BLASTP 2.2.26 [Sep-21-2011]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 014241
(428 letters)
Database: swissprot
539,616 sequences; 191,569,459 total letters
Searching..................................................done
>sp|Q9LD95|SIGF_ARATH RNA polymerase sigma factor sigF, chloroplastic OS=Arabidopsis
thaliana GN=SIGF PE=1 SV=1
Length = 547
Score = 360 bits (923), Expect = 2e-98, Method: Compositional matrix adjust.
Identities = 213/421 (50%), Positives = 274/421 (65%), Gaps = 39/421 (9%)
Query: 1 MEAGRNLLSSPPSFPSRTRVKHSLSSSASSSSSSSVLMHNEQSAPAVASVPTSSVARHFP 60
MEA RNL+SS PSF ++T +K S+ SS SS V++H++ + P V S +S++RHFP
Sbjct: 1 MEATRNLVSSSPSFQTKTHLK-----SSYSSPSSVVMLHDQTTTPVVNSRHLNSLSRHFP 55
Query: 61 TSVLLQEQRDEYRPLLHMFKEDKTSQATSDSRNIETEAFFVEEKNSGDLDQLV-----QD 115
SVL QE R+E RPL H ++D+TSQ T + R D+LV +
Sbjct: 56 ASVLSQEPREESRPLSHALRDDRTSQLTLERRQ---------------FDELVSSREDEK 100
Query: 116 LEHQFLHWPDLWNL--SPPMKRGEDPSVSLTMQSLSNDTEESVDAEPFDAVALARKALSA 173
E Q LH LWNL SP + P+V + DAE D VALA+KALSA
Sbjct: 101 FEQQLLHSTGLWNLLISPLTSETKLPAVVSPL----------ADAELCDVVALAQKALSA 150
Query: 174 SKEAASLAENPKLNGAE-FTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTN 232
SK+AA L ++ + N ++ D TSS E+ R LERR+K R+ K +
Sbjct: 151 SKQAALLVDDTEANPSDNIKDSLSTSSSMSLPEKGNIVRSKRQLERRAKNRRAPKSNDVD 210
Query: 233 HETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEK 292
E Y +K S KKK +G D +D L+LFLWGPET++LLTA EE ELI+ IQ L++LEK K
Sbjct: 211 DEGYVPQKTSAKKKYKQGADNDDALQLFLWGPETKQLLTAKEEAELISHIQHLLKLEKVK 270
Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRG 352
+KL+SQ G EPT+ EWA+A+G+S LKS++H G SSREKLI ANLRLVVH+AKQYQ RG
Sbjct: 271 TKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRSSREKLITANLRLVVHIAKQYQNRG 330
Query: 353 ISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTFN 411
++ DLLQ GSMGLMKSVEKFKPQ+GCRFA+YAYWW+RQ+IRK+IFQ+SRTIRLP +
Sbjct: 331 LNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWWIRQSIRKSIFQNSRTIRLPENVYM 390
Query: 412 L 412
L
Sbjct: 391 L 391
>sp|O22056|SIGB_ARATH RNA polymerase sigma factor sigB OS=Arabidopsis thaliana GN=SIGB
PE=2 SV=2
Length = 572
Score = 158 bits (400), Expect = 7e-38, Method: Compositional matrix adjust.
Identities = 77/195 (39%), Positives = 124/195 (63%), Gaps = 2/195 (1%)
Query: 214 RFLERRSKKRKVSKPQVTNHETYNSRKASVKKKL-SEGFDRNDPLRLFLWGPETRKLLTA 272
R ER++++ K + + + + + KK+L ++ D NDPLR + KLLT
Sbjct: 216 RQTERKARRAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTV 275
Query: 273 DEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREK 332
EE EL A IQDL++LE+ +++L + GR+PT +WA A G+ + L+ +H G ++K
Sbjct: 276 REEHELSAGIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDK 335
Query: 333 LINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQT 391
+I +N+RLV+ +AK YQG G++L DL+Q G GL++ EKF G +F++YA+WW++Q
Sbjct: 336 MIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQA 395
Query: 392 IRKAIFQHSRTIRLP 406
+RK++ SR IRLP
Sbjct: 396 VRKSLSDQSRMIRLP 410
>sp|P26683|RPOD_NOSS1 RNA polymerase sigma factor RpoD OS=Nostoc sp. (strain PCC 7120 /
UTEX 2576) GN=rpoD PE=3 SV=1
Length = 390
Score = 148 bits (373), Expect = 8e-35, Method: Compositional matrix adjust.
Identities = 81/206 (39%), Positives = 124/206 (60%), Gaps = 14/206 (6%)
Query: 206 EVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPE 265
++ +F +P+ E +K K +K + R S KK +E D +RL+L
Sbjct: 44 DIDEFLEPQTDEDDAKSGKAAKSR--------RRTQSKKKHYTE-----DSIRLYLQEIG 90
Query: 266 TRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHS 325
+LL ADEE EL +I DL+ LE+ + +L + R+P EWA+A+ L + LH
Sbjct: 91 RIRLLRADEEIELARKIADLLELERVRERLSEKLERDPRDSEWAEAVQLPLPAFRYRLHI 150
Query: 326 GNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYA 384
G +++K++ +NLRLVV +AK+Y RG+S DL+Q GS+GL+++ EKF + G +F++YA
Sbjct: 151 GRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYA 210
Query: 385 YWWVRQTIRKAIFQHSRTIRLPVMTF 410
WW+RQ I +AI SRTIRLPV +
Sbjct: 211 TWWIRQAITRAIADQSRTIRLPVHLY 236
>sp|Q31ME3|RPOD2_SYNE7 RNA polymerase sigma factor rpoD2 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD2 PE=1 SV=1
Length = 320
Score = 145 bits (365), Expect = 8e-34, Method: Compositional matrix adjust.
