tVk~~l~ra~~~Lr~~ 163 (171) T PRK09645 93 -P--EQSTPDEVDA----ALDRLLIADALAQLSPEHRAVLVRSYYRG--WSTAQIAADLGIPEGTVKSRLHYAVRALRLT 163 (171) T ss_pred -C--CCCCCCHHHH----HHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH T ss_conf -2--5688316889----99999999999759999887989999869--9999999998929999999999999999999 Q ss_pred HHHH Q ss_conf 9974 Q gi|254780611|r 284 IQKQ 287 (302) Q Consensus 284 l~~~ 287 (302) T Consensus 164 L~~~ 167 (171) T PRK09645 164 LQEM 167 (171) T ss_pred HHHC T ss_conf 9970 |
|
| >PRK12517 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.50 E-value=3.2e-12 Score=101.22 Aligned_cols=163 Identities=15% Similarity=0.175 Sum_probs=115.1 Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 28599999999943077875655557999988899999988899898621853456899975778999999853202460 Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123 (302) Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~ 123 (302) T Consensus 19 ~~~~~AFe~L~~~y~~~ly~~a~~~~~d~~~AeDl~QEtFlk~~~~~~~~~~~~--~~~tWL~~-----I~---~~~--- 85 (188) T PRK12517 19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEK--AAKAWLIT-----IL---RRE--- 85 (188) T ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHH-----HH---HHH--- T ss_conf 135999999999999999999999949999999999999999999887647963--18999999-----99---999--- Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC Q ss_conf 01102300358999999997887866244788824677888618983211000000122343355202323453200000 Q gi|254780611|r 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203 (302) Q Consensus 124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~ 203 (302) T Consensus 86 --------------~~~r~~r~~-------~---~~------------------------~~~~~~~------------- 104 (188) T PRK12517 86 --------------NARRFERKQ-------F---DL------------------------VDIEDDS------------- 104 (188) T ss_pred --------------HHHHHHHCC-------C---CC------------------------CCCCCCC------------- T ss_conf --------------889998615-------7---75------------------------6522000------------- Q ss_pred CCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH Q ss_conf 1235-687056556666666777999999621999999999998278888898999999778999999999999999999 Q gi|254780611|r 204 LVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302) Q Consensus 204 l~~~-~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302) T Consensus 105 ~~~~~~~~~e~--------~~~~~~l~~~l~~Lp~~~R~vi~L~~~eg--~s~~EIA~~Lgis~~tVksrl~RAr~~Lr~ 174 (188) T PRK12517 105 IEDDLSSSSEE--------EMEQYWLRRQIAKLDPEYREPLLLQVIGG--FSGEEIAEILDLNKNTVMTRLFRARNQLKE 174 (188) T ss_pred CCCCCCCCCHH--------HHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf 24666788168--------99999999999769999999999999839--999999999893999999999999999999 Q ss_pred HHHHHHCC Q ss_conf 99974012 Q gi|254780611|r 283 SIQKQVEL 290 (302) Q Consensus 283 ~l~~~~~~ 290 (302) T Consensus 175 ~Le~~~e~ 182 (188) T PRK12517 175 ALEKPDEV 182 (188) T ss_pred HHCCHHHH T ss_conf 97420275 |
|
| >PRK09637 RNA polymerase sigma factor SigZ; Provisional | Back alignment and domain information |
|---|
Probab=99.47 E-value=5.5e-12 Score=99.63 Aligned_cols=157 Identities=8% Similarity=0.100 Sum_probs=112.9 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC Q ss_conf 99999943077875655557999988899999988899898621853456899975778999999853202460011023 Q gi|254780611|r 50 AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129 (302) Q Consensus 50 r~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302) T Consensus 3 ~E~Ly~~y~~~l~~~~~~~~~d~~~AEDivQe~flk~~~~~~~~~~~--~~~~~WL~~IarN~~id~~Rk~~r~------ 74 (181) T PRK09637 3 LESIWSEYKAQLKAFLHSRVSNEADVDDLLQEVLIKTHSNLHSLKDG--SSIKSWLYQIANNTIIDFYRKKNRS------ 74 (181) T ss_pred HHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCC--CCHHHHHHHHHHHHHHHHHHHHCCC------ T ss_conf 99999999999999999995999999999999999999852205882--3499999999999999999861555------ Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC Q ss_conf 00358999999997887866244788824677888618983211000000122343355202323453200000123568 Q gi|254780611|r 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209 (302) Q Consensus 130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~ 209 (302) T Consensus 75 -----------------------~-~~~~----------------------------~~-~~~--------------~~~ 87 (181) T PRK09637 75 -----------------------E-ELPD----------------------------DL-LFE--------------DEE 87 (181) T ss_pred -----------------------C-CCCH----------------------------HH-CCC--------------CCC T ss_conf -----------------------6-7742----------------------------22-146--------------798 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 70565566666667779999996219999999999982788888989999997789999999999999999999997401 Q gi|254780611|r 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289 (302) Q Consensus 210 ~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~~ 289 (302) T Consensus 88 -~~~~-----~~~e~~~~l~~~l~~Lp~~~R~v~~L~~~eg--~s~~EIA~~L~is~~tVksrl~RAr~~Lr~~LE~~~~ 159 (181) T PRK09637 88 -REEN-----AKKELAPCLRPFIDALPEKYAEALRLTELEG--LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLEGCCD 159 (181) T ss_pred -CCHH-----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf -3224-----9999999999999769999989979998859--9999999998949999999999999999999971278 |
|
| >PRK12516 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.47 E-value=9.3e-12 Score=98.12 Aligned_cols=168 Identities=10% Similarity=0.085 Sum_probs=117.5 Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 28599999999943077875655557999988899999988899898621853456899975778999999853202460 Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123 (302) Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~ 123 (302) T Consensus 9 ~~~~~~F~~l~~~~~p~L~~~a~~l~~~~~dAEDlvQetflk~~~~~~~~~~~--~~~~aWL~~IarN~~~d~~Rk~~r- 85 (190) T PRK12516 9 VEGTPPFKRELLASLPSLRAFAVSLIGQHDRADDLVQDTIMKAWAKQESFEVG--TNMKAWLFTILRNEFYTQMRKRGR- 85 (190) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHCCC- T ss_conf 99872099999998999999999990999999999999999999998635656--779999999999999999996168- Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC Q ss_conf 01102300358999999997887866244788824677888618983211000000122343355202323453200000 Q gi|254780611|r 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203 (302) Q Consensus 124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~ 203 (302) T Consensus 86 ---------------------~~----------~~~-----------------d~~~~e~------~~------------ 99 (190) T PRK12516 86 ---------------------EV----------QDT-----------------DGMFSEQ------LA------------ 99 (190) T ss_pred ---------------------CC----------CCC-----------------CCCCCCC------CC------------ T ss_conf ---------------------66----------653-----------------2223333------46------------ Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 12356870565566666667779999996219999999999982788888989999997789999999999999999999 Q gi|254780611|r 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302) Q Consensus 204 l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302) T Consensus 100 ---~~~~~~----~~~~----~~~l~~al~~Lp~~~R~vl~L~~~eg--ls~~EIAe~Lgis~~TVksrl~RAr~~Lr~~ 166 (190) T PRK12516 100 ---VHPSQY----GTLD----LQDFRAALDQLPDDQREAIILIGASG--FAYEEAAEICGCAVGTIKSRVSRARARLQEI 166 (190) T ss_pred ---CCCCCC----CHHH----HHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH T ss_conf ---895420----2077----99999999819999989999899829--9999999998949999999999999999999 Q ss_pred HHHHHCCCCC Q ss_conf 9974012246 Q gi|254780611|r 284 IQKQVELSSS 293 (302) Q Consensus 284 l~~~~~~~~~ 293 (302) T Consensus 167 L~~~g~~~~g 176 (190) T PRK12516 167 LQIEGEADYG 176 (190) T ss_pred HHHCCCCCCC T ss_conf 9845998789 |
