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= 012710
(458 letters)
Database: swissprot
539,616 sequences; 191,569,459 total letters
Searching..................................................done
>sp|O22056|SIGB_ARATH RNA polymerase sigma factor sigB OS=Arabidopsis thaliana GN=SIGB
PE=2 SV=2
Length = 572
Score = 437 bits (1124), Expect = e-122, Method: Compositional matrix adjust.
Identities = 259/428 (60%), Positives = 311/428 (72%), Gaps = 26/428 (6%)
Query: 25 SCLLPQFKCQPDTFSIHFRTLHNHQHHSSHPSKSKEPICFRTHCVLSTTSPSTSTAMTTV 84
SCLLPQFKC PD+FSIHFRT P +K + F+ C +ST SP+ +T++
Sbjct: 3 SCLLPQFKCPPDSFSIHFRT------SFCAPKHNKGSVFFQPQCAVST-SPAL---LTSM 52
Query: 85 LDVEKLRLPSLEAHSNAVAANRQWTYFGAVGPSTEENLGTSLATETL-TSDEAVIAAASA 143
LDV KLRLPS + S+++ ++RQWTY GPSTE +LA+ETL TSDEAV+ AA+A
Sbjct: 53 LDVAKLRLPSFDTDSDSLISDRQWTYTRPDGPSTEAKYLEALASETLLTSDEAVVVAAAA 112
Query: 144 EAVALARAAVKVAKDAALMVNHHNSAKPKSKPAISSSADTNTSMWAQLTERERASIIG-- 201
EAVALARAAVKVAKDA L N +N+ ++SS S W Q TE+ERA I+G
Sbjct: 113 EAVALARAAVKVAKDATLFKNSNNTN------LLTSSTADKRSKWDQFTEKERAGILGHL 166
Query: 202 ---DSVIVEAAPEEEYSEQQPLNKSADLEPTHEELKLLEEQV-SQSIAVRSRRQTERKAR 257
D+ IV S ++ + DLE +E L E+ S S+AVRS RQTERKAR
Sbjct: 167 AVSDNGIVSDKITASASNKESI---GDLESEKQEEVELLEEQPSVSLAVRSTRQTERKAR 223
Query: 258 RTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSA 317
R + EK A+ + SVK+GS+ ++KR QEVD++DPLRYLR TTSSS+LLT EE +LSA
Sbjct: 224 RAKGLEKTASGIPSVKTGSSPKKKRLVAQEVDHNDPLRYLRMTTSSSKLLTVREEHELSA 283
Query: 318 GIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRL 377
GIQDLLKLE L+ L+ER G PTFAQWA+AAGVDQ+ LR+R+++G LCKDKMI SNIRL
Sbjct: 284 GIQDLLKLERLQTELTERSGRQPTFAQWASAAGVDQKSLRQRIHHGTLCKDKMIKSNIRL 343
Query: 378 VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQ 437
VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA+KGFKFSTYAHWWIKQAVRKSLSDQ
Sbjct: 344 VISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFSTYAHWWIKQAVRKSLSDQ 403
Query: 438 SRTIRLPV 445
SR IRLP
Sbjct: 404 SRMIRLPF 411
>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 = 169 bits (429), Expect = 3e-41, Method: Compositional matrix adjust.
Identities = 87/175 (49%), Positives = 117/175 (66%), Gaps = 2/175 (1%)
Query: 273 KSG--STSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE 330
KSG + SRR+ S ++ D +R RLL A+EE++L+ I DLL+LE +RE
Sbjct: 59 KSGKAAKSRRRTQSKKKHYTEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRE 118
Query: 331 VLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGM 390
LSE+ P ++WA A + R RL+ G KDKM+ SN+RLV+SIAK Y G+
Sbjct: 119 RLSEKLERDPRDSEWAEAVQLPLPAFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGL 178
Query: 391 NLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
+ QDL+QEG GL+R AEKFD KG+KFSTYA WWI+QA+ ++++DQSRTIRLPV
Sbjct: 179 SFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 233
>sp|Q9LD95|SIGF_ARATH RNA polymerase sigma factor sigF, chloroplastic OS=Arabidopsis
thaliana GN=SIGF PE=1 SV=1
Length = 547
Score = 164 bits (414), Expect = 2e-39, Method: Compositional matrix adjust.
