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= 010092
(518 letters)
Database: swissprot
539,616 sequences; 191,569,459 total letters
Searching..................................................done
>sp|Q9ZNX9|SIGE_ARATH RNA polymerase sigma factor sigE, chloroplastic/mitochondrial
OS=Arabidopsis thaliana GN=SIGE PE=1 SV=1
Length = 517
Score = 673 bits (1737), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 347/529 (65%), Positives = 416/529 (78%), Gaps = 23/529 (4%)
Query: 1 MGVVTISSSPARSPIGLST--ISHRSTSKRPLIVAFKADKSNNQALF-SPQEQIPLPIET 57
MGVV+ISSS ARSP+GL ++HRS+ K+P IVAFKAD S+N AL P+EQ+ +P E
Sbjct: 1 MGVVSISSSAARSPLGLGNDLLTHRSSLKKPSIVAFKADDSSNSALIIPPREQVLIPAE- 59
Query: 58 PKRHQKRRENSRKRLERVK----GVFSDEASPCTLDVDYNEAAAKLENIYKLSPAVTT-S 112
K ++K+RE +R++ + + + A C+L VDYNEAAA+LE+IYKLSPA TT
Sbjct: 60 -KHNEKKREVTRRKPCKTPKKPLSLEHNSAPSCSLGVDYNEAAARLESIYKLSPATTTLV 118
Query: 113 EVKYADGVVKRGRQRRKRIGEVEKKSDDVSGKPVVRNQVKRPKRLSLDKRIELRKNEDEK 172
E DG K RR++ +K K VVRN VK+ KR+SLDKRI L++N EK
Sbjct: 119 EDDVEDGGSKAKVSRRRK-----RKESGEEKKVVVRNNVKKEKRMSLDKRIALKRNVQEK 173
Query: 173 VVTKT---RKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQ 229
V + + T + E EKIE+LVR+YS S D+VSLDWKKMKIPPVLSSTEH WLFKLMQ
Sbjct: 174 PVVASVDKKVTKRQQEEEKIERLVRDYSASNDIVSLDWKKMKIPPVLSSTEHAWLFKLMQ 233
Query: 230 PMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLF 289
PMK ++VK+ LQK LGREP + E+A NM+A +VKK +E+GRAARNKLIKHNLRLVLF
Sbjct: 234 PMKALLEVKDVLQKSLGREPREAEIAGEINMTAGEVKKKIEIGRAARNKLIKHNLRLVLF 293
Query: 290 VIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349
V+ KYF +F NGP+FQDLCQAG++GLITAIDRFEPKR+FRLSTYGLFWIRHAIIRSMT S
Sbjct: 294 VMNKYFHEFTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTYGLFWIRHAIIRSMTTS 353
Query: 350 SFTRVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASK 409
+FTRVPFGLES VR EI +AK EL FE+ R PT++E+++ + I+PERYREV++A+K
Sbjct: 354 NFTRVPFGLES-----VRVEIYKAKTELWFEMGRPPTEDEVVERLKITPERYREVLRAAK 408
Query: 410 PILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRF 469
P+LSL+S+H VTQEEFINGITDVDGV N RQPALLRLALDDVLDSLKPKESLVIRQR+
Sbjct: 409 PVLSLNSKHSVTQEEFINGITDVDGVGANNSRQPALLRLALDDVLDSLKPKESLVIRQRY 468
Query: 470 GLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
GLDGKGDRTLGEIAGNLNISREMVRKHEVK LMKLKH RVDYLRQ++V
Sbjct: 469 GLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHQARVDYLRQYIV 517
>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 = 174 bits (442), Expect = 1e-42, Method: Compositional matrix adjust.
Identities = 120/364 (32%), Positives = 197/364 (54%), Gaps = 24/364 (6%)
Query: 159 LDKRIELRKNEDE----KVVTKTRKTDSKDEHEKIEKLVREYSYSTDLVSLDWKKMKIPP 214
+D+ +E + +ED+ K R+T SK +H Y+ D + L +++
Sbjct: 45 IDEFLEPQTDEDDAKSGKAAKSRRRTQSKKKH-----------YTEDSIRLYLQEIGRIR 93
Query: 215 VLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRA 274
+L + E L + + + +V+E+L + L R+P D E AEA + + L +GR
Sbjct: 94 LLRADEEIELARKIADLLELERVRERLSEKLERDPRDSEWAEAVQLPLPAFRYRLHIGRR 153
Query: 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYG 334
A++K+++ NLRLV+ + KKY G FQDL Q G GLI A ++F+ ++ ++ STY
Sbjct: 154 AKDKMVQSNLRLVVSIAKKYMN---RGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYA 210
Query: 335 LFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQG 393
+WIR AI R++ S T R+P L T I++ L E+ R PT+EEI
Sbjct: 211 TWWIRQAITRAIADQSRTIRLPVHLYETI-----SRIKKTTKLLSQEMGRKPTEEEIATR 265
Query: 394 VNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDV 453
+ ++ E+ R + K+++ +SL + G ++ + + DG E+Q LLR L+ V
Sbjct: 266 MEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIESDGETPEDQVSKNLLREDLEKV 325
Query: 454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 513
LDSL P+E V+R R+GLD +TL EI N++RE +R+ E K L KL+HP R L
Sbjct: 326 LDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSVL 385
Query: 514 RQHM 517
++++
Sbjct: 386 KEYI 389
>sp|P38023|RPOD1_SYNE7 RNA polymerase sigma factor rpoD1 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD1 PE=3 SV=2
Length = 399
Score = 156 bits (395), Expect = 3e-37, Method: Compositional matrix adjust.
Identities = 104/322 (32%), Positives = 179/322 (55%), Gaps = 9/322 (2%)
Query: 197 SYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAE 256
+Y+ D + L +++ +L + E L + + + +++++L + L R P+D E A
Sbjct: 85 TYTEDSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAA 144
Query: 257 ATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLI 316
A + + ++ L GR A++K+++ NLRLV+ + KKY G FQDL Q G GLI
Sbjct: 145 AVDSPLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMN---RGLSFQDLIQEGSLGLI 201
Query: 317 TAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKL 375
A ++F+ ++ ++ STY +WIR AI R++ S T R+P L T I++
Sbjct: 202 RAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI-----SRIKKTTK 256
Query: 376 ELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV 435
L E+ R PT+EEI + ++ E+ R + K+++ +SL + G ++ + + DG
Sbjct: 257 LLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGE 316
Query: 436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRK 495
E++ LLR L+ VL +L P+E V+R R+GLD +TL EI N++RE +R+
Sbjct: 317 TPEDEVAKNLLREDLEGVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQ 376
Query: 496 HEVKGLMKLKHPTRVDYLRQHM 517
E K L KL+HP R L++++
Sbjct: 377 IEAKALRKLRHPNRNSILKEYI 398
>sp|P52322|RPOD_MICAE RNA polymerase sigma factor rpoD1 OS=Microcystis aeruginosa
GN=rpoD1 PE=3 SV=1
Length = 416
Score = 150 bits (379), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 92/256 (35%), Positives = 148/256 (57%), Gaps = 9/256 (3%)
Query: 263 AQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRF 322
+ K+ L GR A+ K+++ NLRLV+ + KKY G FQDL Q G GLI A ++F
Sbjct: 168 SAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKYMN---RGLSFQDLIQEGSLGLIRAAEKF 224
Query: 323 EPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFEL 381
+ ++ ++ STY +WIR AI R++ S T R+P L T I++ L E+
Sbjct: 225 DHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVHLYETI-----SRIKKTTKILSQEM 279
Query: 382 KRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQR 441
+R PT+EEI + ++ E+ R + K+++ +SL + G ++ + + DG E++
Sbjct: 280 RRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPEDEV 339
Query: 442 QPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 501
LLR L++VLD+L P+E V+R R+GLD +TL EI N++RE +R+ E K L
Sbjct: 340 SKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKAL 399
Query: 502 MKLKHPTRVDYLRQHM 517
KL+HP R L++++
Sbjct: 400 RKLRHPNRNSILKEYI 415
>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 = 149 bits (377), Expect = 4e-35, Method: Compositional matrix adjust.
Identities = 88/244 (36%), Positives = 144/244 (59%), Gaps = 9/244 (3%)
Query: 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYG 334
A++K+++ NLRLV+ + KKY G FQDL Q G GLI A ++F+ ++ ++ STY
Sbjct: 189 AKDKMVQSNLRLVVSIAKKYMN---RGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYA 245
Query: 335 LFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQG 393
+WIR AI R++ S T R+P L T I++ L E++R PT+EEI +
Sbjct: 246 TWWIRQAITRAIADQSRTIRLPVHLYETI-----SRIKKTTKLLSQEMRRKPTEEEIAEK 300
Query: 394 VNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPALLRLALDDV 453
+ ++ E+ R + K+++ +SL + G ++ + + DG E++ LLR L++V
Sbjct: 301 MEMTIEKLRFIAKSAQLPISLETPIGKEEDSRLGDFIEADGETPEDEVSKNLLREDLENV 360
Query: 454 LDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYL 513
LD+L P+E V+R R+GLD +TL EI N++RE +R+ E K L KL+HP R L
Sbjct: 361 LDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHPNRNSIL 420
Query: 514 RQHM 517
++++
Sbjct: 421 KEYI 424
>sp|Q59753|RPOD_RHIME RNA polymerase sigma factor RpoD OS=Rhizobium meliloti (strain
1021) GN=rpoD PE=3 SV=1
Length = 684
Score = 145 bits (366), Expect = 7e-34, Method: Compositional matrix adjust.