|
| >PRK09644 RNA polymerase sigma factor SigM; Provisional | Back alignment and domain information |
|---|
Probab=99.46 E-value=7.7e-12 Score=98.64 Aligned_cols=157 Identities=11% Similarity=0.147 Sum_probs=110.1 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC Q ss_conf 99999943077875655557999988899999988899898621853456899975778999999853202460011023 Q gi|254780611|r 50 AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129 (302) Q Consensus 50 r~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302) T Consensus 3 ~E~ly~~y~~~l~~~~~~~~~d~~~AeDl~Qe~flk~~~~~~~~~~~---~~~~WL~~Ia~n~~~d~~Rk~~r~~~---- 75 (165) T PRK09644 3 IEEIYKMYINDVYRYLFSLTKSHHLAEDLLQETFYRAYIYLEDYDNQ---KVKPWLFKVAYHTFIDFVRKEKKVVF---- 75 (165) T ss_pred HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC---CHHHHHHHHHHHHHHHHHHHHCCCCC---- T ss_conf 99999999999999999990999999999999999999988766813---18999999999999999997447577---- Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC Q ss_conf 00358999999997887866244788824677888618983211000000122343355202323453200000123568 Q gi|254780611|r 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209 (302) Q Consensus 130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~ 209 (302) T Consensus 76 --------------------------------------~~~~-------------~~~~---------------~~--~~ 87 (165) T PRK09644 76 --------------------------------------VGTD-------------EIET---------------IQ--AE 87 (165) T ss_pred --------------------------------------CCHH-------------HHCC---------------CC--CC T ss_conf --------------------------------------6521-------------1001---------------13--58 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 705655666666677799999962199999999999827888889899999977899999999999999999999974 Q gi|254780611|r 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 210 ~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 88 ~~~~~~----~~~e~~~~l~~~l~~Lp~~~r~v~~L~~~~~--~s~~EIA~~l~is~~tVk~rl~RAr~~Lr~~L~~e 159 (165) T PRK09644 88 STEEYA----VAKNSYEKLIQIIHTLPVIEAQAILLCDVHE--LTYEEAASVLDLKENTYKSHLFRGRKRLKALLKEE 159 (165) T ss_pred CHHHHH----HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 801499----9899999999998729999999999999988--89999999989399999999999999999999987 |
|
| >PRK12541 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.46 E-value=1.1e-11 Score=97.63 Aligned_cols=160 Identities=11% Similarity=0.142 Sum_probs=108.2 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH Q ss_conf 85999999999430778756555579999888999999888998986218534568999757789999998532024600 Q gi|254780611|r 45 GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124 (302) Q Consensus 45 gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~I 124 (302) T Consensus 2 ~~r~afe~ly~~~~~~l~~~~~~~~~d~~~AeDl~QetFlk~~~~~~~~~---~~~~~~WL~~Ia~N~~~d~~------- 71 (161) T PRK12541 2 KRKQSLEEIYSEHMQDLFRYLLSLTGDSHFAEDLMQETFYRMLVHIDYYK---GEEIRPWLFTIAYNAFIDWY------- 71 (161) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCC---CCCHHHHHHHHHHHHHHHHH------- T ss_conf 63999999999999999999999939999999999999999998361316---67568999999999999999------- Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCC Q ss_conf 11023003589999999978878662447888246778886189832110000001223433552023234532000001 Q gi|254780611|r 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204 (302) Q Consensus 125 RiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l 204 (302) T Consensus 72 ---------------Rk~~~~--------~~-~---------------------------~~~~--------------~~ 86 (161) T PRK12541 72 ---------------RKEKKY--------KT-T---------------------------TVEE--------------FH 86 (161) T ss_pred ---------------HHHHCC--------CC-C---------------------------CHHH--------------HC T ss_conf ---------------986044--------65-5---------------------------2555--------------40 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 23568705655666666677799999962199999999999827888889899999977899999999999999999999 Q gi|254780611|r 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302) Q Consensus 205 ~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302) T Consensus 87 ~~~~~~~~~~~~~~~----~~~~~~~~l~~Lp~~~R~v~~L~~~~g--~s~~EIA~~lgis~~tVk~~l~RArk~Lr~l~ 160 (161) T PRK12541 87 LPNVPSTEHEYFVKH----EIASWLDSLSSLPLERRNVLLLRDYYG--FSYKEIAEMTGLSLAKVKIELHRGRKETKSIK 160 (161) T ss_pred CCCCCCCHHHHHHHH----HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH T ss_conf 468999627789999----999999999819999999999899749--99999999989399999999999999998762 Q ss_pred H Q ss_conf 9 Q gi|254780611|r 285 Q 285 (302) Q Consensus 285 ~ 285 (302) T Consensus 161 E 161 (161) T PRK12541 161 E 161 (161) T ss_pred C T ss_conf 9 |
|
| >COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription] | Back alignment and domain information |
|---|
Probab=99.45 E-value=2.7e-11 Score=95.04 Aligned_cols=170 Identities=16% Similarity=0.183 Sum_probs=121.6 Q ss_pred HHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 82859999999994307787565555799998889999998889989862185345689997577899999985320246 Q gi|254780611|r 43 EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122 (302) Q Consensus 43 ~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~ 122 (302) T Consensus 10 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~dAeDlvQE~~lr~~~~~~~~-~~-~~~~~~wl~~Ia~n~~iD~~R~~~r 87 (182) T COG1595 10 LRGDRAAFEELLERLRPRLRRLARRLLGDRADAEDLVQETFLRAWRAIDSF-RG-RSSFKAWLYRIARNLAIDRLRKRKR 87 (182) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCHHC-CC-CCCHHHHHHHHHHHHHHHHHHHHHH T ss_conf 875178899999999999999999996884309999999999999733311-67-8878999999999999999997610 Q ss_pred CHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHC Q ss_conf 00110230035899999999788786624478882467788861898321100000012234335520232345320000 Q gi|254780611|r 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202 (302) Q Consensus 123 ~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d 202 (302) T Consensus 88 ----------------------~~~~~~~~~------------------------~-----~------~----------- 99 (182) T COG1595 88 ----------------------RRARVEEAD------------------------L-----L------P----------- 99 (182) T ss_pred ----------------------HCCHHHHCC------------------------C-----C------C----------- T ss_conf ----------------------132001000------------------------2-----4------5----------- Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH Q ss_conf 01235687056556666666777999999621999999999998278888898999999778999999999999999999 Q gi|254780611|r 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302) Q Consensus 203 ~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302) T Consensus 100 --~~~~~~~~~~--~~~~~~~~~~~l~~al~~Lp~~~R~~~~l~~~~g--ls~~EIA~~l~i~~~tVks~l~ra~~~l~~ 173 (182) T COG1595 100 --EEADPAPDLA--ELLLAEEELERLRRALARLPPRQREAFLLRYLEG--LSYEEIAEILGISVGTVKSRLHRARKKLRE 173 (182) T ss_pred --CCCCCCCHHH--HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf --4345670267--8887678999999999839999999999999859--999999989599999999999999999999 Q ss_pred HHHHHH Q ss_conf 999740 Q gi|254780611|r 283 SIQKQV 288 (302) Q Consensus 283 ~l~~~~ 288 (302) T Consensus 174 ~l~~~~ 179 (182) T COG1595 174 QLEEAG 179 (182) T ss_pred HHHHHC T ss_conf 875501 |