Identities = 70/154 (45%), Positives = 102/154 (66%), Gaps = 1/154 (0%)
Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
D +R +L +LLTA+EE Q+Q L+ L +++L+ + G EP+ EWA A+ L
Sbjct: 11 DLVRAYLQEIGRVRLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDL 70
Query: 315 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFK 373
+ DL ++ G ++ K+I ANLRLVV +AK+YQ R + DL+Q G++GL + VEKF
Sbjct: 71 NLEDLDRQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFD 130
Query: 374 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
P G +F++YAYWW+RQ I +AI Q SRTIRLP+
Sbjct: 131 PSKGYKFSTYAYWWIRQAITRAIAQQSRTIRLPI 164
>sp|Q31QG5|RPOD3_SYNE7 RNA polymerase sigma factor rpoD3 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD3 PE=3 SV=1
Length = 320
Score = 141 bits (355), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 74/165 (44%), Positives = 111/165 (67%), Gaps = 3/165 (1%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFG-REPTLIEWAKAI 312
+D +R +L LLT +EE L ++Q ++L++ + LQS+ G R+P+ +EWA A
Sbjct: 9 SDLVRTYLREIGRVPLLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAAA 68
Query: 313 GLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEK 371
GLS +L+ + H G ++ K+I ANLRLVV VAK+Y R + L DL+Q G++G+ + VEK
Sbjct: 69 GLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRGVEK 128
Query: 372 FKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV-MTFNLSPI 415
F P G RF++YAYWW+RQ I +AI + +RTIRLP+ +T L+ I
Sbjct: 129 FDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEKLNKI 173
>sp|P38023|RPOD1_SYNE7 RNA polymerase sigma factor rpoD1 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD1 PE=3 SV=2
Length = 399
Score = 138 bits (348), Expect = 7e-32, Method: Compositional matrix adjust.
Identities = 70/157 (44%), Positives = 102/157 (64%), Gaps = 1/157 (0%)
Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
D +RL+L +LL ADEE EL QI DL+ LE+ + +L Q R P+ EWA A+
Sbjct: 89 DSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVDS 148
Query: 315 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFK 373
+ + L G +++K++ +NLRLVV +AK+Y RG+S DL+Q GS+GL+++ EKF
Sbjct: 149 PLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFD 208
Query: 374 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTF 410
+ G +F++YA WW+RQ I +AI SRTIRLPV +
Sbjct: 209 HEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLY 245
>sp|Q03065|RPSB_NOSS1 RNA polymerase sigma-B factor OS=Nostoc sp. (strain PCC 7120 / UTEX
2576) GN=sigB PE=3 SV=1
Length = 332
Score = 130 bits (328), Expect = 1e-29, Method: Compositional matrix adjust.
Identities = 66/154 (42%), Positives = 97/154 (62%), Gaps = 1/154 (0%)
Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
D + ++L LL+ ++E Q+Q ++ + K +L + REPTL EWA + L
Sbjct: 23 DAVSIYLHKIGRVPLLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEWADKMQL 82
Query: 315 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFK 373
L +L G +++K+I ANLRLVV +AK+YQ R + DL+Q G++GL + VEKF
Sbjct: 83 KEDVLLQQLSQGQIAKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQEGALGLERGVEKFD 142
Query: 374 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
P G +F++YAYWW+RQ I +AI Q SRTIRLP+
Sbjct: 143 PTLGYKFSTYAYWWIRQGITRAIAQQSRTIRLPI 176
>sp|Q03066|RPSC_NOSS1 RNA polymerase sigma-C factor OS=Nostoc sp. (strain PCC 7120 / UTEX
2576) GN=sigC PE=3 SV=2
Length = 416
Score = 122 bits (305), Expect = 7e-27, Method: Compositional matrix adjust.
Identities = 77/207 (37%), Positives = 106/207 (51%), Gaps = 45/207 (21%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLE---------------------KEK 292
D +RL+L +LL DEE ++Q ++L + +
Sbjct: 59 TDLVRLYLQEIGRVRLLGRDEEVSEAQKVQRYLKLRIVLANAVKQGDEVATPYLHLIEVQ 118
Query: 293 SKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN----------------------SSR 330
+L S+ G P+L WA G++ DLK L G S+
Sbjct: 119 ERLASELGHRPSLERWAATAGINLCDLKPILSEGKRRWAEIAKMTVEELEKMQSQGLQSK 178
Query: 331 EKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWWVR 389
E +I ANLRLVV VAK+YQ RG+ L DL+Q G++GL ++VEKF P G RF++YAYWW+R
Sbjct: 179 EHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIR 238
Query: 390 QTIRKAIFQHSRTIRLPV-MTFNLSPI 415
Q I +AI SRTIRLPV +T L+ I
Sbjct: 239 QGITRAIATSSRTIRLPVHITEKLNKI 265
>sp|Q59996|RPSC_SYNY3 Probable RNA polymerase sigma-C factor OS=Synechocystis sp. (strain
PCC 6803 / Kazusa) GN=sigC PE=3 SV=1
Length = 404
Score = 120 bits (301), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 75/206 (36%), Positives = 105/206 (50%), Gaps = 44/206 (21%)
Query: 254 NDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSK------------------- 294
D +RL+L LL DEE + Q+Q +RL + +++
Sbjct: 48 TDLVRLYLQDIGRIPLLKRDEEVHIAQQVQSYLRLVEIQNRAAESDAAIDQYQTAIAVHD 107
Query: 295 -LQSQFGREPTLIEWAKAIGLSCRDLKSELHSGN----------------------SSRE 331
L Q G P+ WAK +G + LK L SG +++
Sbjct: 108 QLLVQLGHRPSYERWAKILGQTVATLKQTLKSGKKRWAELAGLTVEELENIEKQGITAKA 167
Query: 332 KLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQ 390
+I ANLRLVV VAK+YQ RG+ L DL+Q G++GL ++VEKF P G RF++Y+YWW+RQ
Sbjct: 168 HMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYSYWWIRQ 227
Query: 391 TIRKAIFQHSRTIRLPV-MTFNLSPI 415
I +AI SR IRLPV +T L+ I
Sbjct: 228 GITRAIATQSRMIRLPVHITEKLNKI 253
>sp|P74565|RPOD_SYNY3 RNA polymerase sigma factor RpoD OS=Synechocystis sp. (strain PCC
6803 / Kazusa) GN=rpoD PE=3 SV=1
Length = 425
Score = 119 bits (297), Expect = 6e-26, Method: Compositional matrix adjust.