Identities = 99/300 (33%), Positives = 163/300 (54%), Gaps = 29/300 (9%)
Query: 232 KVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEV-------GRAARNKLIKHNL 284
K F + + Q +D+ +E + LA T +S A+ ++ + + R A+ ++++ NL
Sbjct: 398 KEFARAENQTIRDIRQEIQN--LATETGISIAEFRRIVSMVQKGEREARIAKKEMVEANL 455
Query: 285 RLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIR 344
RLV+ + KKY G +F DL Q G GL+ A+D+FE +R ++ STY +WIR AI R
Sbjct: 456 RLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 512
Query: 345 SMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYRE 403
S+ + T R+P +++ +I R ++L E+ R PT EE+ + + + E+ R+
Sbjct: 513 SIADQARTIRIPV-----HMIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRK 567
Query: 404 VMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQP------ALLRLALDDVLDSL 457
V+K +K +SL + G ++ + D +E++N P A LR VL SL
Sbjct: 568 VLKIAKEPISLETPVGDEEDSHLG-----DFIEDKNALLPIDAAIQANLRETTTRVLASL 622
Query: 458 KPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
P+E V+R RFG+ D TL E+ +++RE +R+ E K L KLKHP+R LR +
Sbjct: 623 TPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFL 682
>sp|O22056|SIGB_ARATH RNA polymerase sigma factor sigB OS=Arabidopsis thaliana GN=SIGB
PE=2 SV=2
Length = 572
Score = 145 bits (365), Expect = 9e-34, Method: Compositional matrix adjust.
Identities = 93/286 (32%), Positives = 156/286 (54%), Gaps = 14/286 (4%)
Query: 239 EQLQKDL----GREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKY 294
E+LQ +L GR+PT + A A + +++ + G ++K+IK N+RLV+ + K Y
Sbjct: 292 ERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRLVISIAKNY 351
Query: 295 FQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSS-FTR 353
G QDL Q G +GL+ ++F+ + F+ STY +WI+ A+ +S++ S R
Sbjct: 352 ---QGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKSLSDQSRMIR 408
Query: 354 VPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILS 413
+PF + ++ ++ A+ +L E + P +EEI + +S +R V+ + KP S
Sbjct: 409 LPFHM-----VEATYRVKEARKQLYSETGKHPKNEEIAEATGLSMKRLMAVLLSPKPPRS 463
Query: 414 LHSRHGVTQE-EFINGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLD 472
L + G+ Q + I D + V +E+ +R LD VLDSL +E VIR RFG++
Sbjct: 464 LDQKIGMNQNLKPSEVIADPEAVTSEDILIKEFMRQDLDKVLDSLGTREKQVIRWRFGME 523
Query: 473 GKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHMV 518
+TL EI + +SRE VR+ E KLK+ R ++L+Q++V
Sbjct: 524 DGRMKTLQEIGEMMGVSRERVRQIESSAFRKLKNKKRNNHLQQYLV 569
>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 = 144 bits (363), Expect = 2e-33, Method: Compositional matrix adjust.
Identities = 92/262 (35%), Positives = 151/262 (57%), Gaps = 14/262 (5%)
Query: 262 AAQVKKCLEV----GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLIT 317
A ++K+ LE+ GR A+N L++ NLRLV+ + K+Y G F DL Q G GLI
Sbjct: 257 APKLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYT---GRGMLFLDLIQEGNLGLIR 313
Query: 318 AIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLE 376
A+++F+ + ++ STY +WIR AI R+M + T R+P +++V ++ R + +
Sbjct: 314 AVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPV-----HMVEVINKLARVQRQ 368
Query: 377 LLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFINGITDVDGV 435
+L +L R PT EE+ + ++++PE+ EV K + +SLH+ G + EF + I D + V
Sbjct: 369 MLQDLGREPTPEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSEAV 428
Query: 436 ENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRK 495
+ LL+ L VLD+L +E+ V+ RFGL +TL EI ++RE +R+
Sbjct: 429 VPADAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQ 488
Query: 496 HEVKGLMKLKHPTRVDYLRQHM 517
E K + KL+HP+R LR ++
Sbjct: 489 IESKTMSKLRHPSRSQVLRDYL 510
Score = 32.3 bits (72), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 26/40 (65%)
Query: 234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGR 273
+V+ Q+ +DLGREPT ELA+ +M+ +V + + GR
Sbjct: 362 LARVQRQMLQDLGREPTPEELAKELDMTPEKVIEVQKYGR 401
>sp|P77951|HRDB_STRGR RNA polymerase principal sigma factor HrdB OS=Streptomyces griseus
GN=hrdB PE=1 SV=1
Length = 514
Score = 144 bits (363), Expect = 2e-33, Method: Compositional matrix adjust.
Identities = 95/270 (35%), Positives = 155/270 (57%), Gaps = 15/270 (5%)
Query: 254 LAEATNMSAAQVKKCLEV----GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQ 309
LA A + A ++K+ LE+ GR A+N L++ NLRLV+ + K+Y G F DL Q
Sbjct: 253 LANADKL-APKLKRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYT---GRGMLFLDLIQ 308
Query: 310 AGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRG 368
G GLI A+++F+ + ++ STY +WIR AI R+M + T R+P +++V
Sbjct: 309 EGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPV-----HMVEVIN 363
Query: 369 EIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EFIN 427
++ R + ++L +L R PT EE+ + ++++PE+ EV K + +SLH+ G + EF +
Sbjct: 364 KLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEVQKYGREPISLHTPLGEDGDSEFGD 423
Query: 428 GITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLN 487
I D + V + LL+ L VLD+L +E+ V+ RFGL +TL EI
Sbjct: 424 LIEDSEAVVPADAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYG 483
Query: 488 ISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++RE +R+ E K + KL+HP+R LR ++
Sbjct: 484 VTRERIRQIESKTMSKLRHPSRSQVLRDYL 513
Score = 32.3 bits (72), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 26/40 (65%)
Query: 234 FVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGR 273
+V+ Q+ +DLGREPT ELA+ +M+ +V + + GR
Sbjct: 365 LARVQRQMLQDLGREPTPEELAKELDMTPEKVIEVQKYGR 404
>sp|P26480|RPOD_PSEAE RNA polymerase sigma factor RpoD OS=Pseudomonas aeruginosa (strain
ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) GN=rpoD
PE=3 SV=1
Length = 617
Score = 142 bits (359), Expect = 5e-33, Method: Compositional matrix adjust.
Identities = 91/314 (28%), Positives = 173/314 (55%), Gaps = 28/314 (8%)
Query: 219 TEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEA-TNMSAAQVK---KCLEVGRA 274
T+ W+ +++ + + E+L+ D+ R + E+ ++ A++K + + +G A
Sbjct: 315 TDEKWVDSVLKSKPKYAEAIERLRDDILRNQQKLAALESEVELTVAEIKEINRAMSIGEA 374
Query: 275 ----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRL 330
A+ ++++ NLRLV+ + KKY G +F DL Q G GL+ A+D+FE +R ++
Sbjct: 375 KARRAKKEMVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKF 431
Query: 331 STYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEE 389
STY +WIR AI RS+ + T R+P +++ ++ R ++L E+ R PT EE
Sbjct: 432 STYATWWIRQAITRSIADQARTIRIP-----VHMIETINKLNRISRQMLQEMGREPTPEE 486
Query: 390 IIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQP------ 443
+ + +++ ++ R+V+K +K +S+ + G ++ + D +E+ + P
Sbjct: 487 LGERMDMPEDKIRKVLKIAKEPISMETPIGDDEDSHLG-----DFIEDSTMQSPIEMATS 541
Query: 444 ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMK 503
L+ + +VL L +E+ V+R RFG+D D TL E+ +++RE +R+ E K L K
Sbjct: 542 ESLKESTREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRK 601
Query: 504 LKHPTRVDYLRQHM 517
L+HP+R ++LR +
Sbjct: 602 LRHPSRSEHLRSFL 615
>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 = 142 bits (358), Expect = 6e-33, Method: Compositional matrix adjust.
Identities = 99/312 (31%), Positives = 162/312 (51%), Gaps = 9/312 (2%)
Query: 195 EYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVEL 254
E+SY+ D VS+ K+ P+LS + + + +Q M V KE+L + L REPT E
Sbjct: 17 EFSYTADAVSIYLHKIGRVPLLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEW 76
Query: 255 AEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKG 314
A+ + + + L G+ A+ K+I+ NLRLV+ + KKY + F DL Q G G
Sbjct: 77 ADKMQLKEDVLLQQLSQGQIAKQKMIQANLRLVVSIAKKYQK---RNLEFLDLIQEGALG 133
Query: 315 LITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRA 373
L +++F+P ++ STY +WIR I R++ S T R+P + +I+
Sbjct: 134 LERGVEKFDPTLGYKFSTYAYWWIRQGITRAIAQQSRTIRLPIHMADKL-----NKIKCV 188
Query: 374 KLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVD 433
+ EL +L + EI Q +N+ P + RE ++ + +SL R G Q+ + + D
Sbjct: 189 QRELSQKLGYIAGVTEIAQALNLEPSQIREYLQLVRQPVSLDMRIGFEQDTQLQDLLKDD 248
Query: 434 GVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMV 493
G+ E + LL + ++L L P++ V+ RFGL G + TL +I+ + ISRE V
Sbjct: 249 GMSPERYAERELLYQDIHNLLAKLTPQQKEVLILRFGLAGGCELTLVQISQRMGISRERV 308
Query: 494 RKHEVKGLMKLK 505
R+ E + L L+
Sbjct: 309 RQVEKQALTLLR 320
>sp|P33452|RPOD_AGRT5 RNA polymerase sigma factor RpoD OS=Agrobacterium tumefaciens
(strain C58 / ATCC 33970) GN=rpoD PE=3 SV=2
Length = 684
Score = 142 bits (357), Expect = 7e-33, Method: Compositional matrix adjust.