|
| >PRK09642 RNA polymerase sigma factor SigW; Reviewed | Back alignment and domain information |
|---|
Probab=99.44 E-value=7.5e-12 Score=98.74 Aligned_cols=157 Identities=13% Similarity=0.179 Sum_probs=106.4 Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHH Q ss_conf 99430778756555579999888999999888998986218534568999757789999998532024600110230035 Q gi|254780611|r 54 VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133 (302) Q Consensus 54 i~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r 133 (302) T Consensus 1 v~~Y~~~ly~~~~~~~~n~~dAeDi~QevFik~~~~~~~~~~~-~--~~~WL~~Ia~N~~~d~~Rk~~r----------- 66 (160) T PRK09642 1 MQTYRHYIFQVIFSILRHEEDAKDVTQEVFVKIHASLPNYQFR-G--LKTWMARIATNHAIDYKRKKAR----------- 66 (160) T ss_pred CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCC-C--HHHHHHHHHHHHHHHHHHHHHC----------- T ss_conf 9467899999999990999999999999999999845033624-4--9999999999999999998724----------- Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHH Q ss_conf 89999999978878662447888246778886189832110000001223433552023234532000001235687056 Q gi|254780611|r 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213 (302) Q Consensus 134 ~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~ 213 (302) T Consensus 67 -----------~-----------~~------------------------~~~~~~~---~~~--------~~~~~~~~e~ 89 (160) T PRK09642 67 -----------E-----------NE------------------------ELSLCKE---TEE--------NIKSSHNIED 89 (160) T ss_pred -----------C-----------CC------------------------CCCCCHH---HHH--------CCCCCCCHHH T ss_conf -----------5-----------53------------------------1220001---121--------1567799899 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 55666666677799999962199999999999827888889899999977899999999999999999999974 Q gi|254780611|r 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302) Q Consensus 214 ~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302) T Consensus 90 ~~~----~~e~~~~l~~~l~~Lp~~~R~v~~L~~~e~--~s~~EIA~~l~is~~tVk~~l~RArk~Lkk~lkee 157 (160) T PRK09642 90 LLL----TKEQKLLIAQKLRELPENYRDVVLAHYLEE--KSYQEIALQENIEVKTVEMKLYRARKWIKKHWKEE 157 (160) T ss_pred HHH----HHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC T ss_conf 999----899999999999979999999979999829--99999999989199999999999999999999875 |
|
| >PRK12530 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.43 E-value=2.3e-11 Score=95.46 Aligned_cols=173 Identities=16% Similarity=0.184 Sum_probs=110.1 Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHH Q ss_conf 99430778756555579999888999999888998986218534568999757789999998532024600110230035 Q gi|254780611|r 54 VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133 (302) Q Consensus 54 i~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r 133 (302) T Consensus 15 ~e~yr~~L~~fa~~~l~d~~~AEDlvQEtFlka~~~~~~f~~~--~~f~tWL~~Ia~N~~id~lRk~~r~~~~~------ 86 (191) T PRK12530 15 LEEIRLQMLKFATLQLKDADLAEDVVQEAFTSALKNIDSFKGQ--SALKTWIFAILKNKIIDYIRQRKRFVNES------ 86 (191) T ss_pred HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHHCCCCCCC------ T ss_conf 9999999999999993999999999999999999868863787--72999999999999999999846667721------ Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCC-CCCCCCH Q ss_conf 899999999788786624478882467788861898321100000012234335520232345320000012-3568705 Q gi|254780611|r 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV-YDHDGQE 212 (302) Q Consensus 134 ~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~-~~~~~~~ 212 (302) T Consensus 87 ---------------------------~~~------~~~~---------~~~~---~---d~~~~~~~~~~~~~~~~~~e 118 (191) T PRK12530 87 ---------------------------ELI------EEES---------PNSF---F---DEKGHWKPETYEPSELQDVE 118 (191) T ss_pred ---------------------------CCC------CCCC---------CHHH---H---CCCCCCCCCCCCCCCCCCHH T ss_conf ---------------------------001------2224---------1001---0---11122343336830216899 Q ss_pred HHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 6556666666777999999621999999999998278888898999999778999999999999999999999740 Q gi|254780611|r 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288 (302) Q Consensus 213 ~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~ 288 (302) T Consensus 119 ----~~~~~~e~~~~l~~~l~~LP~~~R~v~~Lr~~~~--ls~~EIA~~l~is~~tVksrL~RAR~~Lr~~L~~~~ 188 (191) T PRK12530 119 ----QTVYSEEFWLIFEICLNKLPAQQARVFMMREFLE--LSSEQICQECHITTSNLHVLLYRARLQLQACLSKKW 188 (191) T ss_pred ----HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHC T ss_conf ----9999999999999999869999999999999929--999999999896999999999999999999999845 |
|
| >PRK12546 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.43 E-value=1.5e-11 Score=96.66 Aligned_cols=161 Identities=13% Similarity=0.132 Sum_probs=109.4 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH Q ss_conf 85999999999430778756555579999888999999888998986218534568999757789999998532024600 Q gi|254780611|r 45 GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124 (302) Q Consensus 45 gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~I 124 (302) T Consensus 5 ~~~~~~~~l~e-H~p~L~~fa~r~~~~~~~AEDlvQEtflk~~~~l~~~~~~--~~~~tWL~~IarN~~~d~-------- 73 (188) T PRK12546 5 KHRDPRDELVE-HLPALRAFAISLTRNVAAADDLVQDTVVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSD-------- 73 (188) T ss_pred CCHHHHHHHHH-HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHH-------- T ss_conf 30629999999-9999999999991999999999999999999978764765--313889999999999999-------- Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCC Q ss_conf 11023003589999999978878662447888246778886189832110000001223433552023234532000001 Q gi|254780611|r 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204 (302) Q Consensus 125 RiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l 204 (302) T Consensus 74 --------------~Rk~~r~~--------~-----------------------------~~~~~~~---~-------~~ 92 (188) T PRK12546 74 --------------RRKHKREV--------E-----------------------------DPEGVHA---A-------SL 92 (188) T ss_pred --------------HHHHCCCC--------C-----------------------------CCCCCCC---C-------CC T ss_conf --------------99744777--------7-----------------------------6421112---3-------34 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 23568705655666666677799999962199999999999827888889899999977899999999999999999999 Q gi|254780611|r 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302) Q Consensus 205 ~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302) T Consensus 93 ~-~~~~~~~----~----~~~~~l~~aL~~LP~~~R~vl~L~~~eg--ls~~EIAe~Lgis~gTVKsRL~RAR~~Lr~~L 161 (188) T PRK12546 93 A-VKPAHDG----R----LAMSDFRAAFAQLPDEQREALILVGASG--FSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188) T ss_pred C-CCCCCHH----H----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH T ss_conf 6-8987006----8----9999999999869999988958799829--89999999989399999999999999999987 Q ss_pred HHHH Q ss_conf 9740 Q gi|254780611|r 285 QKQV 288 (302) Q Consensus 285 ~~~~ 288 (302) T Consensus 162 e~~~ 165 (188) T PRK12546 162 QLEE 165 (188) T ss_pred HCCC T ss_conf 2721 |
|
| >PRK07037 extracytoplasmic-function sigma-70 factor; Validated | Back alignment and domain information |
|---|