Identities = 85/199 (42%), Positives = 122/199 (61%), Gaps = 1/199 (0%)
Query: 246 VRSRRQTERKARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSR 305
VRS+RQ ER+A+ RA + + TS +K+ Q D D L+ + +
Sbjct: 188 VRSKRQLERRAKNRRAPKSNDVDDEGYVPQKTSAKKKYK-QGADNDDALQLFLWGPETKQ 246
Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
LLTA EE +L + IQ LLKLE ++ L + G PT +WA A G+ L+ ++ G
Sbjct: 247 LLTAKEEAELISHIQHLLKLEKVKTKLESQNGCEPTIGEWAEAMGISSPVLKSDIHRGRS 306
Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
++K+IT+N+RLV+ IAK YQ G+N QDL+QEG GL++ EKF G +F+TYA+WW
Sbjct: 307 SREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFATYAYWW 366
Query: 426 IKQAVRKSLSDQSRTIRLP 444
I+Q++RKS+ SRTIRLP
Sbjct: 367 IRQSIRKSIFQNSRTIRLP 385
>sp|P38023|RPOD1_SYNE7 RNA polymerase sigma factor rpoD1 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD1 PE=3 SV=2
Length = 399
Score = 159 bits (401), Expect = 5e-38, Method: Compositional matrix adjust.
Identities = 82/154 (53%), Positives = 106/154 (68%)
Query: 292 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGV 351
D +R RLL A+EE++L+ I DLL LE +R+ L E+ P+ A+WAAA
Sbjct: 89 DSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAVDS 148
Query: 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFD 411
E RRRL G KDKM+ SN+RLV+SIAK Y G++ QDL+QEG GL+R AEKFD
Sbjct: 149 PLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFD 208
Query: 412 ASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
KG+KFSTYA WWI+QA+ ++++DQSRTIRLPV
Sbjct: 209 HEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 242
>sp|Q31ME3|RPOD2_SYNE7 RNA polymerase sigma factor rpoD2 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD2 PE=1 SV=1
Length = 320
Score = 150 bits (379), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 71/141 (50%), Positives = 96/141 (68%)
Query: 305 RLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGI 364
RLLTA EE+ +Q L+ L + L +R G P+ +WAAA ++ +L R++ G
Sbjct: 24 RLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDLNLEDLDRQIEQGQ 83
Query: 365 LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHW 424
K KMI +N+RLV+SIAK YQ M DL+QEG GL RG EKFD SKG+KFSTYA+W
Sbjct: 84 RAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFDPSKGYKFSTYAYW 143
Query: 425 WIKQAVRKSLSDQSRTIRLPV 445
WI+QA+ ++++ QSRTIRLP+
Sbjct: 144 WIRQAITRAIAQQSRTIRLPI 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 = 147 bits (370), Expect = 2e-34, Method: Compositional matrix adjust.
Identities = 75/157 (47%), Positives = 108/157 (68%), Gaps = 3/157 (1%)
Query: 291 SDPLR-YLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVL-SERCGGSPTFAQWAAA 348
SD +R YLR LLT EE+ L +Q +KL+ LR+ L SE P+ +WAAA
Sbjct: 9 SDLVRTYLREIGRVP-LLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAA 67
Query: 349 AGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAE 408
AG+ ELR++ + G K KMI +N+RLV+S+AK Y M+L DL+QEG G+ RG E
Sbjct: 68 AGLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRGVE 127
Query: 409 KFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
KFD +KG++FSTYA+WWI+QA+ +++++++RTIRLP+
Sbjct: 128 KFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPI 164
>sp|P52322|RPOD_MICAE RNA polymerase sigma factor rpoD1 OS=Microcystis aeruginosa
GN=rpoD1 PE=3 SV=1
Length = 416
Score = 144 bits (363), Expect = 1e-33, Method: Compositional matrix adjust.