Identities = 98/310 (31%), Positives = 162/310 (52%), Gaps = 36/310 (11%)
Query: 231 MKVFVQVKEQLQKDLGREPTDV---------ELAEATNMSAAQVKKCLEV-------GRA 274
MK + + K+ RE ++ L+ T +S A+ ++ + + R
Sbjct: 386 MKSITNLAARGWKEFAREESNTIREIRQEIQNLSTETGISIAEFRRIVSMVQKGEREARI 445
Query: 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYG 334
A+ ++++ NLRLV+ + KKY G +F DL Q G GL+ A+D+FE +R ++ STY
Sbjct: 446 AKKEMVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 502
Query: 335 LFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQG 393
+WIR AI RS+ + T R+P +++ +I R ++L E+ R PT EE+ +
Sbjct: 503 TWWIRQAITRSIADQARTIRIPV-----HMIETINKIVRTSRQMLHEIGREPTPEELAEK 557
Query: 394 VNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQP------ALLR 447
+ + E+ R+V+K +K +SL + G ++ + D +E++N P A LR
Sbjct: 558 LAMPLEKVRKVLKIAKEPISLETPVGDEEDSHLG-----DFIEDKNALLPIDAAIQANLR 612
Query: 448 LALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHP 507
VL SL P+E V+R RFG+ D TL E+ +++RE +R+ E K L KLKHP
Sbjct: 613 ETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHP 672
Query: 508 TRVDYLRQHM 517
+R LR +
Sbjct: 673 SRSRKLRSFL 682
>sp|P52327|RPOD_PSEPU RNA polymerase sigma factor RpoD OS=Pseudomonas putida GN=rpoD PE=3
SV=1
Length = 614
Score = 142 bits (357), Expect = 8e-33, Method: Compositional matrix adjust.
Identities = 88/280 (31%), Positives = 156/280 (55%), Gaps = 27/280 (9%)
Query: 252 VELAEATNMSAAQVKKC---LEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRF 304
++L T ++ A++K+ + +G A A+ ++++ NLRLV+ + KKY G +F
Sbjct: 346 IDLETETGLTVAEIKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQF 402
Query: 305 QDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSI 363
DL Q G GL+ A+D+FE +R ++ STY +WIR AI RS+ + T R+P +
Sbjct: 403 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP-----VHM 457
Query: 364 MQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423
++ ++ R ++L E+ R PT EE+ + + + ++ R+V+K +K +S+ + G ++
Sbjct: 458 IETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKIAKEPISMETPIGDDED 517
Query: 424 EFINGITDVDGVENENQRQPAL------LRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 477
+ D +E+ + P L+ A DVL L +E+ V+R RFG+D D
Sbjct: 518 SHLG-----DFIEDSTMQSPIYVATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDH 572
Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
TL E+ +++RE +R+ E K KL+HPTR ++LR +
Sbjct: 573 TLEEVGKQFDVTRERIRQIEAKAWRKLRHPTRSEHLRSFL 612
>sp|Q2K619|RPOD_RHIEC RNA polymerase sigma factor rpoD OS=Rhizobium etli (strain CFN 42 /
ATCC 51251) GN=sigA PE=1 SV=1
Length = 685
Score = 142 bits (357), Expect = 9e-33, Method: Compositional matrix adjust.
Identities = 93/278 (33%), Positives = 152/278 (54%), Gaps = 27/278 (9%)
Query: 254 LAEATNMSAAQVKKCLEV-------GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQD 306
LA T +S ++ ++ + + R A+ ++++ NLRLV+ + KKY G +F D
Sbjct: 419 LATETGISISEFRRIVHMVQKGEREARIAKKEMVEANLRLVISIAKKYTN---RGLQFLD 475
Query: 307 LCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQ 365
L Q G GL+ A+D+FE +R ++ STY +WIR AI RS+ + T R+P +++
Sbjct: 476 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV-----HMIE 530
Query: 366 VRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEF 425
+I R ++L E+ R PT EE+ + + + E+ R+V+K +K +SL + G ++
Sbjct: 531 TINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPVGDEEDSH 590
Query: 426 INGITDVDGVENENQRQP------ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTL 479
+ D +E++N P A LR VL SL P+E V+R RFG+ D TL
Sbjct: 591 LG-----DFIEDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTL 645
Query: 480 GEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
E+ +++RE +R+ E K L KLKHP+R LR +
Sbjct: 646 EEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKLRSFL 683
>sp|D5AQI9|RPOD_RHOCB RNA polymerase sigma factor rpoD OS=Rhodobacter capsulatus (strain
ATCC BAA-309 / NBRC 16581 / SB1003) GN=rpoD PE=3 SV=1
Length = 674
Score = 142 bits (357), Expect = 9e-33, Method: Compositional matrix adjust.
Identities = 103/313 (32%), Positives = 168/313 (53%), Gaps = 31/313 (9%)
Query: 222 TWLFKL-MQPMKVFVQVKEQLQ---KDLGREPTDVELAEATNMS-----AAQVKKCLEVG 272
TW+ ++ +P + +V + E+ + +DL E V ++S QV+K +
Sbjct: 374 TWMDRMSAKPARAWVTLFEKSRDKVEDLRHEMAQVGQYVGVDISEFRRIVNQVQKGEKEA 433
Query: 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLST 332
R A+ ++++ NLRLV+ + KKY G +F DL Q G GL+ A+D+FE +R ++ ST
Sbjct: 434 RQAKKEMVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 490
Query: 333 YGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEII 391
Y +WIR AI RS+ + T R+P +++ ++ R ++L E+ R PT EE+
Sbjct: 491 YATWWIRQAITRSIADQARTIRIP-----VHMIETINKLVRTGRQMLHEIGREPTPEELA 545
Query: 392 QGVNISPERYREVMKASKPILSLHSRHGVTQE----EFI---NGITDVDGVENENQRQPA 444
+ + + E+ R+VMK +K +SL + G ++ +FI N I +D EN
Sbjct: 546 EKLQMPLEKVRKVMKIAKEPISLETPIGDEEDSQLGDFIEDKNAILPLDSAIQEN----- 600
Query: 445 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504
L+ VL SL P+E V+R RFG+ D TL E+ +++RE +R+ E K L KL
Sbjct: 601 -LKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 659
Query: 505 KHPTRVDYLRQHM 517
KHP+R LR +
Sbjct: 660 KHPSRSRKLRSFL 672
>sp|P06224|RPOD_BACSU RNA polymerase sigma factor RpoD OS=Bacillus subtilis (strain 168)
GN=sigA PE=1 SV=2
Length = 371
Score = 141 bits (356), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 99/315 (31%), Positives = 167/315 (53%), Gaps = 31/315 (9%)
Query: 205 LDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQ 264
D + +PP + K+ P+++++ K++GR V L A A
Sbjct: 85 FDLNDLSVPPGV---------KINDPVRMYL-------KEIGR----VNLLSAKE-EIAY 123
Query: 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEP 324
+K E ++ +L + NLRLV+ + K+Y G F DL Q G GL+ A+++F+
Sbjct: 124 AQKIEEGDEESKRRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGNMGLMKAVEKFDY 180
Query: 325 KRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKR 383
++ ++ STY +WIR AI R++ + T R+P + T +R +QR +LL +L R
Sbjct: 181 RKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR--VQR---QLLQDLGR 235
Query: 384 VPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING-ITDVDGVENENQRQ 442
PT EEI + ++++PE+ RE++K ++ +SL + G + + I D + +
Sbjct: 236 EPTPEEIAEDMDLTPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEATSPSDHAA 295
Query: 443 PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502
LL+ L+DVLD+L +E V+R RFGLD RTL E+ ++RE +R+ E K L
Sbjct: 296 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 355
Query: 503 KLKHPTRVDYLRQHM 517
KL+HP+R L+ +
Sbjct: 356 KLRHPSRSKRLKDFL 370
>sp|Q04506|RPOD_LACLA RNA polymerase sigma factor RpoD OS=Lactococcus lactis subsp.