Probab=99.41 E-value=3.2e-11 Score=94.56 Aligned_cols=166 Identities=18% Similarity=0.222 Sum_probs=116.5 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH Q ss_conf 85999999999430778756555579999888999999888998986218534568999757789999998532024600 Q gi|254780611|r 45 GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124 (302) Q Consensus 45 gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~I 124 (302) T Consensus 9 ~~e~al~elf~~~~~~L~~~a~r~~~~~~~AEDivQe~Flkl~~~~~~~~~~~--~~-awL~~iarN~~id~lRr~~--- 82 (183) T PRK07037 9 ACDGALLDVFVDNRSMLVKIARGIVGCASRAEDVVQDAFVKLVEAPNQDAVKQ--PV-AYLFQMVRNLAIDHCRRQS--- 82 (183) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCC--HH-HHHHHHHHHHHHHHHHHHH--- T ss_conf 60899999999999999999999979998899999999999997454344136--99-9999999999999999777--- Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCC Q ss_conf 11023003589999999978878662447888246778886189832110000001223433552023234532000001 Q gi|254780611|r 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204 (302) Q Consensus 125 RiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l 204 (302) T Consensus 83 -------------------~~~~-----~~~-----------------------------~--------~~~~~----~~ 97 (183) T PRK07037 83 -------------------LENK-----YHG-----------------------------D--------EDDGL----DV 97 (183) T ss_pred -------------------HHHH-----CCC-----------------------------C--------HHHHC----CC T ss_conf -------------------6650-----134-----------------------------2--------44421----26 Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 23568705655666666677799999962199999999999827888889899999977899999999999999999999 Q gi|254780611|r 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302) Q Consensus 205 ~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302) T Consensus 98 ~~~~~~pe~~~~~~e----~~~~l~~ai~~LP~~~R~v~~L~~~eg--~s~~EIAe~LgiS~~tVk~~l~rAl~~LR~~L 171 (183) T PRK07037 98 PSPEASPEAALINRD----TLRHVADALDELPARTRAAFEMVRLRG--ETLQDIARELNVSQTLVNFMIRDALRHCRKCL 171 (183) T ss_pred CCCCCCHHHHHHHHH----HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH T ss_conf 788999899999999----999999999819999999989898739--89999999989299999999999999999999 Q ss_pred HHH Q ss_conf 974 Q gi|254780611|r 285 QKQ 287 (302) Q Consensus 285 ~~~ 287 (302) T Consensus 172 e~~ 174 (183) T PRK07037 172 DAC 174 (183) T ss_pred HHH T ss_conf 876 |
|
| >PRK12547 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.39 E-value=7.7e-11 Score=91.96 Aligned_cols=160 Identities=12% Similarity=0.139 Sum_probs=111.0 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHH Q ss_conf 59999999994307787565555799998889999998889989862185345689997577899999985320246001 Q gi|254780611|r 46 DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125 (302) Q Consensus 46 d~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IR 125 (302) T Consensus 4 ~~~~F~~l~~~~~p~L~~~a~~l~~~~~~AeDlvQe~flk~~~~~~~~~~~--~~~~~Wl~~IarN~~~d~~-------- 73 (164) T PRK12547 4 TSKNFKQELLAALPSLRAFAVSLSSKHDKADDLVQDTLMKAWAKQDSFQPG--TNLKAWLFTILRNEFYSQM-------- 73 (164) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHH-------- T ss_conf 799999999998999999999994999999999999999999988876998--8699999999999999999-------- Q ss_pred HCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCC Q ss_conf 10230035899999999788786624478882467788861898321100000012234335520232345320000012 Q gi|254780611|r 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205 (302) Q Consensus 126 iP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~ 205 (302) T Consensus 74 --------------Rk~~r~~--------~--~------------~-----~~~~~------~------~--------~- 91 (164) T PRK12547 74 --------------RKRGREV--------Q--D------------S-----DGVFT------A------R--------L- 91 (164) T ss_pred --------------HHHCCCC--------C--C------------C-----CCCCC------C------C--------C- T ss_conf --------------9727877--------6--5------------2-----10110------1------2--------5- Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 35687056556666666777999999621999999999998278888898999999778999999999999999999999 Q gi|254780611|r 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302) Q Consensus 206 ~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302) T Consensus 92 ~~~~~~~----~~~~----~~~l~~al~~Lp~~~r~v~~L~~~~g--~s~~EIA~~lgis~~tVksrl~rAr~~Lr~~Lk 161 (164) T PRK12547 92 AVHPAQY----GSLD----LQDFRKALNLLPADQREAIILIGASG--FSYEEAAEICGCAVGTIKSRVSRARNRLQELLK 161 (164) T ss_pred CCCCHHH----HHHH----HHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH T ss_conf 6894024----3689----99999999858999999999899849--999999999893999999999999999999987 Q ss_pred HH Q ss_conf 74 Q gi|254780611|r 286 KQ 287 (302) Q Consensus 286 ~~ 287 (302) T Consensus 162 ~~ 163 (164) T PRK12547 162 ID 163 (164) T ss_pred HC T ss_conf 67 |
|
| >PRK09639 RNA polymerase sigma factor SigX; Provisional | Back alignment and domain information |
|---|
Probab=99.39 E-value=7.3e-11 Score=92.14 Aligned_cols=161 Identities=12% Similarity=0.103 Sum_probs=108.6 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH Q ss_conf 99999999943077875655557999988899999988899898621853456899975778999999853202460011 Q gi|254780611|r 47 LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126 (302) Q Consensus 47 ~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRi 126 (302) T Consensus 2 eeAF~~ly~~y~~~l~~~~~~~~~d~~~AeDl~Qe~flk~~~~--~~~~--~~~~~~wL~~ia~n~~~d~~R~~~----- 72 (166) T PRK09639 2 EETFEDLFKQYYQDVVQQIIYIVKDRTQAEDLAQEVFLRLLRS--DWKG--IENEKGWLIKSARNVAYNYFRSEK----- 72 (166) T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC--CCCC--CCCHHHHHHHHHHHHHHHHHHHHH----- T ss_conf 8999999999999999999999299999999999999999872--6354--467899999999999999999884----- Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCC Q ss_conf 02300358999999997887866244788824677888618983211000000122343355202323453200000123 Q gi|254780611|r 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206 (302) Q Consensus 127 P~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~ 206 (302) T Consensus 73 -----------------~~~~~~~---------------------------------~~~~-------~~~-------~~ 88 (166) T PRK09639 73 -----------------RHRARIL---------------------------------GEFQ-------WQE-------EQ 88 (166) T ss_pred -----------------HHHHHHC---------------------------------CCHH-------CCC-------CC T ss_conf -----------------0201000---------------------------------0100-------013-------45 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 56870565566666667779999996219999999999982788888989999997789999999999999999999997 Q gi|254780611|r 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 207 ~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 89 ~~~~~e~~~~~----~~~~~~l~~~l~~Lp~~~r~v~~l~~-~g--~s~~EIA~~l~is~~tVk~~l~RA~~~Lr~~le~ 161 (166) T PRK09639 89 IDSSPEEIWIR----KEEITKVQEVLAKMTERDRTVLLLRF-SG--YSYKEIAQALGIDESSVGTTLHRAKKKFRKIYEQ 161 (166) T ss_pred CCCCHHHHHHH----HHHHHHHHHHHHHCCHHHHHHHHHHH-HC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 57997899998----99999999998839999999999999-38--9999999998919999999999999999999998 Q ss_pred H Q ss_conf 4 Q gi|254780611|r 287 Q 287 (302) Q Consensus 287 ~ 287 (302) T Consensus 162 ~ 162 (166) T PRK09639 162 M 162 (166) T ss_pred H T ss_conf 7 |
|
| >PRK09651 RNA polymerase sigma factor FecI; Provisional | Back alignment and domain information |
|---|