Identities = 75/218 (34%), Positives = 114/218 (52%), Gaps = 51/218 (23%)
Query: 239 RKASVKKK-LSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQS 297
RK +VKKK +E D +R++L +LL A+EE EL QI DL+ LE + L
Sbjct: 59 RKDAVKKKPYTE-----DSIRIYLQEIGRIRLLRAEEEIELARQIADLLELELIRDNLTL 113
Query: 298 QFGREPTLIEWAKAI----------------GLSCRDLKSELHSGNS------------- 328
Q R+P+ +EW K + +D+ S L + ++
Sbjct: 114 QLERQPSELEWGKQVWKLETAKQRLVGDKKKEPKKKDIDSYLANPDNELSLENEWSQQPN 173
Query: 329 ---------------SREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKF 372
+++K++ +NLRLVV +AK+Y RG+S DL+Q GS+GL+++ EKF
Sbjct: 174 KNFAAFRRRLFLDRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKF 233
Query: 373 KPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPVMTF 410
+ G +F++YA WW+RQ I +AI SRTIRLPV +
Sbjct: 234 DHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLY 271
>sp|P52322|RPOD_MICAE RNA polymerase sigma factor rpoD1 OS=Microcystis aeruginosa
GN=rpoD1 PE=3 SV=1
Length = 416
Score = 115 bits (289), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 69/196 (35%), Positives = 104/196 (53%), Gaps = 40/196 (20%)
Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEK------------------------ 290
D +R++L +LL A+EE EL +I DL++LE+
Sbjct: 67 DSIRIYLQEIGRIRLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIE 126
Query: 291 ----EKSK-------LQSQFGRE----PTLIEWAKAIGLSCRDLKSELHSGNSSREKLIN 335
EKS+ +++ G+ P L EW K L+ G ++EK++
Sbjct: 127 KIIVEKSEKEPKLSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQ 186
Query: 336 ANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRK 394
+NLRLVV +AK+Y RG+S DL+Q GS+GL+++ EKF + G +F++YA WW+RQ I +
Sbjct: 187 SNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITR 246
Query: 395 AIFQHSRTIRLPVMTF 410
AI SRTIRLPV +
Sbjct: 247 AIADQSRTIRLPVHLY 262
>sp|Q31QR8|RPOD4_SYNE7 RNA polymerase sigma factor rpoD4 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD4 PE=3 SV=1
Length = 311
Score = 109 bits (272), Expect = 4e-23, Method: Compositional matrix adjust.
Identities = 60/140 (42%), Positives = 90/140 (64%), Gaps = 20/140 (14%)
Query: 269 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 328
LLTA+EE EL ++Q ++ L+E A S + ++ L +G
Sbjct: 33 LLTAEEEVELSRKVQLMM-----------------ALLENPDAESNS--ENQAVLQAGQR 73
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWW 387
++ K++ ANLRLVV VAK+YQ +G+ L DL+Q GS+GL ++VEKF P G +F++YAYWW
Sbjct: 74 AKTKMLKANLRLVVSVAKKYQNQGLELLDLIQEGSLGLERAVEKFDPALGYKFSTYAYWW 133
Query: 388 VRQTIRKAIFQHSRTIRLPV 407
+RQ++ +AI H+RTIRLP+
Sbjct: 134 IRQSMTRAIDNHARTIRLPI 153
>sp|P35540|RPOS_SHIFL RNA polymerase sigma factor RpoS OS=Shigella flexneri GN=rpoS PE=3
SV=3
Length = 330
Score = 108 bits (269), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 45/96 (46%), Positives = 70/96 (72%), Gaps = 1/96 (1%)
Query: 323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFA 381
L +SR ++I +NLRLVV +A++Y RG++L DL++ G++GL+++VEKF P+ G RF+
Sbjct: 84 LRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFS 143
Query: 382 SYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYI 417
+YA WW+RQTI +AI +RTIRLP+ +Y+
Sbjct: 144 TYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179
>sp|P0A2E5|RPOS_SALTY RNA polymerase sigma factor RpoS OS=Salmonella typhimurium (strain
LT2 / SGSC1412 / ATCC 700720) GN=rpoS PE=3 SV=1
Length = 330
Score = 108 bits (269), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 45/96 (46%), Positives = 70/96 (72%), Gaps = 1/96 (1%)
Query: 323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFA 381
L +SR ++I +NLRLVV +A++Y RG++L DL++ G++GL+++VEKF P+ G RF+
Sbjct: 84 LRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFS 143
Query: 382 SYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYI 417
+YA WW+RQTI +AI +RTIRLP+ +Y+
Sbjct: 144 TYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179
>sp|P0A2E6|RPOS_SALTI RNA polymerase sigma factor RpoS OS=Salmonella typhi GN=rpoS PE=3
SV=1
Length = 330
Score = 108 bits (269), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 45/96 (46%), Positives = 70/96 (72%), Gaps = 1/96 (1%)
Query: 323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFA 381
L +SR ++I +NLRLVV +A++Y RG++L DL++ G++GL+++VEKF P+ G RF+
Sbjct: 84 LRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFS 143
Query: 382 SYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYI 417
+YA WW+RQTI +AI +RTIRLP+ +Y+
Sbjct: 144 TYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179
>sp|P0A2E7|RPOS_SALDU RNA polymerase sigma factor RpoS OS=Salmonella dublin GN=rpoS PE=3
SV=1
Length = 330
Score = 108 bits (269), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 45/96 (46%), Positives = 70/96 (72%), Gaps = 1/96 (1%)