lactis (strain IL1403) GN=rpoD PE=3 SV=2
Length = 386
Score = 141 bits (356), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 96/277 (34%), Positives = 154/277 (55%), Gaps = 12/277 (4%)
Query: 243 KDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP 302
K++GR P + L E T ++ A + E A+ L + NLRLV+ + K+Y G
Sbjct: 120 KEIGRYPL-ISLDEETKLAEAIIAGG-EGAEFAKQMLAEANLRLVVSIAKRYS---GRGM 174
Query: 303 RFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLEST 361
+F DL Q G GL+ A+D+F+ + F+ STY +WIR AI R++ + T R+P + T
Sbjct: 175 QFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 234
Query: 362 SIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVT 421
+R +QR LL EL R P+ EEI + ++++P++ REV+K ++ +SL + G
Sbjct: 235 INKLIR--VQR---NLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEE 289
Query: 422 QEEFINGITDVDGVENE-NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLG 480
+ + + D +E+ + LLR LD+V+D+L +E V+R RFGLD TL
Sbjct: 290 DDSHLGDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLE 349
Query: 481 EIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++ ++RE +R+ E K + KL+HP R LR M
Sbjct: 350 DVGKQFKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 386
>sp|P58290|RPOD_LACLC RNA polymerase sigma factor RpoD (Fragment) OS=Lactococcus lactis
subsp. cremoris GN=rpoD PE=3 SV=1
Length = 364
Score = 141 bits (355), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 96/277 (34%), Positives = 154/277 (55%), Gaps = 12/277 (4%)
Query: 243 KDLGREPTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGP 302
K++GR P + L E T ++ A + E A+ L + NLRLV+ + K+Y G
Sbjct: 98 KEIGRYPL-ISLDEETKLAEAIIAGG-EGAEFAKQMLAEANLRLVVSIAKRYS---GRGM 152
Query: 303 RFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLEST 361
+F DL Q G GL+ A+D+F+ + F+ STY +WIR AI R++ + T R+P + T
Sbjct: 153 QFLDLIQEGNMGLMKAVDKFDQTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVET 212
Query: 362 SIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVT 421
+R +QR LL EL R P+ EEI + ++++P++ REV+K ++ +SL + G
Sbjct: 213 INKLIR--VQR---NLLQELGRDPSPEEIGKELHMAPDKVREVLKIAQEPVSLETPIGEE 267
Query: 422 QEEFINGITDVDGVENE-NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLG 480
+ + + D +E+ + LLR LD+V+D+L +E V+R RFGLD TL
Sbjct: 268 DDSHLGDFIEDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDGRMHTLE 327
Query: 481 EIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++ ++RE +R+ E K + KL+HP R LR M
Sbjct: 328 DVGKQFKVTRERIRQIEAKAIKKLRHPRRSKPLRDFM 364
>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 = 141 bits (355), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 100/315 (31%), Positives = 170/315 (53%), Gaps = 31/315 (9%)
Query: 205 LDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQ 264
D + +PP + K+ P+++++ K++GR P + AE A +
Sbjct: 86 FDLNDLSVPPGV---------KINDPVRMYL-------KEIGRVP--LLTAEEEIELATR 127
Query: 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEP 324
+++ E A+ +L + NLRLV+ + K+Y G F DL Q G GLI A+++F+
Sbjct: 128 IEQGDE---EAKRRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGNMGLIKAVEKFDY 181
Query: 325 KRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKR 383
+ F+ STY +WIR AI R++ + T R+P + T +R +QR +LL +L R
Sbjct: 182 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR--VQR---QLLQDLGR 236
Query: 384 VPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFING-ITDVDGVENENQRQ 442
P+ EE+ + ++++PE+ RE++K ++ +SL + G + + I D D + +
Sbjct: 237 EPSPEEVAEEMDLTPEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQDALAPSDAAA 296
Query: 443 PALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLM 502
LL+ L+DVLD+L +E V+R RFGLD RTL E+ ++RE +R+ E K L
Sbjct: 297 YELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALR 356
Query: 503 KLKHPTRVDYLRQHM 517
KL+HP+R L+ +
Sbjct: 357 KLRHPSRSKRLKDFL 371
>sp|P57163|RPOD_BUCAI RNA polymerase sigma factor RpoD OS=Buchnera aphidicola subsp.
Acyrthosiphon pisum (strain APS) GN=rpoD PE=3 SV=1
Length = 612
Score = 141 bits (355), Expect = 1e-32, Method: Compositional matrix adjust.
Identities = 94/281 (33%), Positives = 157/281 (55%), Gaps = 29/281 (10%)
Query: 252 VELAEATNMSAAQVK---KCLEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRF 304
+++ E T ++ QVK K + +G A A+ ++++ NLRLV+ + KKY G +F
Sbjct: 344 IKIEEETGLTIEQVKDINKRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQF 400
Query: 305 QDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSI 363
DL Q G GL+ A+D+FE +R ++ STY +WIR AI RS+ + T R+P +
Sbjct: 401 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM----- 455
Query: 364 MQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE 423
++ ++ R ++L E+ R PT EE+ + + I ++ R+V+K +K +S+ + G +
Sbjct: 456 IETINKLNRISRQMLQEIGREPTPEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDD 515
Query: 424 ----EFINGIT---DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGD 476
+FI T +D +E+ LR A DVL L +E+ V+R RFG+D D
Sbjct: 516 SHLGDFIEDTTLELPLDSATSES------LRSATHDVLSGLTAREAKVLRMRFGIDMNTD 569
Query: 477 RTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
TL E+ +++RE +R+ E K L KL+HP+R + LR +
Sbjct: 570 HTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 610
>sp|P0A2E3|RPOD_SALTY RNA polymerase sigma factor RpoD OS=Salmonella typhimurium (strain
LT2 / SGSC1412 / ATCC 700720) GN=rpoD PE=3 SV=1
Length = 615
Score = 140 bits (354), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 92/280 (32%), Positives = 155/280 (55%), Gaps = 29/280 (10%)
Query: 253 ELAEATNMSAAQVKKC---LEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQ 305
++ E T ++ QVK + +G A A+ ++++ NLRLV+ + KKY G +F
Sbjct: 348 QIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFL 404
Query: 306 DLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIM 364
DL Q G GL+ A+D+FE +R ++ STY +WIR AI RS+ + T R+P + +
Sbjct: 405 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM-----I 459
Query: 365 QVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE- 423
+ ++ R ++L E+ R PT EE+ + + + ++ R+V+K +K +S+ + G ++
Sbjct: 460 ETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 519
Query: 424 ---EFINGIT---DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 477
+FI T +D E+ LR A DVL L +E+ V+R RFG+D D
Sbjct: 520 HLGDFIEDTTLELPLDSATTES------LRAATHDVLAGLTAREAKVLRMRFGIDMNTDH 573
Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
TL E+ +++RE +R+ E K L KL+HP+R + LR +
Sbjct: 574 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 613
>sp|P0A2E4|RPOD_SALTI RNA polymerase sigma factor RpoD OS=Salmonella typhi GN=rpoD PE=3
SV=1
Length = 615
Score = 140 bits (354), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 92/280 (32%), Positives = 155/280 (55%), Gaps = 29/280 (10%)
Query: 253 ELAEATNMSAAQVKKC---LEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQ 305
++ E T ++ QVK + +G A A+ ++++ NLRLV+ + KKY G +F
Sbjct: 348 QIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFL 404
Query: 306 DLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIM 364
DL Q G GL+ A+D+FE +R ++ STY +WIR AI RS+ + T R+P + +
Sbjct: 405 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM-----I 459
Query: 365 QVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE- 423
+ ++ R ++L E+ R PT EE+ + + + ++ R+V+K +K +S+ + G ++
Sbjct: 460 ETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 519
Query: 424 ---EFINGIT---DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 477
+FI T +D E+ LR A DVL L +E+ V+R RFG+D D
Sbjct: 520 HLGDFIEDTTLELPLDSATTES------LRAATHDVLAGLTAREAKVLRMRFGIDMNTDH 573
Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
TL E+ +++RE +R+ E K L KL+HP+R + LR +
Sbjct: 574 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 613
>sp|P52328|RPSD2_BACSP RNA polymerase sigma factor RpoD OS=Bacillus sp. GN=sigA PE=3 SV=1
Length = 377
Score = 140 bits (354), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 100/305 (32%), Positives = 161/305 (52%), Gaps = 42/305 (13%)
Query: 225 FKLMQPMKVFVQVKEQLQKDLGREP-----TDVELAEATNMSAAQVKKCLEVGRAARNKL 279
K+ P+++++ K++GR P +VELA K+ + A+ +L
Sbjct: 102 IKINDPVRMYL-------KEIGRVPLLSADDEVELA----------KRIMNGDEEAKRRL 144
Query: 280 IKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIR 339
+ NLRLV+ + K+Y G F DL Q G GLI A+++F+ + F+ STY +WIR
Sbjct: 145 AEANLRLVVSIAKRYV---GRGMLFLDLIQEGNMGLIKAVEKFDHNKGFKFSTYATWWIR 201
Query: 340 HAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISP 398