Probab=99.37 E-value=7.7e-11 Score=91.99 Aligned_cols=165 Identities=13% Similarity=0.097 Sum_probs=118.1 Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 28599999999943077875655557999988899999988899898621853456899975778999999853202460 Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123 (302) Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~ 123 (302) T Consensus 6 ~~~~~AFe~Ly~~~~~~l~~~~~~~~~~~~~AeDivQe~Flr~~~~-~~~~~~~--~~~a~L~~iarn~~id~~Rr~~~- 81 (172) T PRK09651 6 TTASLTFESLYGTHHGWLKSWLTRKLQSAFDADDIAQDTFLRVMVS-ETLSTIR--DPRSFLCTIAKRVMVDLFRRNAL- 81 (172) T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC-CCCCCCC--CHHHHHHHHHHHHHHHHHHHHHH- T ss_conf 5586699999999999999999999598868999999999999863-8523346--88999999999999999999888- Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC Q ss_conf 01102300358999999997887866244788824677888618983211000000122343355202323453200000 Q gi|254780611|r 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203 (302) Q Consensus 124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~ 203 (302) T Consensus 82 -------------------~~~~------------~~~~~~-------------------------~~------------ 93 (172) T PRK09651 82 -------------------EKAY------------LEMLAL-------------------------MP------------ 93 (172) T ss_pred -------------------HHHH------------HHHHHH-------------------------CC------------ T ss_conf -------------------8878------------888874-------------------------75------------ Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 12356870565566666667779999996219999999999982788888989999997789999999999999999999 Q gi|254780611|r 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302) Q Consensus 204 l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302) T Consensus 94 -~~~~~~~e~~~----~~~e~~~~l~~~l~~Lp~~~R~v~~L~~~eg--ls~~EIA~~lgiS~~tVk~~l~rAlk~c~~~ 166 (172) T PRK09651 94 -EGGAPSPEERE----SQLETLQLLDSMLDGLNGKTREAFLLSQLDG--LTYSEIAHKLGVSISSVKKYVAKAVEHCLLF 166 (172) T ss_pred -CCCCCCHHHHH----HHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH T ss_conf -54599988999----9999999999998709999999999998839--9999999998939999999999999999999 Q ss_pred HHHH Q ss_conf 9974 Q gi|254780611|r 284 IQKQ 287 (302) Q Consensus 284 l~~~ 287 (302) T Consensus 167 ~~~~ 170 (172) T PRK09651 167 RLEY 170 (172) T ss_pred HHHC T ss_conf 9873 |
|
| >PRK12540 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.31 E-value=3.1e-10 Score=87.90 Aligned_cols=160 Identities=12% Similarity=0.154 Sum_probs=107.9 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHH Q ss_conf 99999999943077875655557999988899999988899898621853456899975778999999853202460011 Q gi|254780611|r 47 LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126 (302) Q Consensus 47 ~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRi 126 (302) T Consensus 4 ~~~f~~~~l~~~P~L~~fa~~l~~n~~dAEDlvQEtflk~~~~~~~~~~~--~~~~tWL~~IarN~~~~~---------- 71 (181) T PRK12540 4 TDSLRDDILAAVPSLRAFAISLSGNGDRADDLVQETLLRALANIDSFQPG--SNLPAWLFTILRNLFRSD---------- 71 (181) T ss_pred CHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHH---------- T ss_conf 08899999998799999999993999999999999999999849875987--624899999999999999---------- Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCC Q ss_conf 02300358999999997887866244788824677888618983211000000122343355202323453200000123 Q gi|254780611|r 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206 (302) Q Consensus 127 P~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~ 206 (302) T Consensus 72 ------------~Rk~~r~~~----------~-----------------~~------~~~~~--------------~~-~ 91 (181) T PRK12540 72 ------------YRKRRREVE----------D-----------------AD------GSYAK--------------TL-K 91 (181) T ss_pred ------------HHHHCCCCC----------C-----------------CC------CCCCC--------------CC-C T ss_conf ------------998357666----------4-----------------32------11000--------------14-6 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 56870565566666667779999996219999999999982788888989999997789999999999999999999997 Q gi|254780611|r 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 207 ~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 92 ~~~~~~----~~~----~~~~l~~al~~Lp~~~R~vl~L~~~eg--ls~~EIA~iL~is~gTVKsRL~RAr~kLr~~L~~ 161 (181) T PRK12540 92 SQPGQN----AHL----EFEEFRAALEKLPQDQREALILVGASG--FSYEDAAAICGCAVGTIKSRVNRARSKLSALLYV 161 (181) T ss_pred CCCCHH----HHH----HHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH T ss_conf 899735----677----899999999819999989988799809--9999999998949999999999999999999874 Q ss_pred HH Q ss_conf 40 Q gi|254780611|r 287 QV 288 (302) Q Consensus 287 ~~ 288 (302) T Consensus 162 ~g 163 (181) T PRK12540 162 DG 163 (181) T ss_pred CC T ss_conf 65 |
|
| >TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1; InterPro: IPR014327 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=99.25 E-value=4.4e-10 Score=86.95 Aligned_cols=166 Identities=14% Similarity=0.214 Sum_probs=121.1 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCC Q ss_conf 99999994307787565555799998889999998889989862185345689997577899999985320246001102 Q gi|254780611|r 49 AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128 (302) Q Consensus 49 Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~ 128 (302) T Consensus 2 aF~~ly~~Yy~~l~~fA~~yv~~~e~AEdIVqdvF~~lWe~r~~l~~~~--~~~~YL~~~v~N~~ln~Lr~~~--~~--- 74 (167) T TIGR02985 2 AFEQLYRRYYPKLCAFARRYVKDEEDAEDIVQDVFLKLWENRESLEESE--SIKAYLFTIVKNRCLNYLRHKQ--VE--- 74 (167) T ss_pred HHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHH--HH--- T ss_conf 4889999987999999999836899999999999999973145256213--5217999999998998998899--99--- Q ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCC Q ss_conf 30035899999999788786624478882467788861898321100000012234335520232345320000012356 Q gi|254780611|r 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208 (302) Q Consensus 129 ~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~ 208 (302) T Consensus 75 -----------~~~~~~~~---~~~-----------------------------~~~~~~~--------------~~~l~ 97 (167) T TIGR02985 75 -----------EKYQEELS---EIE-----------------------------EDEIELR--------------LQSLE 97 (167) T ss_pred -----------HHHHHHHH---HHH-----------------------------HHHHHHH--------------HHHCC T ss_conf -----------99999999---865-----------------------------5678763--------------10036 Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH Q ss_conf 8705655666666677799999962199999999999827888889899999977899999999999999999999 Q gi|254780611|r 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302) Q Consensus 209 ~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302) T Consensus 98 ~~~~~~~----~~~El~~~i~~~~~~LPe~~R~iF~lsr~--eg~s~~EIA~~L~iS~~TVe~hi~~ALk~LR~~L 167 (167) T TIGR02985 98 ADPEEDI----YSKELEEIIEEAIEKLPEQCREIFILSRF--EGLSNKEIAEELGISVKTVEYHITKALKFLRKEL 167 (167) T ss_pred CCCHHHH----HHHHHHHHHHHHHHHCCHHHHHHHHHHHH--HCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHC T ss_conf 8974578----79999999999987568989999999886--1798678998848988899999999999998739 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of sigma factors are members of the sigma-70 family and are found primarily in the genus Bacteroides. This appears to have resulted from a lineage-specific expansion as Bacteroides thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037 (Tannerella forsythensis ATCC 43037), Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currently only two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >PRK12523 RNA polymerase sigma factor; Reviewed | Back alignment and domain information |