Identities = 79/193 (40%), Positives = 104/193 (53%), Gaps = 39/193 (20%)
Query: 292 DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLRE--------------VLSERCG 337
D +R RLL A EE++L+ I DLLKLE +RE L ER
Sbjct: 67 DSIRIYLQEIGRIRLLRAEEEIELARKIADLLKLERIREDFCLYSDAEWGKQVFLFERIE 126
Query: 338 G-------------------------SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMIT 372
+P +W A + +RRL +G K+KM+
Sbjct: 127 KIIVEKSEKEPKLSDIKAYLGKTELTAPLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQ 186
Query: 373 SNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRK 432
SN+RLV+SIAK Y G++ QDL+QEG GL+R AEKFD KG+KFSTYA WWI+QA+ +
Sbjct: 187 SNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITR 246
Query: 433 SLSDQSRTIRLPV 445
+++DQSRTIRLPV
Sbjct: 247 AIADQSRTIRLPV 259
>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 = 134 bits (336), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 60/140 (42%), Positives = 93/140 (66%)
Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
LL+ +E+ + +Q ++ + +E L+E+ PT +WA + + L ++L+ G +
Sbjct: 37 LLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEWADKMQLKEDVLLQQLSQGQI 96
Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
K KMI +N+RLV+SIAK YQ + DL+QEG GL RG EKFD + G+KFSTYA+WW
Sbjct: 97 AKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQEGALGLERGVEKFDPTLGYKFSTYAYWW 156
Query: 426 IKQAVRKSLSDQSRTIRLPV 445
I+Q + ++++ QSRTIRLP+
Sbjct: 157 IRQGITRAIAQQSRTIRLPI 176
>sp|O24629|SIGA_ARATH RNA polymerase sigma factor sigA OS=Arabidopsis thaliana GN=SIGA
PE=1 SV=1
Length = 502
Score = 127 bits (319), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 76/199 (38%), Positives = 112/199 (56%), Gaps = 12/199 (6%)
Query: 256 ARRTRAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLR-YLRATTSSSRLLTANEEMQ 314
AR+ R K N+ VK+ V +V +R Y++ S +L+ E ++
Sbjct: 159 ARQRRIGAKKKTNMTHVKA----------VSDVSSGKQVRGYVKGVISED-VLSHVEVVR 207
Query: 315 LSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSN 374
LS I+ L+L+ + L +R G P+ Q A + + + EL+ L L ++K+ SN
Sbjct: 208 LSKKIKSGLRLDDHKSRLKDRLGCEPSDEQLAVSLKISRAELQAWLMECHLAREKLAMSN 267
Query: 375 IRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSL 434
+RLV+SIA+ Y G + DLVQ G GL+RG EKFD+SKGF+ STY +WWI+Q V ++L
Sbjct: 268 VRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWWIRQGVSRAL 327
Query: 435 SDQSRTIRLPVISHGRGNL 453
D SRT+RLP H R L
Sbjct: 328 VDNSRTLRLPTHLHERLGL 346
>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 = 126 bits (317), Expect = 3e-28, Method: Compositional matrix adjust.
Identities = 52/80 (65%), Positives = 66/80 (82%)
Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
KDKM+ SN+RLV+SIAK Y G++ QDL+QEG GL+R AEKFD KG+KFSTYA WW
Sbjct: 189 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 248
Query: 426 IKQAVRKSLSDQSRTIRLPV 445
I+QA+ ++++DQSRTIRLPV
Sbjct: 249 IRQAITRAIADQSRTIRLPV 268
Score = 35.8 bits (81), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 273 KSGSTSRRKRPSVQEVDYS-DPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREV 331
K + ++ +V++ Y+ D +R RLL A EE++L+ I DLL+LE +R+
Sbjct: 51 KEKKVRKIRKDAVKKKPYTEDSIRIYLQEIGRIRLLRAEEEIELARQIADLLELELIRDN 110
Query: 332 LSERCGGSPTFAQWA 346
L+ + P+ +W
Sbjct: 111 LTLQLERQPSELEWG 125
>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 = 123 bits (309), Expect = 2e-27, Method: Compositional matrix adjust.
Identities = 67/173 (38%), Positives = 96/173 (55%), Gaps = 27/173 (15%)
Query: 295 RYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ- 353
RYL+ R++ AN Q L L ++E L+ G P+ +WAA AG++
Sbjct: 89 RYLKL-----RIVLANAVKQGDEVATPYLHLIEVQERLASELGHRPSLERWAATAGINLC 143
Query: 354 ---------------------RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNL 392
EL + + G+ K+ MI +N+RLV+S+AK YQ G+ L
Sbjct: 144 DLKPILSEGKRRWAEIAKMTVEELEKMQSQGLQSKEHMIKANLRLVVSVAKKYQNRGLEL 203
Query: 393 QDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
DLVQEG GL R EKFD +KG++FSTYA+WWI+Q + ++++ SRTIRLPV
Sbjct: 204 LDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPV 256
>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 = 123 bits (309), Expect = 3e-27, Method: Compositional matrix adjust.