Query: 323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFA 381
L +SR ++I +NLRLVV +A++Y RG++L DL++ G++GL+++VEKF P+ G RF+
Sbjct: 84 LRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFS 143
Query: 382 SYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYI 417
+YA WW+RQTI +AI +RTIRLP+ +Y+
Sbjct: 144 TYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179
>sp|P13445|RPOS_ECOLI RNA polymerase sigma factor RpoS OS=Escherichia coli (strain K12)
GN=rpoS PE=3 SV=3
Length = 330
Score = 108 bits (269), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 45/96 (46%), Positives = 70/96 (72%), Gaps = 1/96 (1%)
Query: 323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFA 381
L +SR ++I +NLRLVV +A++Y RG++L DL++ G++GL+++VEKF P+ G RF+
Sbjct: 84 LRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFS 143
Query: 382 SYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYI 417
+YA WW+RQTI +AI +RTIRLP+ +Y+
Sbjct: 144 TYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179
>sp|P33118|RPSB_CORDI RNA polymerase sigma factor SigB OS=Corynebacterium diphtheriae
(strain ATCC 700971 / NCTC 13129 / Biotype gravis)
GN=sigB PE=3 SV=2
Length = 329
Score = 107 bits (268), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 61/154 (39%), Positives = 92/154 (59%), Gaps = 13/154 (8%)
Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
D +R++L G LL A++E EL I+ L +++ E + +A+
Sbjct: 30 DLVRVYLNGIGKTALLNAEDEVELAQTIE---------VGLYAEYLLENSQEPLTRAM-- 78
Query: 315 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFK 373
RDLK + G +R L+ ANLRLVV +AK+Y GRG+ L DL+Q G++GL++++EKF
Sbjct: 79 -KRDLKVLVKEGRKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFD 137
Query: 374 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
G +F++YA WW+RQ I + + SRTIRLPV
Sbjct: 138 YSKGFKFSTYATWWIRQAITRGMADQSRTIRLPV 171
>sp|P47765|RPOS_YEREN RNA polymerase sigma factor RpoS OS=Yersinia enterocolitica GN=rpoS
PE=3 SV=1
Length = 331
Score = 107 bits (268), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 44/90 (48%), Positives = 68/90 (75%), Gaps = 1/90 (1%)
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWW 387
SR ++I +NLRLVV +A++Y RG++L DL++ G++GL+++VEKF P+ G RF++YA WW
Sbjct: 91 SRRRMIESNLRLVVKIARRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWW 150
Query: 388 VRQTIRKAIFQHSRTIRLPVMTFNLSPIYI 417
+RQTI +AI +RTIRLP+ +Y+
Sbjct: 151 IRQTIERAIMNQTRTIRLPIHIVKELNVYL 180
>sp|O51804|RPOS_VIBCH RNA polymerase sigma factor RpoS OS=Vibrio cholerae serotype O1
(strain ATCC 39315 / El Tor Inaba N16961) GN=rpoS PE=3
SV=1
Length = 335
Score = 107 bits (267), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 43/96 (44%), Positives = 71/96 (73%), Gaps = 1/96 (1%)
Query: 323 LHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFA 381
L ++R+++I +NLRLVV ++++Y RG++L DL++ G++GL+++VEKF P+ G RF+
Sbjct: 85 LRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFS 144
Query: 382 SYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYI 417
+YA WW+RQTI +A+ +RTIRLP+ IY+
Sbjct: 145 TYATWWIRQTIERALMNQTRTIRLPIHVVKELNIYL 180
>sp|P45684|RPOS_PSEAE RNA polymerase sigma factor RpoS OS=Pseudomonas aeruginosa (strain
ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) GN=rpoS
PE=3 SV=1
Length = 334
Score = 107 bits (266), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 44/91 (48%), Positives = 69/91 (75%), Gaps = 1/91 (1%)
Query: 328 SSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYW 386
+ R+++I +NLRLVV +A++Y RG+SL DL++ G++GL+++VEKF P+ G RF++YA W
Sbjct: 94 AGRKRMIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATW 153
Query: 387 WVRQTIRKAIFQHSRTIRLPVMTFNLSPIYI 417
W+RQTI +AI +RTIRLP+ +Y+
Sbjct: 154 WIRQTIERAIMNQTRTIRLPIHVVKELNVYL 184
>sp|P52329|RPOD_ENTFA RNA polymerase sigma factor RpoD OS=Enterococcus faecalis (strain
ATCC 700802 / V583) GN=rpoD PE=3 SV=2
Length = 368
Score = 107 bits (266), Expect = 2e-22, Method: Compositional matrix adjust.
Identities = 59/159 (37%), Positives = 84/159 (52%), Gaps = 41/159 (25%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L +LLTA EE EL +I++
Sbjct: 92 GVKINDPVRMYLKEIGRVQLLTAAEEVELALKIEE------------------------- 126
Query: 310 KAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKS 368
++++L ANLRLVV +AK+Y GRG+ DL+Q G+MGLMK+
Sbjct: 127 ---------------GDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKA 171
Query: 369 VEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
VEKF + G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 172 VEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|O24629|SIGA_ARATH RNA polymerase sigma factor sigA OS=Arabidopsis thaliana GN=SIGA
PE=1 SV=1
Length = 502
Score = 106 bits (265), Expect = 3e-22, Method: Compositional matrix adjust.