|---|
Probab=99.24 E-value=1.4e-09 Score=83.53 Aligned_cols=165 Identities=13% Similarity=0.113 Sum_probs=111.2 Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC Q ss_conf 28599999999943077875655557999988899999988899898621853456899975778999999853202460 Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123 (302) Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~ 123 (302) T Consensus 6 ~p~~~~~~~Ly~~~~~~L~~~~~r~~~~~e~AEDivQd~Flrl~~~-~~~~~~--~~~~a~Lf~iarNl~~D~~Rr~--- 79 (172) T PRK12523 6 SPHSELVGALYRDHRGWLLAWLRRNLACRQRAEDLSQDTFVRLLGR-PELPTP--REPRAFLAAVAKGLMFDHFRRA--- 79 (172) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHC-CCCCCC--CCHHHHHHHHHHHHHHHHHHHH--- T ss_conf 9739999999999999999999999498868999999999999827-765673--4599999999999999999989--- Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC Q ss_conf 01102300358999999997887866244788824677888618983211000000122343355202323453200000 Q gi|254780611|r 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203 (302) Q Consensus 124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~ 203 (302) T Consensus 80 -------------------~~~~~~----------~~~~~~-------------------------~~------------ 93 (172) T PRK12523 80 -------------------ALEQAY----------LAELAL-------------------------VP------------ 93 (172) T ss_pred -------------------HHHHHH----------HHHHHC-------------------------CC------------ T ss_conf -------------------988500----------888862-------------------------66------------ Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 12356870565566666667779999996219999999999982788888989999997789999999999999999999 Q gi|254780611|r 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302) Q Consensus 204 l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302) T Consensus 94 -~~~~~~~e~~~~~~----e~~~~l~~al~~Lp~~~R~v~~L~~~eG--ls~~EIA~~LgiS~~tVk~~l~rAl~~~~~~ 166 (172) T PRK12523 94 -EAEQPSPEEQHLIL----EDLKAIDRLLGKLSSKARAAFLYNRLDG--MGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172) T ss_pred -CCCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH T ss_conf -54689979999999----9999999998649999999999999939--9999999998939999999999999999998 Q ss_pred HHHH Q ss_conf 9974 Q gi|254780611|r 284 IQKQ 287 (302) Q Consensus 284 l~~~ 287 (302) T Consensus 167 l~~~ 170 (172) T PRK12523 167 LYGE 170 (172) T ss_pred HHCC T ss_conf 6079 |
|
| >PRK12511 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.23 E-value=4.4e-10 Score=86.94 Aligned_cols=158 Identities=9% Similarity=0.091 Sum_probs=102.8 Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCC Q ss_conf 99999943077875655557999988899999988899898621853456899975778999999853202460011023 Q gi|254780611|r 50 AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129 (302) Q Consensus 50 r~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~ 129 (302) T Consensus 7 ~~~~~~~-~P~L~rfa~~l~~d~~dAEDlvQetflk~~~~~~~~~~~--~~~~~WL~~IarN~~id~~Rr~~-------- 75 (182) T PRK12511 7 RFDVIDQ-LVPLRRYARSLTRDSAEAEDLVHDALVRALERRASFRSG--GNLRTWLMSILHNAFIDELRRRR-------- 75 (182) T ss_pred HHHHHHH-HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHCC-------- T ss_conf 9999998-999999999992999999999999999999998866886--64999999999999999998433-------- Q ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCC Q ss_conf 00358999999997887866244788824677888618983211000000122343355202323453200000123568 Q gi|254780611|r 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209 (302) Q Consensus 130 ~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~ 209 (302) T Consensus 76 --------------~----------~~~~~------------------------~~~~---~~~-~----------~~~~ 93 (182) T PRK12511 76 --------------A----------EARRA------------------------DELV---VEA-D----------ASAP 93 (182) T ss_pred --------------C----------CCCCC------------------------CCCC---CCC-C----------CCCC T ss_conf --------------4----------43433------------------------3101---235-5----------5689 Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHC Q ss_conf 70565566666667779999996219999999999982788888989999997789999999999999999999997401 Q gi|254780611|r 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289 (302) Q Consensus 210 ~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~~~ 289 (302) T Consensus 94 ~~~e~-------~~~~~~l~~al~~Lp~~~R~vl~L~~~eg--ls~~EIAe~Lgis~gTVKsrl~RAr~~LR~~le~~g~ 164 (182) T PRK12511 94 AGQEH-------AVRLAQIRDAFFDLPEEQRAALHLVAIEG--LSYQEAANVLGIPIGTLMSRIGRARAALRAFEEGTGP 164 (182) T ss_pred CCHHH-------HHHHHHHHHHHHCCCHHHHHHEEEEEECC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCC T ss_conf 63568-------99999999999869998950112410079--9999999998939999999999999999998631288 |
|
| >PRK12528 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.07 E-value=1.2e-08 Score=77.21 Aligned_cols=162 Identities=12% Similarity=0.080 Sum_probs=108.6 Q ss_pred HHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 82859999999994307787565555799998889999998889989862185345689997577899999985320246 Q gi|254780611|r 43 EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122 (302) Q Consensus 43 ~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~ 122 (302) T Consensus 5 ~~~~~~~~e~ly~~~~~~L~~~~~r~~g~~~~AEDivQd~Flrl~~~~~~~~~~---~~~ayL~~iA~n~~id~~R~~~- 80 (167) T PRK12528 5 DSAHAATVEGLYSAHHHWLTGWLRRRLGCPQSAADLAQDTFVKVLVARETAQII---EPRAFLTTIAKRVLCNHYRRQD- 80 (167) T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCC---CHHHHHHHHHHHHHHHHHHHHH- T ss_conf 655789999999999999999999993988579999999999999656544656---7999999999999999999999- Q ss_pred CHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHC Q ss_conf 00110230035899999999788786624478882467788861898321100000012234335520232345320000 Q gi|254780611|r 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202 (302) Q Consensus 123 ~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d 202 (302) T Consensus 81 ---------------------~~~~~~----------~~~~------------------------~-~~----------- 93 (167) T PRK12528 81 ---------------------LERAYL----------EALA------------------------Q-LP----------- 93 (167) T ss_pred ---------------------HHHHHH----------HHHH------------------------C-CC----------- T ss_conf ---------------------899899----------8876------------------------3-65----------- Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH Q ss_conf 01235687056556666666777999999621999999999998278888898999999778999999999999999999 Q gi|254780611|r 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302) Q Consensus 203 ~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302) T Consensus 94 --~~~~~~~e~~~~~~----e~~~~l~~~l~~LP~~~R~vf~L~r~~g--ls~~EIA~~LgiS~~tVk~~l~rA~~~c~~ 165 (167) T PRK12528 94 --ERVAPSEEERAIIL----ETLVELDRLLDGLPPLVKRAFLLAQVDG--LGYGEIATELGISLATVKRYLNKAAMRCYF 165 (167) T ss_pred --CCCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf --32469857899999----9999999998709999999999999829--899999999797999999999999999997 Q ss_pred H Q ss_conf 9 Q gi|254780611|r 283 S 283 (302) Q Consensus 283 ~ 283 (302) T Consensus 166 ~ 166 (167) T PRK12528 166 A 166 (167) T ss_pred H T ss_conf 6 |
|