Identities = 55/94 (58%), Positives = 74/94 (78%), Gaps = 1/94 (1%)
Query: 353 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFD 411
+REL RR G K+K+ITSN+RLV+SIAK Y G G++ QDL+QEG GL++ EKFD
Sbjct: 141 ERELARRAQMGDKKAKEKLITSNLRLVVSIAKRYMGRGLSFQDLIQEGNIGLLKAVEKFD 200
Query: 412 ASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
KG+KFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 201 WRKGYKFSTYATWWIRQAITRAIADQARTIRIPV 234
>sp|P27785|RPOD_STRAU RNA polymerase sigma factor RpoD OS=Streptomyces aureofaciens
GN=rpoD PE=3 SV=1
Length = 317
Score = 121 bits (304), Expect = 1e-26, Method: Compositional matrix adjust.
Identities = 63/140 (45%), Positives = 90/140 (64%), Gaps = 13/140 (9%)
Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
LLTA EE+ L+ ++ L E E+ GG+ A +L R + G +
Sbjct: 33 LLTAAEEVDLARRVEAGLFAE-------EKLGGAADLDSQLAV------DLDRLVVMGRM 79
Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
K ++I SN+RLV+S+AK Y G G+ + DLVQEG GL+R EKFD ++G+KFSTYA WW
Sbjct: 80 AKRRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWW 139
Query: 426 IKQAVRKSLSDQSRTIRLPV 445
I+QA+ ++L+DQ+RTIR+PV
Sbjct: 140 IRQAMSRALADQARTIRVPV 159
>sp|P0A602|RPOD_MYCTU RNA polymerase sigma factor RpoD OS=Mycobacterium tuberculosis
GN=rpoD PE=1 SV=1
Length = 528
Score = 120 bits (302), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 64/155 (41%), Positives = 93/155 (60%), Gaps = 13/155 (8%)
Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
LL A EE++L+ I+ L L LSER P +R++ G
Sbjct: 240 LLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP---------AAQRRDMMWICRDGDR 290
Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
K+ ++ +N+RLV+S+AK Y G GM DL+QEG GL+R EKFD +KG+KFSTYA WW
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 350
Query: 426 IKQAVRKSLSDQSRTIRLPV----ISHGRGNLQSE 456
I+QA+ ++++DQ+RTIR+PV + + G +Q E
Sbjct: 351 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRE 385
>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 = 120 bits (302), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 64/155 (41%), Positives = 93/155 (60%), Gaps = 13/155 (8%)
Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
LL A EE++L+ I+ L L LSER P +R++ G
Sbjct: 240 LLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP---------AAQRRDMMWICRDGDR 290
Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
K+ ++ +N+RLV+S+AK Y G GM DL+QEG GL+R EKFD +KG+KFSTYA WW
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 350
Query: 426 IKQAVRKSLSDQSRTIRLPV----ISHGRGNLQSE 456
I+QA+ ++++DQ+RTIR+PV + + G +Q E
Sbjct: 351 IRQAITRAMADQARTIRIPVHMVEVINKLGRIQRE 385
>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 = 52/101 (51%), Positives = 70/101 (69%)
Query: 345 WAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLV 404
WA AG+ EL GI K MI +N+RLV+S+AK YQ G+ L DL+QEG GL
Sbjct: 144 WAELAGLTVEELENIEKQGITAKAHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLE 203
Query: 405 RGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
R EKFD +KG++FSTY++WWI+Q + ++++ QSR IRLPV
Sbjct: 204 RAVEKFDPTKGYRFSTYSYWWIRQGITRAIATQSRMIRLPV 244
>sp|Q59914|HRDD_STRGR RNA polymerase principal sigma factor HrdD OS=Streptomyces griseus
GN=hrdD PE=3 SV=1
Length = 332
Score = 120 bits (301), Expect = 2e-26, Method: Compositional matrix adjust.