Identities = 53/151 (35%), Positives = 96/151 (63%), Gaps = 1/151 (0%)
Query: 257 LRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSC 316
+R ++ G + +L+ E L +I+ +RL+ KS+L+ + G EP+ + A ++ +S
Sbjct: 187 VRGYVKGVISEDVLSHVEVVRLSKKIKSGLRLDDHKSRLKDRLGCEPSDEQLAVSLKISR 246
Query: 317 RDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQGSM-GLMKSVEKFKPQ 375
+L++ L + +REKL +N+RLV+ +A++Y G + DL+QG + GL++ +EKF
Sbjct: 247 AELQAWLMECHLAREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSS 306
Query: 376 AGCRFASYAYWWVRQTIRKAIFQHSRTIRLP 406
G R ++Y YWW+RQ + +A+ +SRT+RLP
Sbjct: 307 KGFRISTYVYWWIRQGVSRALVDNSRTLRLP 337
>sp|Q9KI19|RPOS_COXBU RNA polymerase sigma factor RpoS OS=Coxiella burnetii (strain RSA
493 / Nine Mile phase I) GN=rpoS PE=1 SV=1
Length = 352
Score = 105 bits (261), Expect = 8e-22, Method: Compositional matrix adjust.
Identities = 45/97 (46%), Positives = 69/97 (71%), Gaps = 2/97 (2%)
Query: 323 LHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRF 380
+H G+ +R+++I ANLRLVV +A+ Y RG+ DL++ G++GL+ +VEKF P+ G RF
Sbjct: 106 VHKGDPKARKQMIEANLRLVVKIARHYVNRGLPFLDLIEEGNLGLLTAVEKFDPERGFRF 165
Query: 381 ASYAYWWVRQTIRKAIFQHSRTIRLPVMTFNLSPIYI 417
++YA WW+RQTI +AI SRT+RLP+ +Y+
Sbjct: 166 STYATWWIRQTIERAIMNQSRTVRLPIHVIKELNVYL 202
>sp|P77994|RPOD_THEMA RNA polymerase sigma factor RpoD OS=Thermotoga maritima (strain
ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) GN=rpoD PE=1
SV=3
Length = 399
Score = 104 bits (259), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 48/93 (51%), Positives = 69/93 (74%), Gaps = 2/93 (2%)
Query: 317 RDLKSELHSGNS-SREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKP 374
R+L G+ ++EKLI +NLRLVV +AK+Y GRG+S DL+Q G++GL+K+VEKF
Sbjct: 142 RELARRAQMGDKKAKEKLITSNLRLVVSIAKRYMGRGLSFQDLIQEGNIGLLKAVEKFDW 201
Query: 375 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
+ G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 202 RKGYKFSTYATWWIRQAITRAIADQARTIRIPV 234
>sp|P0A602|RPOD_MYCTU RNA polymerase sigma factor RpoD OS=Mycobacterium tuberculosis
GN=rpoD PE=1 SV=1
Length = 528
Score = 103 bits (258), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 61/161 (37%), Positives = 91/161 (56%), Gaps = 24/161 (14%)
Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQI-------QDLIRLEKEKSKLQSQFGREPTLIE 307
D +R +L LL A+EE EL +I Q + L + KL + R+ I
Sbjct: 226 DSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWI- 284
Query: 308 WAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLM 366
CRD G+ ++ L+ ANLRLVV +AK+Y GRG++ DL+Q G++GL+
Sbjct: 285 --------CRD-------GDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLI 329
Query: 367 KSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
++VEKF G +F++YA WW+RQ I +A+ +RTIR+PV
Sbjct: 330 RAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPV 370
>sp|P0A603|RPOD_MYCBO RNA polymerase sigma factor RpoD OS=Mycobacterium bovis (strain
ATCC BAA-935 / AF2122/97) GN=rpoD PE=3 SV=1
Length = 528
Score = 103 bits (258), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 61/161 (37%), Positives = 91/161 (56%), Gaps = 24/161 (14%)
Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQI-------QDLIRLEKEKSKLQSQFGREPTLIE 307
D +R +L LL A+EE EL +I Q + L + KL + R+ I
Sbjct: 226 DSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLPAAQRRDMMWI- 284
Query: 308 WAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLM 366
CRD G+ ++ L+ ANLRLVV +AK+Y GRG++ DL+Q G++GL+
Sbjct: 285 --------CRD-------GDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLI 329
Query: 367 KSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
++VEKF G +F++YA WW+RQ I +A+ +RTIR+PV
Sbjct: 330 RAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPV 370
>sp|O33662|RPOD_STRMU RNA polymerase sigma factor RpoD OS=Streptococcus mutans serotype c
(strain ATCC 700610 / UA159) GN=rpoD PE=3 SV=1
Length = 371
Score = 103 bits (256), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 72/221 (32%), Positives = 101/221 (45%), Gaps = 69/221 (31%)
Query: 188 GAEFTDISLTSSLGYPLEEVKQFSQPRFLERRSKKRKVSKPQVTNHETYNSRKASVKKKL 247
G TD S Y +EE+K ++T+ E S A V
Sbjct: 60 GISITDREGNPSTKYAVEEIK------------------PEELTDEELLGSNSAKV---- 97
Query: 248 SEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIE 307
NDP+R++L LLT +EE EL
Sbjct: 98 ------NDPVRMYLKEIGVVPLLTNEEEKEL----------------------------- 122
Query: 308 WAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLM 366
AI + DL++ +++L ANLRLVV +AK+Y GRG+ DL+Q G+MGLM
Sbjct: 123 ---AIAVENGDLEA--------KQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLM 171
Query: 367 KSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
K+V+KF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 172 KAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPV 212
>sp|O66381|RPOD_BACHD RNA polymerase sigma factor RpoD OS=Bacillus halodurans (strain
ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)
GN=sigA PE=3 SV=2
Length = 372
Score = 103 bits (256), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 58/159 (36%), Positives = 81/159 (50%), Gaps = 41/159 (25%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L LLTA+EE EL +I+