AI R++ + T R+P +++ ++ R +LL EL R PT EEI + +S
Sbjct: 202 QAITRAIADQARTIRIP-----VHMVETINKLIRVSRQLLQELGREPTPEEIAAEMELSV 256
Query: 399 ERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA------LLRLALDD 452
E+ RE+MK ++ +SL + G + + D +E++ PA LL+ L+D
Sbjct: 257 EKVREIMKIAQEPVSLETPIGEEDDSHLG-----DFIEDQEALTPADAAAYELLKEQLED 311
Query: 453 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDY 512
VLD+L +E V+R RFGLD RTL E+ ++RE +R+ E K L KL+HP+R
Sbjct: 312 VLDTLTEREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKR 371
Query: 513 LRQHM 517
L+ +
Sbjct: 372 LKDFL 376
>sp|P52326|RPOD_PSEFL RNA polymerase sigma factor RpoD OS=Pseudomonas fluorescens GN=rpoD
PE=3 SV=1
Length = 615
Score = 140 bits (353), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 94/316 (29%), Positives = 168/316 (53%), Gaps = 28/316 (8%)
Query: 217 SSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEA-TNMSAAQVKKC---LEVG 272
+ + +W L + + + +LQ D+ R + E T + A++K + +G
Sbjct: 311 NEVDESWTDALAKGKSKYAEAIARLQPDIIRCQQKLTALEVETGLKIAEIKDINRRMSIG 370
Query: 273 RA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRF 328
A A+ ++++ NLRLV+ + KKY G +F DL Q G GL+ A+D+FE +R +
Sbjct: 371 EAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGY 427
Query: 329 RLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTD 387
+ STY +WIR AI RS+ + T R+P +++ ++ R ++L E+ R PT
Sbjct: 428 KFSTYATWWIRQAITRSIADQARTIRIP-----VHMIETINKLNRISRQMLQEMGREPTP 482
Query: 388 EEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQP---- 443
EE+ + + + ++ R+V+K +K +S+ + G ++ + D +E+ + P
Sbjct: 483 EELGERMEMPEDKIRKVLKIAKEPISMETPIGDDEDSHLG-----DFIEDSTMQSPIDVA 537
Query: 444 --ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGL 501
L+ A +VL L +E+ V+R RFG+D D TL E+ +++RE +R+ E K L
Sbjct: 538 TVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 597
Query: 502 MKLKHPTRVDYLRQHM 517
KL+HPTR ++LR +
Sbjct: 598 RKLRHPTRSEHLRSFL 613
>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 = 140 bits (353), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 91/258 (35%), Positives = 146/258 (56%), Gaps = 20/258 (7%)
Query: 267 KCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKR 326
K E + A+ +L + NLRLV+ + K+Y G +F DL Q G GL+ A+++F+ ++
Sbjct: 123 KIEEGDQEAKQRLAEANLRLVVSIAKRYV---GRGMQFLDLIQEGNMGLMKAVEKFDYRK 179
Query: 327 RFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVP 385
F+ STY +WIR AI R++ + T R+P + T +R IQR +LL +L R P
Sbjct: 180 GFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR--IQR---QLLQDLGREP 234
Query: 386 TDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA- 444
T EEI +++ E+ RE++K ++ +SL + G + + D +E+++ PA
Sbjct: 235 TPEEIGAEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHLG-----DFIEDQDATSPAE 289
Query: 445 -----LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499
LL+ L+DVLD+L +E V+R RFGLD RTL E+ ++RE +R+ E K
Sbjct: 290 HAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAK 349
Query: 500 GLMKLKHPTRVDYLRQHM 517
L KL+HP+R L+ +
Sbjct: 350 ALRKLRHPSRSKQLKDFL 367
>sp|P00579|RPOD_ECOLI RNA polymerase sigma factor RpoD OS=Escherichia coli (strain K12)
GN=rpoD PE=1 SV=2
Length = 613
Score = 140 bits (353), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 92/280 (32%), Positives = 155/280 (55%), Gaps = 29/280 (10%)
Query: 253 ELAEATNMSAAQVKKC---LEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQ 305
++ E T ++ QVK + +G A A+ ++++ NLRLV+ + KKY G +F
Sbjct: 346 QIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN---RGLQFL 402
Query: 306 DLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIM 364
DL Q G GL+ A+D+FE +R ++ STY +WIR AI RS+ + T R+P + +
Sbjct: 403 DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM-----I 457
Query: 365 QVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE- 423
+ ++ R ++L E+ R PT EE+ + + + ++ R+V+K +K +S+ + G ++
Sbjct: 458 ETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS 517
Query: 424 ---EFINGIT---DVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDR 477
+FI T +D E+ LR A DVL L +E+ V+R RFG+D D
Sbjct: 518 HLGDFIEDTTLELPLDSATTES------LRAATHDVLAGLTAREAKVLRMRFGIDMNTDY 571
Query: 478 TLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
TL E+ +++RE +R+ E K L KL+HP+R + LR +
Sbjct: 572 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFL 611
>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 = 140 bits (353), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 105/331 (31%), Positives = 173/331 (52%), Gaps = 42/331 (12%)
Query: 192 LVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGRE--- 248
LV+E + S DL M +PP + K+ P+++++ K++GR
Sbjct: 80 LVKEETESFDLTD-----MSVPPGV---------KINDPVRMYL-------KEIGRVDLL 118
Query: 249 PTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLC 308
D E+A A + A ++ A+ +L + NLRLV+ + K+Y G F DL
Sbjct: 119 TADEEIALAKRIEAGDIE--------AKGRLAEANLRLVVSIAKRYV---GRGMLFLDLI 167
Query: 309 QAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVR 367
Q G GL+ A+++F+ + F+ STY +WIR AI R++ + T R+P + T +R
Sbjct: 168 QEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR 227
Query: 368 GEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 427
+QR+ LL +L R P+ EEI + +++ E+ RE++K ++ +SL + G + +
Sbjct: 228 --VQRS---LLQDLGRDPSPEEIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHLG 282
Query: 428 G-ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNL 486
I D D + LL+ L+DVLD+L +E V+R RFGLD RTL E+
Sbjct: 283 DFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRVF 342
Query: 487 NISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++RE +R+ E K L KL+HP+R L+ +
Sbjct: 343 GVTRERIRQIEAKALRKLRHPSRSKQLKDFL 373
>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 = 140 bits (352), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 105/331 (31%), Positives = 173/331 (52%), Gaps = 42/331 (12%)
Query: 192 LVREYSYSTDLVSLDWKKMKIPPVLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGRE--- 248
LV+E + S DL M +PP + K+ P+++++ K++GR
Sbjct: 80 LVKEETESFDLTD-----MSVPPGV---------KINDPVRMYL-------KEIGRVDLL 118
Query: 249 PTDVELAEATNMSAAQVKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLC 308
D E+A A + A ++ A+ +L + NLRLV+ + K+Y G F DL
Sbjct: 119 TADEEIALAKRIEAGDIE--------AKGRLAEANLRLVVSIAKRYV---GRGMLFLDLI 167
Query: 309 QAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVR 367
Q G GL+ A+++F+ + F+ STY +WIR AI R++ + T R+P + T +R
Sbjct: 168 QEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR 227
Query: 368 GEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 427
+QR+ LL +L R P+ EEI + +++ E+ RE++K ++ +SL + G + +
Sbjct: 228 --VQRS---LLQDLGRDPSPEEIGEEMDLPTEKVREILKIAQEPVSLETPIGEEDDSHLG 282
Query: 428 G-ITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNL 486
I D D + LL+ L+DVLD+L +E V+R RFGLD RTL E+
Sbjct: 283 DFIEDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGRVF 342
Query: 487 NISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++RE +R+ E K L KL+HP+R L+ +
Sbjct: 343 GVTRERIRQIEAKALRKLRHPSRSKQLKDFL 373
>sp|P0CZ15|RPOD_RHOCA RNA polymerase sigma factor rpoD OS=Rhodobacter capsulatus GN=rpoD
PE=2 SV=1
Length = 674
Score = 140 bits (352), Expect = 3e-32, Method: Compositional matrix adjust.
Identities = 101/305 (33%), Positives = 165/305 (54%), Gaps = 31/305 (10%)
Query: 222 TWLFKL-MQPMKVFVQVKEQLQ---KDLGREPTDVELAEATNMS-----AAQVKKCLEVG 272
TW+ ++ +P + +V + E+ + +DL E V ++S QV+K +
Sbjct: 374 TWMDRMSAKPARAWVTLFEKSRHKVEDLRHEMAQVGQYVGVDISEFRRIVNQVQKGEKEA 433
Query: 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLST 332
R A+ ++++ NLRLV+ + KKY G +F DL Q G GL+ A+D+FE +R ++ ST
Sbjct: 434 RQAKKEMVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFST 490
Query: 333 YGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEII 391
Y +WIR AI RS+ + T R+P +++ ++ R ++L E+ R PT EE+
Sbjct: 491 YATWWIRQAITRSIADQARTIRIP-----VHMIETINKLVRTGRQMLHEIGREPTPEELA 545
Query: 392 QGVNISPERYREVMKASKPILSLHSRHGVTQE----EFI---NGITDVDGVENENQRQPA 444
+ + + E+ R+VMK +K +SL + G ++ +FI N I +D EN
Sbjct: 546 EKLQMPLEKVRKVMKIAKEPISLETPIGHEEDSQLGDFIEDKNAILPLDSAIQEN----- 600
Query: 445 LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKL 504
L+ VL SL P+E V+R RFG+ D TL E+ +++RE +R+ E K L KL
Sbjct: 601 -LKETTTRVLPSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 659
Query: 505 KHPTR 509
KHP+R
Sbjct: 660 KHPSR 664
>sp|P32001|RPOD_BUCAP RNA polymerase sigma factor RpoD OS=Buchnera aphidicola subsp.