| >PRK12525 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=99.02 E-value=4.1e-08 Score=73.74 Aligned_cols=164 Identities=15% Similarity=0.102 Sum_probs=97.4 Q ss_pred HCCHHHH-HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC Q ss_conf 2859999-999994307787565555799998889999998889989862185345689997577899999985320246 Q gi|254780611|r 44 HGDLSAA-HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122 (302) Q Consensus 44 ~gd~~Ar-~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~ 122 (302) T Consensus 4 ~~~~~~~l~~Lf~~~y~~L~~~~~r~lg~~~~AeDivQe~Flr~~~~~~~~~~---~~~~a~L~~iArnl~~d~------ 74 (168) T PRK12525 4 GSIKNTLIGQMFQQDYDWLCKKLSRQLGCPHSAEDIASETFLQVLALPDPASI---REPRALLTTIARRLMYEG------ 74 (168) T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCC---CCHHHHHHHHHHHHHHHH------ T ss_conf 31898999999999999999999999498857999999999999867774554---588999999999999999------ Q ss_pred CHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHC Q ss_conf 00110230035899999999788786624478882467788861898321100000012234335520232345320000 Q gi|254780611|r 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202 (302) Q Consensus 123 ~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d 202 (302) T Consensus 75 ----------------~Rr~~~~~~----------~~~------------------------~~~----~~~~------- 93 (168) T PRK12525 75 ----------------WRRQDLERA----------YLQ------------------------SLA----EAPE------- 93 (168) T ss_pred ----------------HHHHHHHHH----------HHH------------------------HHH----CCCC------- T ss_conf ----------------999999998----------888------------------------885----1666------- Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH Q ss_conf 01235687056556666666777999999621999999999998278888898999999778999999999999999999 Q gi|254780611|r 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302) Q Consensus 203 ~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302) T Consensus 94 ---~~~~~pe~~~~~~----e~~~~l~~al~~LP~~~R~vflL~~~eG--lsy~EIAe~LgIS~~tV~~~l~rAl~~c~~ 164 (168) T PRK12525 94 ---AVQPSPEEQWMVI----ETLLAIDRLLDGLSGKARAAFLMSQLEG--LTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168) T ss_pred ---CCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH T ss_conf ---5689867899999----9999999998639999999999999929--999999999897999999999999999999 Q ss_pred HHHH Q ss_conf 9997 Q gi|254780611|r 283 SIQK 286 (302) Q Consensus 283 ~l~~ 286 (302) T Consensus 165 ~lq~ 168 (168) T PRK12525 165 GFQE 168 (168) T ss_pred HHHC T ss_conf 8409 |
|
| >PRK12529 RNA polymerase sigma factor; Provisional | Back alignment and domain information |
|---|
Probab=98.94 E-value=1.7e-07 Score=69.59 Aligned_cols=165 Identities=13% Similarity=0.118 Sum_probs=102.0 Q ss_pred HCCHHHHHHHHHHHHHHH-HHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCC Q ss_conf 285999999999430778-75655557999-9888999999888998986218534568999757789999998532024 Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLV-VKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121 (302) Q Consensus 44 ~gd~~Ar~~Li~~nlrlV-~~iA~~y~~~g-~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~ 121 (302) T Consensus 9 ~~D~~a~~~Ly~~h~~~L~~~l~~Rl~~~~~~~AeDl~QDvFlrl~~~~~~~~~~~i~~p~a~L~rIA~Nl~id------ 82 (178) T PRK12529 9 SADRDKVATLYRENHAWLRNWLAYRLRSWGRGVADDLAHDIFLRILASRDGGQREAIRQPRAYLARIANCVLVS------ 82 (178) T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHH------ T ss_conf 44799999999999999999999982899835469999999999997344456432334899999999999999------ Q ss_pred CCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHH Q ss_conf 60011023003589999999978878662447888246778886189832110000001223433552023234532000 Q gi|254780611|r 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201 (302) Q Consensus 122 ~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~ 201 (302) T Consensus 83 ----------------~~Rr~~~~~~~----------le~~------------------------~-------------- 98 (178) T PRK12529 83 ----------------WRRRQSLELAW----------LEAL------------------------A-------------- 98 (178) T ss_pred ----------------HHHHHHHHHHH----------HHHH------------------------H-------------- T ss_conf ----------------99988889878----------9988------------------------6-------------- Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH Q ss_conf 00123568705655666666677799999962199999999999827888889899999977899999999999999999 Q gi|254780611|r 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281 (302) Q Consensus 202 d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR 281 (302) T Consensus 99 ~~~~~~~pspE~~~~~~----e~l~~l~~al~~Lp~r~R~vF~L~r~eG--ls~~EIAe~LgiS~~tV~~~l~rAl~~C~ 172 (178) T PRK12529 99 TLPEPLHPSPEQQSVIL----ETLHEIDALLDTLRPRVKQAFLMATLDG--MKQKDIAQALDIALPTVKKYIHQAYVTCL 172 (178) T ss_pred CCCCCCCCCHHHHHHHH----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHH T ss_conf 47866689989999999----9999999998569978889987998829--99999999989599999999999999999 Q ss_pred HHH Q ss_conf 999 Q gi|254780611|r 282 ESI 284 (302) Q Consensus 282 ~~l 284 (302) T Consensus 173 ~~~ 175 (178) T PRK12529 173 SLM 175 (178) T ss_pred HHC T ss_conf 867 |
|
| >PRK09636 RNA polymerase sigma factor SigJ; Provisional | Back alignment and domain information |
|---|
Probab=98.78 E-value=6.1e-07 Score=65.90 Aligned_cols=153 Identities=18% Similarity=0.182 Sum_probs=92.0 Q ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHH Q ss_conf 99430778756555579999888999999888998986218534568999757789999998532024600110230035 Q gi|254780611|r 54 VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133 (302) Q Consensus 54 i~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r 133 (302) T Consensus 6 fe~~R~~L~~~AyRmlGs~~DAEDvvQEt~lr~~~~----~~~~~~~~~aWL~rI~~n~~ld~----------------- 64 (289) T PRK09636 6 FEPLRPHLLSVAYRMLGSVADAEDIVQEAWLRWNNA----DRAEIRDPRAFLTRVVTRLCLDR----------------- 64 (289) T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCC----CCCCCCCHHHHHHHHHHHHHHHH----------------- T ss_conf 998799999999998099978999999999998506----84223478999999999999999----------------- Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHH Q ss_conf 89999999978878662447888246778886189832110000001223433552023234532000001235687056 Q gi|254780611|r 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213 (302) Q Consensus 134 ~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~ 213 (302) T Consensus 65 -----LR~ar~rre~~~g~--------------------------------wlpep--------------~~~~~~~p~~ 93 (289) T PRK09636 65 -----LRSARHRRETYVGP--------------------------------WLPEP--------------VVEDSDDPLE 93 (289) T ss_pred -----HHHHHCCCCCCCCC--------------------------------CCCCC--------------CCCCCCCCHH T ss_conf -----98540165546787--------------------------------78876--------------6788899356 Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 5566666667779999996219999999999982788888989999997789999999999999999999 Q gi|254780611|r 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302) Q Consensus 214 ~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302) T Consensus 94 ~~~~---~e~~~~al~~~L~~L~p~qRav~vLrdv~g--~s~~EIA~iLg~s~~avR~~l~RAR~~l~~~ 158 (289) T PRK09636 94 AVVA---AEDLSLALMLALERLSPLERAAFLLHDVFG--VPFDEIASTLGRSEAACRQLASRARKHVRAA 158 (289) T ss_pred HHHH---HHHHHHHHHHHHHHCCHHHHHHHHHHHHHC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHCC T ss_conf 7887---788999999999739998962540498609--9999999998179999999999999987344 |
|