Sbjct: 96 GVKINDPVRMYLKEIGRVPLLTAEEEIELATRIE-------------------------- 129
Query: 310 KAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKS 368
++ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGL+K+
Sbjct: 130 --------------QGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 175
Query: 369 VEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
VEKF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 176 VEKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 214
>sp|P52331|RPOD_LISMO RNA polymerase sigma factor RpoD OS=Listeria monocytogenes serovar
1/2a (strain ATCC BAA-679 / EGD-e) GN=rpoD PE=3 SV=1
Length = 374
Score = 103 bits (256), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 60/160 (37%), Positives = 83/160 (51%), Gaps = 43/160 (26%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L LLTADEE L +I+
Sbjct: 98 GVKINDPVRMYLKEIGRVDLLTADEEIALAKRIE-------------------------- 131
Query: 310 KAIGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMK 367
+G+ ++ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGLMK
Sbjct: 132 ---------------AGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMK 176
Query: 368 SVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
+VEKF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 177 AVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 216
>sp|Q92BQ6|RPOD_LISIN RNA polymerase sigma factor RpoD OS=Listeria innocua serovar 6a
(strain CLIP 11262) GN=rpoD PE=3 SV=1
Length = 374
Score = 103 bits (256), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 60/160 (37%), Positives = 83/160 (51%), Gaps = 43/160 (26%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L LLTADEE L +I+
Sbjct: 98 GVKINDPVRMYLKEIGRVDLLTADEEIALAKRIE-------------------------- 131
Query: 310 KAIGLSCRDLKSELHSGN-SSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMK 367
+G+ ++ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGLMK
Sbjct: 132 ---------------AGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMK 176
Query: 368 SVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
+VEKF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 177 AVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 216
>sp|P18184|HRDC_STRCO RNA polymerase principal sigma factor HrdC OS=Streptomyces
coelicolor (strain ATCC BAA-471 / A3(2) / M145) GN=hrdC
PE=3 SV=1
Length = 339
Score = 102 bits (255), Expect = 4e-21, Method: Compositional matrix adjust.
Identities = 53/140 (37%), Positives = 88/140 (62%), Gaps = 10/140 (7%)
Query: 269 LLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNS 328
LLTA++E L +I+ +R +E L++ EP + R L+ +H G
Sbjct: 51 LLTAEDEVRLATRIEAGVRAREE---LETADTGEPAPTPRRR------RTLEETVHDGQE 101
Query: 329 SREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWW 387
+++ ++ ANLRLVV +AK++ RG+ L D++Q G++GL+++VEKF G +F++YA WW
Sbjct: 102 AKDHMVRANLRLVVSMAKRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKGFKFSTYATWW 161
Query: 388 VRQTIRKAIFQHSRTIRLPV 407
+RQ I + + H+RT+RLPV
Sbjct: 162 IRQAIERGLATHARTVRLPV 181
>sp|P52328|RPSD2_BACSP RNA polymerase sigma factor RpoD OS=Bacillus sp. GN=sigA PE=3 SV=1
Length = 377
Score = 102 bits (254), Expect = 6e-21, Method: Compositional matrix adjust.
Identities = 57/159 (35%), Positives = 82/159 (51%), Gaps = 41/159 (25%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L LL+AD+E EL +I
Sbjct: 101 GIKINDPVRMYLKEIGRVPLLSADDEVELAKRI--------------------------- 133
Query: 310 KAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKS 368
++ ++ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGL+K+
Sbjct: 134 -------------MNGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 180
Query: 369 VEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
VEKF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 181 VEKFDHNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 219
>sp|P0A4J0|RPOD_STRR6 RNA polymerase sigma factor RpoD OS=Streptococcus pneumoniae
(strain ATCC BAA-255 / R6) GN=rpoD PE=3 SV=1
Length = 369
Score = 102 bits (253), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 61/182 (33%), Positives = 93/182 (51%), Gaps = 51/182 (28%)
Query: 227 KPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI 286
+P++++ + S A V NDP+R++L LLT +EE EL
Sbjct: 79 EPELSDEDLIGSTSAKV----------NDPVRMYLKEIGVVPLLTNEEEKEL-------- 120
Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAK 346
A+ + D+++ +++L ANLRLVV +AK
Sbjct: 121 ------------------------ALAVEAGDIEA--------KQRLAEANLRLVVSIAK 148
Query: 347 QYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 405
+Y GRG+ DL+Q G+MGLMK+V+KF G +F++YA WW+RQ I +AI +RTIR+
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208
Query: 406 PV 407
PV
Sbjct: 209 PV 210
>sp|P0A4I9|RPOD_STRPN RNA polymerase sigma factor RpoD OS=Streptococcus pneumoniae
serotype 4 (strain ATCC BAA-334 / TIGR4) GN=rpoD PE=3
SV=1
Length = 369
Score = 102 bits (253), Expect = 7e-21, Method: Compositional matrix adjust.