Schizaphis graminum (strain Sg) GN=rpoD PE=3 SV=1
Length = 617
Score = 139 bits (351), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 103/318 (32%), Positives = 171/318 (53%), Gaps = 45/318 (14%)
Query: 218 STEHTWLFKLMQ-PMKVFVQVKE--QLQKDLGREPTDVELAEATNMSAAQVK---KCLEV 271
S+ +W KL + KVF +K+ Q++K+ G ++ QVK K + +
Sbjct: 325 SSNQSWSKKLEEIKEKVFSSMKKLKQIEKETG-------------LTIEQVKDINKRMSI 371
Query: 272 GRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRR 327
G A A+ ++++ NLRLV+ + KKY G +F DL Q G GL+ A+D+FE +R
Sbjct: 372 GEAKAKRAKKEMVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRG 428
Query: 328 FRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPT 386
++ STY +WIR AI RS+ + T R+P + ++ ++ R ++L E+ R PT
Sbjct: 429 YKFSTYATWWIRQAITRSIADQARTIRIPVHM-----IETINKLNRISRQMLQEIGREPT 483
Query: 387 DEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE----EFINGIT---DVDGVENEN 439
EE+ + + I ++ R+V+K +K +S+ + G + +FI T +D +E+
Sbjct: 484 PEELSEKMLIPEDKIRKVLKIAKEPISMETPIGDDDDSHLGDFIEDTTLELPLDSATSES 543
Query: 440 QRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVK 499
LR A DVL L +E+ V+R RFG+D D TL E+ +++RE +R+ E K
Sbjct: 544 ------LRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 597
Query: 500 GLMKLKHPTRVDYLRQHM 517
L KL+HP+R + LR +
Sbjct: 598 ALRKLRHPSRSEVLRSFL 615
>sp|Q9LD95|SIGF_ARATH RNA polymerase sigma factor sigF, chloroplastic OS=Arabidopsis
thaliana GN=SIGF PE=1 SV=1
Length = 547
Score = 139 bits (351), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 94/294 (31%), Positives = 158/294 (53%), Gaps = 10/294 (3%)
Query: 215 VLSSTEHTWLFKLMQPMKVFVQVKEQLQKDLGREPTDVELAEATNMSAAQVKKCLEVGRA 274
+L++ E L +Q + +VK +L+ G EPT E AEA +S+ +K + GR+
Sbjct: 247 LLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRS 306
Query: 275 ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYG 334
+R KLI NLRLV+ + K+Y G FQDL Q G GL+ ++++F+P+ R +TY
Sbjct: 307 SREKLITANLRLVVHIAKQYQN---RGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYA 363
Query: 335 LFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQG 393
+WIR +I +S+ +S T R+P ++ + G++ A+ + E P+ EE+
Sbjct: 364 YWWIRQSIRKSIFQNSRTIRLP-----ENVYMLLGKVSEARKTCVQEGNYRPSKEELAGH 418
Query: 394 VNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVENENQR-QPALLRLALDD 452
V +S E+ +++ ++ LS+ Q+ IT G+E L+R + +
Sbjct: 419 VGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDSGIETPTMSVGKQLMRNHVRN 478
Query: 453 VLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKH 506
+L+ L PKE +I+ RFG+DG R+L EI +S+E VR+ E + L +LK
Sbjct: 479 LLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLKQ 532
>sp|P0A602|RPOD_MYCTU RNA polymerase sigma factor RpoD OS=Mycobacterium tuberculosis
GN=rpoD PE=1 SV=1
Length = 528
Score = 139 bits (351), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 95/272 (34%), Positives = 151/272 (55%), Gaps = 14/272 (5%)
Query: 252 VELAE-ATNMSAAQVKKCLEV---GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDL 307
EL+E + AAQ + + + G A+N L++ NLRLV+ + K+Y G F DL
Sbjct: 264 TELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYT---GRGMAFLDL 320
Query: 308 CQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQV 366
Q G GLI A+++F+ + ++ STY +WIR AI R+M + T R+P + ++
Sbjct: 321 IQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHM--VEVINK 378
Query: 367 RGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EF 425
G IQR ELL +L R PT EE+ + ++I+PE+ E+ + ++ +SL G + +
Sbjct: 379 LGRIQR---ELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQL 435
Query: 426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGN 485
+ I D + V + LL+ L VLD+L +E+ V+R RFGL RTL EI
Sbjct: 436 GDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQV 495
Query: 486 LNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++RE +R+ E K + KL+HP+R LR ++
Sbjct: 496 YGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 527
>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 = 139 bits (351), Expect = 4e-32, Method: Compositional matrix adjust.
Identities = 95/272 (34%), Positives = 151/272 (55%), Gaps = 14/272 (5%)
Query: 252 VELAE-ATNMSAAQVKKCLEV---GRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDL 307
EL+E + AAQ + + + G A+N L++ NLRLV+ + K+Y G F DL
Sbjct: 264 TELSERGEKLPAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYT---GRGMAFLDL 320
Query: 308 CQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQV 366
Q G GLI A+++F+ + ++ STY +WIR AI R+M + T R+P + ++
Sbjct: 321 IQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHM--VEVINK 378
Query: 367 RGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE-EF 425
G IQR ELL +L R PT EE+ + ++I+PE+ E+ + ++ +SL G + +
Sbjct: 379 LGRIQR---ELLQDLGREPTPEELAKEMDITPEKVLEIQQYAREPISLDQTIGDEGDSQL 435
Query: 426 INGITDVDGVENENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGN 485
+ I D + V + LL+ L VLD+L +E+ V+R RFGL RTL EI
Sbjct: 436 GDFIEDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQV 495
Query: 486 LNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++RE +R+ E K + KL+HP+R LR ++
Sbjct: 496 YGVTRERIRQIESKTMSKLRHPSRSQVLRDYL 527
>sp|Q8CP24|RPOD_STAES RNA polymerase sigma factor RpoD OS=Staphylococcus epidermidis
(strain ATCC 12228) GN=rpoD PE=3 SV=1
Length = 368
Score = 139 bits (350), Expect = 5e-32, Method: Compositional matrix adjust.
Identities = 95/272 (34%), Positives = 153/272 (56%), Gaps = 25/272 (9%)
Query: 258 TNMSAAQ----VKKCLEVG-RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV 312
N+ +AQ + K +E G A+++L + NLRLV+ + K+Y G F DL Q G
Sbjct: 109 VNLLSAQEEIELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGN 165
Query: 313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQ 371
GLI A+++F+ + F+ STY +WIR AI R++ + T R+P + T +R +Q
Sbjct: 166 MGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR--VQ 223
Query: 372 RAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD 431
R +LL +L R P EEI + +++ PE+ RE++K ++ +SL + G + +
Sbjct: 224 R---QLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHLG---- 276
Query: 432 VDGVENENQRQPA------LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGN 485
D +E++ + P+ LL+ L+DVLD+L +E V+R RFGLD RTL E+
Sbjct: 277 -DFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335
Query: 486 LNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++RE +R+ E K L KL+HP+R L+ M
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFM 367
>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 = 139 bits (350), Expect = 5e-32, Method: Compositional matrix adjust.
Identities = 95/272 (34%), Positives = 153/272 (56%), Gaps = 25/272 (9%)
Query: 258 TNMSAAQ----VKKCLEVG-RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV 312
N+ +AQ + K +E G A+++L + NLRLV+ + K+Y G F DL Q G
Sbjct: 109 VNLLSAQEEIELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGN 165
Query: 313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQ 371
GLI A+++F+ + F+ STY +WIR AI R++ + T R+P + T +R +Q
Sbjct: 166 MGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR--VQ 223
Query: 372 RAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD 431
R +LL +L R P EEI + +++ PE+ RE++K ++ +SL + G + +
Sbjct: 224 R---QLLQDLGRDPAPEEIGEEMDLPPEKVREILKIAQEPVSLETPIGEEDDSHLG---- 276
Query: 432 VDGVENENQRQPA------LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGN 485
D +E++ + P+ LL+ L+DVLD+L +E V+R RFGLD RTL E+
Sbjct: 277 -DFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335
Query: 486 LNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++RE +R+ E K L KL+HP+R L+ M
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFM 367
>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 = 139 bits (350), Expect = 5e-32, Method: Compositional matrix adjust.
Identities = 87/263 (33%), Positives = 150/263 (57%), Gaps = 11/263 (4%)
Query: 258 TNMSAAQVKKCLEVGR-AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLI 316
TN ++ +E G A+ +L + NLRLV+ + K+Y G +F DL Q G GL+
Sbjct: 115 TNEEEKELAIAVENGDLEAKQRLAEANLRLVVSIAKRYV---GRGMQFLDLIQEGNMGLM 171
Query: 317 TAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKL 375
A+D+F+ + F+ STY +WIR AI R++ + T R+P +++ ++ R +
Sbjct: 172 KAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIP-----VHMVETINKLVREQR 226
Query: 376 ELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV 435
LL EL + PT E+I + ++++P++ RE++K ++ +SL + G + + + + +
Sbjct: 227 NLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVI 286
Query: 436 ENE-NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVR 494
EN + +LR LD+VLD+L +E V+R RFGLD RTL ++ +++RE +R
Sbjct: 287 ENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFDVTRERIR 346
Query: 495 KHEVKGLMKLKHPTRVDYLRQHM 517
+ E K L KL+HP+R LR +
Sbjct: 347 QIEAKALRKLRHPSRSKQLRDFV 369
>sp|Q8P4H2|RPOD_XANCP RNA polymerase sigma factor RpoD OS=Xanthomonas campestris pv.
campestris (strain ATCC 33913 / NCPPB 528 / LMG 568)
GN=rpoD PE=3 SV=1
Length = 624
Score = 139 bits (350), Expect = 5e-32, Method: Compositional matrix adjust.
Identities = 91/295 (30%), Positives = 162/295 (54%), Gaps = 30/295 (10%)
Query: 237 VKEQLQKDLGREPTDVELAEATNMSAAQVK---KCLEVGRA----ARNKLIKHNLRLVLF 289
VK+Q+ + + +E+ +A ++ A++K + + G A A+ ++++ NLRLV+
Sbjct: 343 VKDQI---VSEQQGSIEMEKANYLTLAEIKDISRAMAYGEAKARKAKKEMVEANLRLVIS 399
Query: 290 VIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349
+ KKY G +F DL Q G GL+ A+D+FE +R ++ STY +WIR AI RS+
Sbjct: 400 IAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 456
Query: 350 SFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS 408
+ T R+P +++ ++ R ++L + R T EE+ + +++ ++ R+VMK +
Sbjct: 457 ARTIRIP-----VHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIA 511
Query: 409 KPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA------LLRLALDDVLDSLKPKES 462
K +S+ + G ++ + D +E+ N P L + DVL L P+E+
Sbjct: 512 KEPISMETPIGDDEDSHLG-----DFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREA 566
Query: 463 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
V+R RFG+D D TL E+ +++RE +R+ E K L KL+HP+R + LR +
Sbjct: 567 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFL 621
>sp|P52324|RPOD_CAUCR RNA polymerase sigma factor RpoD OS=Caulobacter crescentus (strain
ATCC 19089 / CB15) GN=rpoD PE=3 SV=1
Length = 652
Score = 139 bits (350), Expect = 6e-32, Method: Compositional matrix adjust.