| >TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family; InterPro: IPR014331 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=98.69 E-value=1.1e-06 Score=64.11 Aligned_cols=156 Identities=17% Similarity=0.238 Sum_probs=93.2 Q ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCH Q ss_conf 99994307787565555799998889999998889989862185345689997577899999985320246001102300 Q gi|254780611|r 52 RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131 (302) Q Consensus 52 ~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~ 131 (302) T Consensus 5 ~ll~~h~~~~rafv~~L~~~~~dadDv~QEt~v~~~~k~~~f~~~~~--F~aWa~~iArn~vl~~~r~~~R~-------- 74 (163) T TIGR02989 5 RLLTRHQRSLRAFVRSLVPDRDDADDVLQETFVTAWRKFDEFDPGTD--FGAWARGIARNKVLNHRRKLGRD-------- 74 (163) T ss_pred HHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHHHHHHHHHHHHHCCCC-------- T ss_conf 99999989999999997179565888999999999860775178989--76789999999999998730244-------- Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCC Q ss_conf 35899999999788786624478882467788861898321100000012234335520232345320000012356870 Q gi|254780611|r 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211 (302) Q Consensus 132 ~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~ 211 (302) T Consensus 75 -~----------~~l~~f~D~-----l~e~lA~~~--------------------~~~---------------------- 96 (163) T TIGR02989 75 -R----------ERLVVFDDE-----LLEALAAEL--------------------EEA---------------------- 96 (163) T ss_pred -C----------HHHHHHHHH-----HHHHHHHHH--------------------HHH---------------------- T ss_conf -1----------277762599-----999999987--------------------555---------------------- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH Q ss_conf 56556666666777999999621999999999998278888898999999778999999999999999999999 Q gi|254780611|r 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285 (302) Q Consensus 212 ~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~ 285 (302) T Consensus 97 ----~~~~~~~~~~~AL~~C~~~L~~~~R~Ll~~rY~~G--~~~~~~A~~~g~~~~A~~~----~L~R~R~~L~ 160 (163) T TIGR02989 97 ----EEADRSEDELQALEGCLEKLPERQRELLQLRYQRG--VSLEALAEQLGRTVNAVYK----ALSRLRVRLR 160 (163) T ss_pred ----HCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHCCC--CCHHHHHHHHCCHHHHHHH----HHHHHHHHHH T ss_conf ----22788178999999878635978899999982279--7878999884713899999----9999999975 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry of sigma factors are members of the sigma-70 family and are abundantly found in the species Rhodopirellula baltica, and Verrucomicrobium spinosum and to a lesser extent in Gemmata obscuriglobus.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent. |
| >PRK09635 sigI RNA polymerase sigma factor SigI; Provisional | Back alignment and domain information |
|---|
Probab=98.50 E-value=2e-05 Score=55.85 Aligned_cols=158 Identities=15% Similarity=0.105 Sum_probs=92.1 Q ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCC Q ss_conf 99999430778756555579999888999999888998986218534568999757789999998532024600110230 Q gi|254780611|r 51 HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130 (302) Q Consensus 51 ~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~ 130 (302) T Consensus 8 ~~~fe~hR~~L~~~ayRmlGs~~dAED~VQEa~lr~~~~~~~~---~-~~~~awL~ri~tn~c----------------- 66 (290) T PRK09635 8 SAAWRAHRAYLVDLAFRMVGDIGVAEDMVQEAFSRLLRAPVGD---I-DDERGWLIVVTSRLC----------------- 66 (290) T ss_pred HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCC---C-CCHHHHHHHHHHHHH----------------- T ss_conf 9999998999999999980898789999999999997477312---3-578889999999999----------------- Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCC Q ss_conf 03589999999978878662447888246778886189832110000001223433552023234532000001235687 Q gi|254780611|r 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210 (302) Q Consensus 131 ~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~ 210 (302) T Consensus 67 -----ld~LR~~r~rre~--------~~~------~~----------------~~~-----~~--------~~-~~~~~d 97 (290) T PRK09635 67 -----LDHIKSASTRRER--------PQD------IA----------------AWH-----DG--------DA-SVSSVD 97 (290) T ss_pred -----HHHHHHHHHCCCC--------CCC------CC----------------CCC-----CC--------CC-CCCCCC T ss_conf -----9998766522678--------766------67----------------778-----76--------77-788898 Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH Q ss_conf 0565566666667779999996219999999999982788888989999997789999999999999999999 Q gi|254780611|r 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283 (302) Q Consensus 211 ~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~ 283 (302) T Consensus 98 p~~~~---~~~~~v~~All~~Le~L~P~eRaa~vLrdvfg--~~~~EIA~~Lg~s~~a~Rqll~RAR~~l~~~ 165 (290) T PRK09635 98 PADRV---TLDDEVRLALLIMLERLGPAERVVFVLHEIFG--LPYQQIATTIGSQASTCRQLAHRARRKINES 165 (290) T ss_pred HHHHH---HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHCC T ss_conf 28898---87778999999998629986854552698608--9889999996899899999999999987323 |
|
| >TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family; InterPro: IPR014325 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription | Back alignment and domain information |
|---|
Probab=98.41 E-value=1.7e-07 Score=69.57 Aligned_cols=152 Identities=14% Similarity=0.252 Sum_probs=94.6 Q ss_pred HHHHHHHHHHHHHHHHC-CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCH Q ss_conf 99943077875655557-99998889999998889989862185345689997577899999985320246001102300 Q gi|254780611|r 53 LVTSHLRLVVKIAMGYR-GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131 (302) Q Consensus 53 Li~~nlrlV~~iA~~y~-~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~ 131 (302) T Consensus 11 f~~~r~~~L~r~A~lLt~GD~~~AEDLvQ~Al~~~y~rW~Ri-~~~~~-~~a----YvR~vl~n~~~s~w---------- 74 (165) T TIGR02983 11 FVAARYPRLLRTAYLLTAGDPHEAEDLVQEALVRTYVRWDRI-RDADA-PDA----YVRRVLVNLAISRW---------- 74 (165) T ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC-CCCCC-CHH----HHHHHHHHHHHHHH---------- T ss_conf 999999999999999827887569999999999998862215-88254-057----89999999999999---------- Q ss_pred HHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCC Q ss_conf 35899999999788786624478882467788861898321100000012234335520232345320000012356870 Q gi|254780611|r 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211 (302) Q Consensus 132 ~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~ 211 (302) T Consensus 75 --------RrR~~~~e~~~~~~Pd~---------------------------------------------------~ga~ 95 (165) T TIGR02983 75 --------RRRRVRLELPTEELPDA---------------------------------------------------AGAP 95 (165) T ss_pred --------HHHHHHHHCCCCCCCCC---------------------------------------------------CCCC T ss_conf --------98876442146686488---------------------------------------------------8898 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH Q ss_conf 565566666667779999996219999999999982788888989999997789999999999999999999997 Q gi|254780611|r 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286 (302) Q Consensus 212 ~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~ 286 (302) T Consensus 96 d~-~----~~~~~r~~l~~AL~~LP~rQR~vvVLRY~eD--lSe~~~A~~LG~SvGTVKS~~sRal~~LR~~~~~ 163 (165) T TIGR02983 96 DP-A----ADVALRAALARALRRLPARQRAVVVLRYYED--LSEAEVAEVLGISVGTVKSRLSRALARLRELLEE 163 (165) T ss_pred CC-C----CCHHHHHHHHHHHHHCCHHCCEEEEEECCCC--CCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCC T ss_conf 75-3----1122699999999735641236723204578--9868999881999322899899999998873257 |
Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This group of similar sigma-70 factors includes the s |