Identities = 61/182 (33%), Positives = 93/182 (51%), Gaps = 51/182 (28%)
Query: 227 KPQVTNHETYNSRKASVKKKLSEGFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLI 286
+P++++ + S A V NDP+R++L LLT +EE EL
Sbjct: 79 EPELSDEDLIGSTSAKV----------NDPVRMYLKEIGVVPLLTNEEEKEL-------- 120
Query: 287 RLEKEKSKLQSQFGREPTLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAK 346
A+ + D+++ +++L ANLRLVV +AK
Sbjct: 121 ------------------------ALAVEAGDIEA--------KQRLAEANLRLVVSIAK 148
Query: 347 QYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRL 405
+Y GRG+ DL+Q G+MGLMK+V+KF G +F++YA WW+RQ I +AI +RTIR+
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208
Query: 406 PV 407
PV
Sbjct: 209 PV 210
>sp|P06224|RPOD_BACSU RNA polymerase sigma factor RpoD OS=Bacillus subtilis (strain 168)
GN=sigA PE=1 SV=2
Length = 371
Score = 101 bits (252), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 61/153 (39%), Positives = 89/153 (58%), Gaps = 21/153 (13%)
Query: 264 PETRKLLTADEEFEL-------IAQIQDLIRLE-KEKSKLQSQFGREPTLIEWAKAIGLS 315
P ++L A+EEF+L +I D +R+ KE ++ +E I +A+ I
Sbjct: 73 PNIQQLAKAEEEFDLNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEE--IAYAQKIE-- 128
Query: 316 CRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKP 374
S+ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGLMK+VEKF
Sbjct: 129 --------EGDEESKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDY 180
Query: 375 QAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
+ G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 181 RKGYKFSTYATWWIRQAITRAIADQARTIRIPV 213
>sp|P0A0I9|RPOD_STAAW RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
MW2) GN=rpoD PE=3 SV=1
Length = 368
Score = 100 bits (249), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 57/159 (35%), Positives = 80/159 (50%), Gaps = 41/159 (25%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L LL+A EE EL +I+
Sbjct: 92 GVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE-------------------------- 125
Query: 310 KAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKS 368
++ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGL+K+
Sbjct: 126 --------------QGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 171
Query: 369 VEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
VEKF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 172 VEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|Q6G905|RPOD_STAAS RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
MSSA476) GN=rpoD PE=3 SV=1
Length = 368
Score = 100 bits (249), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 57/159 (35%), Positives = 80/159 (50%), Gaps = 41/159 (25%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L LL+A EE EL +I+
Sbjct: 92 GVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE-------------------------- 125
Query: 310 KAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKS 368
++ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGL+K+
Sbjct: 126 --------------QGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 171
Query: 369 VEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
VEKF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 172 VEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|Q6GGD8|RPOD_STAAR RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
MRSA252) GN=rpoD PE=3 SV=1
Length = 368
Score = 100 bits (249), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 57/159 (35%), Positives = 80/159 (50%), Gaps = 41/159 (25%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L LL+A EE EL +I+
Sbjct: 92 GVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE-------------------------- 125
Query: 310 KAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKS 368
++ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGL+K+
Sbjct: 126 --------------QGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 171
Query: 369 VEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
VEKF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 172 VEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|P0A0I8|RPOD_STAAM RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
Mu50 / ATCC 700699) GN=rpoD PE=1 SV=1
Length = 368
Score = 100 bits (249), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 57/159 (35%), Positives = 80/159 (50%), Gaps = 41/159 (25%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L LL+A EE EL +I+
Sbjct: 92 GVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE-------------------------- 125
Query: 310 KAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKS 368
++ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGL+K+
Sbjct: 126 --------------QGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 171
Query: 369 VEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
VEKF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 172 VEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|Q5HFJ9|RPOD_STAAC RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
COL) GN=rpoD PE=3 SV=1
Length = 368
Score = 100 bits (249), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 57/159 (35%), Positives = 80/159 (50%), Gaps = 41/159 (25%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L LL+A EE EL +I+
Sbjct: 92 GVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE-------------------------- 125
Query: 310 KAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKS 368
++ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGL+K+
Sbjct: 126 --------------QGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 171
Query: 369 VEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
VEKF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 172 VEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|P0A0J0|RPOD_STAA8 RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
NCTC 8325) GN=rpoD PE=3 SV=1
Length = 368
Score = 100 bits (249), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 57/159 (35%), Positives = 80/159 (50%), Gaps = 41/159 (25%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L LL+A EE EL +I+
Sbjct: 92 GVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE-------------------------- 125
Query: 310 KAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKS 368
++ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGL+K+
Sbjct: 126 --------------QGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 171
Query: 369 VEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
VEKF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 172 VEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|Q99TT5|RPOD_STAAN RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
N315) GN=rpoD PE=1 SV=1
Length = 368
Score = 100 bits (249), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 57/159 (35%), Positives = 80/159 (50%), Gaps = 41/159 (25%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L LL+A EE EL +I+
Sbjct: 92 GVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE-------------------------- 125
Query: 310 KAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKS 368
++ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGL+K+
Sbjct: 126 --------------QGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 171
Query: 369 VEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
VEKF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 172 VEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|P56835|RPOD_CHLMU RNA polymerase sigma factor RpoD OS=Chlamydia muridarum (strain
MoPn / Nigg) GN=rpoD PE=3 SV=1
Length = 571
Score = 100 bits (248), Expect = 3e-20, Method: Compositional matrix adjust.