Identities = 92/261 (35%), Positives = 143/261 (54%), Gaps = 22/261 (8%)
Query: 265 VKKCLEVGRAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEP 324
V+K R A+ ++++ NLRLV+ + KKY G +F DL Q G GL+ A+D+FE
Sbjct: 404 VQKGEREARQAKKEMVEANLRLVISIAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEY 460
Query: 325 KRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKR 383
+R ++ STY +WIR AI RS+ + T R+P +++ +I R ++L E+ R
Sbjct: 461 RRGYKFSTYATWWIRQAITRSIADQARTIRIP-----VHMIETINKIVRTSRQMLHEIGR 515
Query: 384 VPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQE----EFI---NGITDVDGVE 436
PT EE+ + + + E+ R+V+K +K +SL + G ++ +FI N I +D
Sbjct: 516 EPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPIGDEEDSHLGDFIEDKNAILPIDAAI 575
Query: 437 NENQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKH 496
N LR VL SL P+E V+R RFG+ D TL E+ +++RE +R+
Sbjct: 576 QSN------LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQI 629
Query: 497 EVKGLMKLKHPTRVDYLRQHM 517
E K L KLKHP+R LR +
Sbjct: 630 EAKALRKLKHPSRSRKLRSFL 650
Score = 32.3 bits (72), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 194 REYSYSTDLVSLDWKKMKIPPVLSSTEHTWLF--KLMQPMKVFVQVKEQLQKDLGREPTD 251
R Y +ST + W + I ++ T +++ + V+ Q+ ++GREPT
Sbjct: 462 RGYKFST--YATWWIRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTP 519
Query: 252 VELAEATNMSAAQVKKCLEVGR 273
ELAE M +V+K L++ +
Sbjct: 520 EELAEKLAMPLEKVRKVLKIAK 541
>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 = 139 bits (349), Expect = 8e-32, Method: Compositional matrix adjust.
Identities = 84/245 (34%), Positives = 144/245 (58%), Gaps = 12/245 (4%)
Query: 273 RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLST 332
+ A+ KLI NLRLV+ + K+Y G FQDL Q G GL+ A+++F+ ++ ++ ST
Sbjct: 153 KKAKEKLITSNLRLVVSIAKRYM---GRGLSFQDLIQEGNIGLLKAVEKFDWRKGYKFST 209
Query: 333 YGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEII 391
Y +WIR AI R++ + T R+P +++ ++ R + E + P+ EE+
Sbjct: 210 YATWWIRQAITRAIADQARTIRIP-----VHMVETINKLNRLRREYYQKHGEEPSIEELA 264
Query: 392 QGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGVEN-ENQRQPALLRLAL 450
+ + PE+ +E+++A+K +SL S G ++ I D + + + + L+R L
Sbjct: 265 KMMGKPPEKIKEILEAAKETISLESPIGEDEDSSIEDFVADDSIASPKKEAMRMLMREEL 324
Query: 451 DDVLDSLKPKESLVIRQRFGL-DGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTR 509
+ VL +L P+E++V+R R+GL DGK +TL E+ N++RE +R+ EVK L KL+HP+R
Sbjct: 325 EKVLKTLSPREAMVLRMRYGLLDGK-PKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSR 383
Query: 510 VDYLR 514
YL+
Sbjct: 384 SKYLK 388
>sp|Q89B10|RPOD_BUCBP RNA polymerase sigma factor RpoD OS=Buchnera aphidicola subsp.
Baizongia pistaciae (strain Bp) GN=rpoD PE=3 SV=1
Length = 609
Score = 138 bits (348), Expect = 8e-32, Method: Compositional matrix adjust.
Identities = 93/276 (33%), Positives = 153/276 (55%), Gaps = 27/276 (9%)
Query: 256 EATNMSAAQVK---KCLEVGRA----ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLC 308
E T ++ QVK K + +G A A+ ++++ NLRLV+ + KKY G +F DL
Sbjct: 345 EETGLTIHQVKNINKRISLGEAKAKRAKKEMVEANLRLVISIAKKYTN---RGLQFLDLI 401
Query: 309 QAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVR 367
Q G GL+ A+D+FE +R ++ STY +WIR AI RS+ + T R+P + ++
Sbjct: 402 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM-----IETI 456
Query: 368 GEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 427
++ R ++L E+ R PT EE+ + + I ++ R+V+K +K +S+ + G + +
Sbjct: 457 NKLNRISRQILQEIGREPTPEELSERMLIPEDKIRKVLKIAKEPISMETPIGEDDDSHLG 516
Query: 428 GITDVDGVENENQRQP------ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGE 481
D +E+ N P A LR A +VL L +E+ V+R RFG+D D TL E
Sbjct: 517 -----DFLEDTNIELPLDSATSASLRSATKNVLSGLTTREAKVLRMRFGIDMNTDHTLEE 571
Query: 482 IAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
+ +++RE +R+ E K L KL+HP+R + LR +
Sbjct: 572 VGKQFDVTRERIRQIEAKALRKLRHPSRSEILRSFL 607
>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 = 138 bits (347), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 86/263 (32%), Positives = 149/263 (56%), Gaps = 11/263 (4%)
Query: 258 TNMSAAQVKKCLEVGR-AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLI 316
TN ++ +E G A+ +L + NLRLV+ + K+Y G +F DL Q G GL+
Sbjct: 113 TNEEEKELALAVEAGDIEAKQRLAEANLRLVVSIAKRYV---GRGMQFLDLIQEGNMGLM 169
Query: 317 TAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKL 375
A+D+F+ + F+ STY +WIR AI R++ + T R+P +++ ++ R +
Sbjct: 170 KAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIP-----VHMVETINKLVREQR 224
Query: 376 ELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV 435
LL EL + PT E+I + ++++P++ RE++K ++ +SL + G + + + + +
Sbjct: 225 NLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVI 284
Query: 436 ENE-NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVR 494
EN + +LR LD++LD+L +E V+R RFGLD RTL ++ N++RE +R
Sbjct: 285 ENPVDYTTRIVLREQLDEILDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIR 344
Query: 495 KHEVKGLMKLKHPTRVDYLRQHM 517
+ E K L KL+ P+R LR +
Sbjct: 345 QIEAKALRKLRQPSRSKPLRDFI 367
>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 = 138 bits (347), Expect = 1e-31, Method: Compositional matrix adjust.
Identities = 86/263 (32%), Positives = 149/263 (56%), Gaps = 11/263 (4%)
Query: 258 TNMSAAQVKKCLEVGR-AARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGVKGLI 316
TN ++ +E G A+ +L + NLRLV+ + K+Y G +F DL Q G GL+
Sbjct: 113 TNEEEKELALAVEAGDIEAKQRLAEANLRLVVSIAKRYV---GRGMQFLDLIQEGNMGLM 169
Query: 317 TAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQRAKL 375
A+D+F+ + F+ STY +WIR AI R++ + T R+P +++ ++ R +
Sbjct: 170 KAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIP-----VHMVETINKLVREQR 224
Query: 376 ELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITDVDGV 435
LL EL + PT E+I + ++++P++ RE++K ++ +SL + G + + + + +
Sbjct: 225 NLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVI 284
Query: 436 ENE-NQRQPALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGNLNISREMVR 494
EN + +LR LD++LD+L +E V+R RFGLD RTL ++ N++RE +R
Sbjct: 285 ENPVDYTTRIVLREQLDEILDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIR 344
Query: 495 KHEVKGLMKLKHPTRVDYLRQHM 517
+ E K L KL+ P+R LR +
Sbjct: 345 QIEAKALRKLRQPSRSKPLRDFI 367
>sp|P43766|RPOD_HAEIN RNA polymerase sigma factor RpoD OS=Haemophilus influenzae (strain
ATCC 51907 / DSM 11121 / KW20 / Rd) GN=rpoD PE=3 SV=1
Length = 629
Score = 137 bits (346), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 88/276 (31%), Positives = 151/276 (54%), Gaps = 27/276 (9%)
Query: 256 EATNMSAAQVKK-CLEVGRA------ARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLC 308
E T ++ Q++ C V R A+ ++++ NLRLV+ + KKY G +F DL
Sbjct: 365 ENTKLTITQMRDICDAVARGEQKARRAKKEMVEANLRLVISIAKKYTN---RGLQFLDLI 421
Query: 309 QAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVR 367
Q G GL+ A+D+FE +R ++ STY +WIR AI RS+ + T R+P +++
Sbjct: 422 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIP-----VHMIETI 476
Query: 368 GEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFIN 427
++ R +LL E+ R T EE+ + + + ++ R+V+K +K +S+ + G + +
Sbjct: 477 NKLNRISRQLLQEMGREATPEELAERMGMPEDKIRKVLKIAKEPISMETPIGDDDDSHLG 536
Query: 428 GITDVDGVENENQRQP------ALLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGE 481
D +E+ P L++A +VL+ L P+E+ V+R RFG+D D TL E
Sbjct: 537 -----DFIEDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEE 591
Query: 482 IAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
+ +++RE +R+ E K L KL+HP+R + LR +
Sbjct: 592 VGKQFDVTRERIRQIEAKALRKLRHPSRSETLRSFL 627
>sp|Q8PG33|RPOD_XANAC RNA polymerase sigma factor RpoD OS=Xanthomonas axonopodis pv.