Identities = 46/105 (43%), Positives = 74/105 (70%), Gaps = 5/105 (4%)
Query: 304 TLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GS 362
TL E+ K + R L+ + ++++++ +NLRLV+ +AK+Y RG+S DL+Q G+
Sbjct: 296 TLEEFKKDV----RMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGN 351
Query: 363 MGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
MGLMK+VEKF+ + G +F++YA WW+RQ + +AI +RTIR+PV
Sbjct: 352 MGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPV 396
>sp|Q9Z7F0|RPOD_CHLPN RNA polymerase sigma factor RpoD OS=Chlamydia pneumoniae GN=rpoD
PE=3 SV=1
Length = 572
Score = 99.8 bits (247), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 46/105 (43%), Positives = 74/105 (70%), Gaps = 5/105 (4%)
Query: 304 TLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GS 362
TL E+ K + R L+ + ++++++ +NLRLV+ +AK+Y RG+S DL+Q G+
Sbjct: 296 TLEEFKKDV----RMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGN 351
Query: 363 MGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
MGLMK+VEKF+ + G +F++YA WW+RQ + +AI +RTIR+PV
Sbjct: 352 MGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPV 396
>sp|O83506|RPOD_TREPA RNA polymerase sigma factor RpoD OS=Treponema pallidum (strain
Nichols) GN=rpoD PE=3 SV=1
Length = 611
Score = 99.8 bits (247), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 45/90 (50%), Positives = 68/90 (75%), Gaps = 5/90 (5%)
Query: 323 LHSGN----SSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFKPQAG 377
+H G+ +++KLINANLRLVV +AK+Y RG+ DL+Q G++GL+K+VEKF+ + G
Sbjct: 363 IHRGHVMLKKAKDKLINANLRLVVSIAKKYTNRGLLFFDLVQEGNIGLIKAVEKFEYRKG 422
Query: 378 CRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
+F++YA WW+RQ I ++I +RTIR+PV
Sbjct: 423 YKFSTYATWWIRQAITRSISDQARTIRVPV 452
>sp|P18333|RPOD_CHLTR RNA polymerase sigma factor RpoD OS=Chlamydia trachomatis (strain
D/UW-3/Cx) GN=rpoD PE=3 SV=2
Length = 571
Score = 99.8 bits (247), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 46/105 (43%), Positives = 74/105 (70%), Gaps = 5/105 (4%)
Query: 304 TLIEWAKAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GS 362
TL E+ K + R L+ + ++++++ +NLRLV+ +AK+Y RG+S DL+Q G+
Sbjct: 296 TLEEFKKDV----RMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGN 351
Query: 363 MGLMKSVEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
MGLMK+VEKF+ + G +F++YA WW+RQ + +AI +RTIR+PV
Sbjct: 352 MGLMKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQARTIRIPV 396
>sp|Q8CP24|RPOD_STAES RNA polymerase sigma factor RpoD OS=Staphylococcus epidermidis
(strain ATCC 12228) GN=rpoD PE=3 SV=1
Length = 368
Score = 99.8 bits (247), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 57/159 (35%), Positives = 80/159 (50%), Gaps = 41/159 (25%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L LL+A EE EL +I+
Sbjct: 92 GVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE-------------------------- 125
Query: 310 KAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKS 368
++ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGL+K+
Sbjct: 126 --------------QGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 171
Query: 369 VEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
VEKF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 172 VEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|Q5HNY7|RPOD_STAEQ RNA polymerase sigma factor RpoD OS=Staphylococcus epidermidis
(strain ATCC 35984 / RP62A) GN=rpoD PE=3 SV=1
Length = 368
Score = 99.8 bits (247), Expect = 4e-20, Method: Compositional matrix adjust.
Identities = 57/159 (35%), Positives = 80/159 (50%), Gaps = 41/159 (25%)
Query: 250 GFDRNDPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWA 309
G NDP+R++L LL+A EE EL +I+
Sbjct: 92 GVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIE-------------------------- 125
Query: 310 KAIGLSCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKS 368
++ +L ANLRLVV +AK+Y GRG+ DL+Q G+MGL+K+
Sbjct: 126 --------------QGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKA 171
Query: 369 VEKFKPQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
VEKF G +F++YA WW+RQ I +AI +RTIR+PV
Sbjct: 172 VEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|P18183|HRDB_STRCO RNA polymerase principal sigma factor HrdB OS=Streptomyces
coelicolor (strain ATCC BAA-471 / A3(2) / M145) GN=hrdB
PE=3 SV=2
Length = 511
Score = 99.4 bits (246), Expect = 5e-20, Method: Compositional matrix adjust.
Identities = 58/154 (37%), Positives = 89/154 (57%), Gaps = 14/154 (9%)
Query: 255 DPLRLFLWGPETRKLLTADEEFELIAQIQDLIRLEKEKSKLQSQFGREPTLIEWAKAIGL 314
DP++ +L LL A++E EL +I+ + E KL + P L
Sbjct: 213 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAE---DKLANSDKLAPKL--------- 260
Query: 315 SCRDLKSELHSGNSSREKLINANLRLVVHVAKQYQGRGISLHDLLQ-GSMGLMKSVEKFK 373
R+L+ G ++ L+ ANLRLVV +AK+Y GRG+ DL+Q G++GL+++VEKF
Sbjct: 261 -KRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFD 319
Query: 374 PQAGCRFASYAYWWVRQTIRKAIFQHSRTIRLPV 407
G +F++YA WW+RQ I +A+ +RTIR+PV
Sbjct: 320 YTKGYKFSTYATWWIRQAITRAMADQARTIRIPV 353
Database: swissprot
Posted date: Mar 23, 2013 2:32 AM
Number of letters in database: 191,569,459
Number of sequences in database: 539,616
Lambda K H
0.314 0.128 0.362
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 143,992,353
Number of Sequences: 539616
Number of extensions: 5684242
Number of successful extensions: 28116
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 140
Number of HSP's successfully gapped in prelim test: 73
Number of HSP's that attempted gapping in prelim test: 27245
Number of HSP's gapped (non-prelim): 627
length of query: 428
length of database: 191,569,459
effective HSP length: 120
effective length of query: 308
effective length of database: 126,815,539
effective search space: 39059186012
effective search space used: 39059186012
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 63 (28.9 bits)