citri (strain 306) GN=rpoD PE=3 SV=1
Length = 625
Score = 137 bits (346), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 90/295 (30%), Positives = 161/295 (54%), Gaps = 30/295 (10%)
Query: 237 VKEQLQKDLGREPTDVELAEATNMSAAQVK---KCLEVGRA----ARNKLIKHNLRLVLF 289
VK+Q+ + + +E+ +A ++ ++K + + G A A+ ++++ NLRLV+
Sbjct: 344 VKDQI---ISEQQGSIEMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVIS 400
Query: 290 VIKKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVS 349
+ KKY G +F DL Q G GL+ A+D+FE +R ++ STY +WIR AI RS+
Sbjct: 401 IAKKYTN---RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 457
Query: 350 SFT-RVPFGLESTSIMQVRGEIQRAKLELLFELKRVPTDEEIIQGVNISPERYREVMKAS 408
+ T R+P +++ ++ R ++L + R T EE+ + +++ ++ R+VMK +
Sbjct: 458 ARTIRIP-----VHMIETINKLNRISRQMLQQFGREATPEELAKEMDMPEDKIRKVMKIA 512
Query: 409 KPILSLHSRHGVTQEEFINGITDVDGVENENQRQPA------LLRLALDDVLDSLKPKES 462
K +S+ + G ++ + D +E+ N P L + DVL L P+E+
Sbjct: 513 KEPISMETPIGDDEDSHLG-----DFIEDTNVESPIDNTTNINLSETVRDVLAGLTPREA 567
Query: 463 LVIRQRFGLDGKGDRTLGEIAGNLNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
V+R RFG+D D TL E+ +++RE +R+ E K L KL+HP+R + LR +
Sbjct: 568 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEQLRSFL 622
>sp|Q99TT5|RPOD_STAAN RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
N315) GN=rpoD PE=1 SV=1
Length = 368
Score = 137 bits (345), Expect = 2e-31, Method: Compositional matrix adjust.
Identities = 95/272 (34%), Positives = 152/272 (55%), Gaps = 25/272 (9%)
Query: 258 TNMSAAQ----VKKCLEVG-RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV 312
N+ +AQ + K +E G A+++L + NLRLV+ + K+Y G F DL Q G
Sbjct: 109 VNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGN 165
Query: 313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQ 371
GLI A+++F+ + F+ STY +WIR AI R++ + T R+P + T +R +Q
Sbjct: 166 MGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR--VQ 223
Query: 372 RAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD 431
R +LL +L R P EEI + +++ E+ REV+K ++ +SL + G + +
Sbjct: 224 R---QLLQDLGRDPAPEEIGEEMDLPAEKVREVLKIAQEPVSLETPIGEEDDSHLG---- 276
Query: 432 VDGVENENQRQPA------LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGN 485
D +E++ + P+ LL+ L+DVLD+L +E V+R RFGLD RTL E+
Sbjct: 277 -DFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335
Query: 486 LNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++RE +R+ E K L KL+HP+R L+ M
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFM 367
>sp|P0A0I9|RPOD_STAAW RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
MW2) GN=rpoD PE=3 SV=1
Length = 368
Score = 136 bits (343), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 94/272 (34%), Positives = 152/272 (55%), Gaps = 25/272 (9%)
Query: 258 TNMSAAQ----VKKCLEVG-RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV 312
N+ +AQ + K +E G A+++L + NLRLV+ + K+Y G F DL Q G
Sbjct: 109 VNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGN 165
Query: 313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQ 371
GLI A+++F+ + F+ STY +WIR AI R++ + T R+P + T +R +Q
Sbjct: 166 MGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR--VQ 223
Query: 372 RAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD 431
R +LL +L R P EEI + +++ E+ RE++K ++ +SL + G + +
Sbjct: 224 R---QLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLG---- 276
Query: 432 VDGVENENQRQPA------LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGN 485
D +E++ + P+ LL+ L+DVLD+L +E V+R RFGLD RTL E+
Sbjct: 277 -DFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335
Query: 486 LNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++RE +R+ E K L KL+HP+R L+ M
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFM 367
>sp|Q6G905|RPOD_STAAS RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
MSSA476) GN=rpoD PE=3 SV=1
Length = 368
Score = 136 bits (343), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 94/272 (34%), Positives = 152/272 (55%), Gaps = 25/272 (9%)
Query: 258 TNMSAAQ----VKKCLEVG-RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV 312
N+ +AQ + K +E G A+++L + NLRLV+ + K+Y G F DL Q G
Sbjct: 109 VNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGN 165
Query: 313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQ 371
GLI A+++F+ + F+ STY +WIR AI R++ + T R+P + T +R +Q
Sbjct: 166 MGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR--VQ 223
Query: 372 RAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD 431
R +LL +L R P EEI + +++ E+ RE++K ++ +SL + G + +
Sbjct: 224 R---QLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLG---- 276
Query: 432 VDGVENENQRQPA------LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGN 485
D +E++ + P+ LL+ L+DVLD+L +E V+R RFGLD RTL E+
Sbjct: 277 -DFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335
Query: 486 LNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++RE +R+ E K L KL+HP+R L+ M
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFM 367
>sp|Q6GGD8|RPOD_STAAR RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
MRSA252) GN=rpoD PE=3 SV=1
Length = 368
Score = 136 bits (343), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 94/272 (34%), Positives = 152/272 (55%), Gaps = 25/272 (9%)
Query: 258 TNMSAAQ----VKKCLEVG-RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV 312
N+ +AQ + K +E G A+++L + NLRLV+ + K+Y G F DL Q G
Sbjct: 109 VNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGN 165
Query: 313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQ 371
GLI A+++F+ + F+ STY +WIR AI R++ + T R+P + T +R +Q
Sbjct: 166 MGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR--VQ 223
Query: 372 RAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD 431
R +LL +L R P EEI + +++ E+ RE++K ++ +SL + G + +
Sbjct: 224 R---QLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLG---- 276
Query: 432 VDGVENENQRQPA------LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGN 485
D +E++ + P+ LL+ L+DVLD+L +E V+R RFGLD RTL E+
Sbjct: 277 -DFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335
Query: 486 LNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++RE +R+ E K L KL+HP+R L+ M
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFM 367
>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 = 136 bits (343), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 94/272 (34%), Positives = 152/272 (55%), Gaps = 25/272 (9%)
Query: 258 TNMSAAQ----VKKCLEVG-RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV 312
N+ +AQ + K +E G A+++L + NLRLV+ + K+Y G F DL Q G
Sbjct: 109 VNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGN 165
Query: 313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQ 371
GLI A+++F+ + F+ STY +WIR AI R++ + T R+P + T +R +Q
Sbjct: 166 MGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR--VQ 223
Query: 372 RAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD 431
R +LL +L R P EEI + +++ E+ RE++K ++ +SL + G + +
Sbjct: 224 R---QLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLG---- 276
Query: 432 VDGVENENQRQPA------LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGN 485
D +E++ + P+ LL+ L+DVLD+L +E V+R RFGLD RTL E+
Sbjct: 277 -DFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335
Query: 486 LNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++RE +R+ E K L KL+HP+R L+ M
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFM 367
>sp|Q5HFJ9|RPOD_STAAC RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
COL) GN=rpoD PE=3 SV=1
Length = 368
Score = 136 bits (343), Expect = 3e-31, Method: Compositional matrix adjust.
Identities = 94/272 (34%), Positives = 152/272 (55%), Gaps = 25/272 (9%)
Query: 258 TNMSAAQ----VKKCLEVG-RAARNKLIKHNLRLVLFVIKKYFQDFANGPRFQDLCQAGV 312
N+ +AQ + K +E G A+++L + NLRLV+ + K+Y G F DL Q G
Sbjct: 109 VNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYV---GRGMLFLDLIQEGN 165
Query: 313 KGLITAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTVSSFT-RVPFGLESTSIMQVRGEIQ 371
GLI A+++F+ + F+ STY +WIR AI R++ + T R+P + T +R +Q
Sbjct: 166 MGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIR--VQ 223
Query: 372 RAKLELLFELKRVPTDEEIIQGVNISPERYREVMKASKPILSLHSRHGVTQEEFINGITD 431
R +LL +L R P EEI + +++ E+ RE++K ++ +SL + G + +
Sbjct: 224 R---QLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLG---- 276
Query: 432 VDGVENENQRQPA------LLRLALDDVLDSLKPKESLVIRQRFGLDGKGDRTLGEIAGN 485
D +E++ + P+ LL+ L+DVLD+L +E V+R RFGLD RTL E+
Sbjct: 277 -DFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKV 335
Query: 486 LNISREMVRKHEVKGLMKLKHPTRVDYLRQHM 517
++RE +R+ E K L KL+HP+R L+ M
Sbjct: 336 FGVTRERIRQIEAKALRKLRHPSRSKRLKDFM 367
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
0.317 0.134 0.373
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 183,376,969
Number of Sequences: 539616
Number of extensions: 7738013
Number of successful extensions: 28558
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 130
Number of HSP's successfully gapped in prelim test: 167
Number of HSP's that attempted gapping in prelim test: 27794
Number of HSP's gapped (non-prelim): 553
length of query: 518
length of database: 191,569,459
effective HSP length: 122
effective length of query: 396
effective length of database: 125,736,307
effective search space: 49791577572
effective search space used: 49791577572
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 64 (29.3 bits)