Identities = 55/98 (56%), Positives = 72/98 (73%)
Query: 348 AAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGA 407
+AG + EL + G KD I SN+RLV+++A+ Y +G+ L DL+QEG GLVR
Sbjct: 78 SAGASREELEALVAEGERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAV 137
Query: 408 EKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
EKFD +KGFKFSTYA WWI+QA+ +S++DQSRTIRLPV
Sbjct: 138 EKFDYAKGFKFSTYATWWIRQAITRSIADQSRTIRLPV 175
>sp|O24621|SIGC_ARATH RNA polymerase sigma factor sigC OS=Arabidopsis thaliana GN=SIGC
PE=2 SV=1
Length = 571
Score = 119 bits (299), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 50/133 (37%), Positives = 91/133 (68%)
Query: 312 EMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMI 371
E ++S G++ + +E +R L E G + + WAAAAG++++ L R L+YG C+D+++
Sbjct: 278 ETEMSTGVKIVADMERIRTQLEEESGKVASLSCWAAAAGMNEKLLMRNLHYGWYCRDELV 337
Query: 372 TSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVR 431
S LV+ +A+NY+G G+ +DL+Q G G+++GAE+FD ++G+KFSTY +WI++++
Sbjct: 338 KSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKSMS 397
Query: 432 KSLSDQSRTIRLP 444
+S +R + +P
Sbjct: 398 TMVSRHARGVHIP 410
>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 = 119 bits (298), Expect = 4e-26, Method: Compositional matrix adjust.
Identities = 52/93 (55%), Positives = 70/93 (75%)
Query: 353 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA 412
+R+L+ + G + ++ +N+RLV+S+AK Y G GM L DL+QEG GL+R EKFD
Sbjct: 79 KRDLKVLVKEGRKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 138
Query: 413 SKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
SKGFKFSTYA WWI+QA+ + ++DQSRTIRLPV
Sbjct: 139 SKGFKFSTYATWWIRQAITRGMADQSRTIRLPV 171
>sp|Q60012|HRDD_STRVF RNA polymerase principal sigma factor HrdD OS=Streptomyces
viridifaciens GN=hrdD PE=3 SV=1
Length = 332
Score = 118 bits (296), Expect = 9e-26, Method: Compositional matrix adjust.
Identities = 53/91 (58%), Positives = 69/91 (75%)
Query: 355 ELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASK 414
EL+ ++ G KD I SN+RLV+++A+ Y +G+ L DL+QEG GLVR EKFD K
Sbjct: 85 ELQALVDAGERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRK 144
Query: 415 GFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
GFKFSTYA WWI+QA+ +S++DQSRTIRLPV
Sbjct: 145 GFKFSTYATWWIRQAITRSIADQSRTIRLPV 175
>sp|P18249|HRDD_STRCO RNA polymerase principal sigma factor HrdD OS=Streptomyces
coelicolor (strain ATCC BAA-471 / A3(2) / M145) GN=hrdD
PE=3 SV=2
Length = 332
Score = 117 bits (292), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 50/80 (62%), Positives = 63/80 (78%)
Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
KD I SN+RLV+++A+ Y +G+ L DL+QEG GLVR EKFD KGFKFSTYA WW
Sbjct: 96 AKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155
Query: 426 IKQAVRKSLSDQSRTIRLPV 445
I+QA+ +S++DQSRTIRLPV
Sbjct: 156 IRQAITRSIADQSRTIRLPV 175
>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 = 116 bits (291), Expect = 3e-25, Method: Compositional matrix adjust.
Identities = 68/186 (36%), Positives = 95/186 (51%), Gaps = 52/186 (27%)
Query: 260 RAAEKAAANVMSVKSGSTSRRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGI 319
+ AEKA A +S +G V +DP+R +LLTA EE++L+ I
Sbjct: 77 KEAEKAQAEDLSAPTG------------VKINDPVRMYLKEIGRVQLLTAAEEVELALKI 124
Query: 320 QDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVI 379
+ EG +E K ++ +N+RLV+
Sbjct: 125 E-----EGDQE-----------------------------------AKQRLAEANLRLVV 144
Query: 380 SIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSR 439
SIAK Y G GM DL+QEG GL++ EKFD KGFKFSTYA WWI+QA+ ++++DQ+R
Sbjct: 145 SIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQAR 204
Query: 440 TIRLPV 445
TIR+PV
Sbjct: 205 TIRIPV 210
>sp|P18182|HRDA_STRCO RNA polymerase principal sigma factor HrdA OS=Streptomyces
coelicolor (strain ATCC BAA-471 / A3(2) / M145) GN=hrdA
PE=3 SV=2
Length = 396
Score = 116 bits (291), Expect = 4e-25, Method: Compositional matrix adjust.
Identities = 48/83 (57%), Positives = 67/83 (80%)
Query: 363 GILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYA 422
G L K ++I +N+RLV+S+AK Y G G+ + DLVQEG GL+R EKFD ++G+KFSTYA
Sbjct: 156 GRLAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYA 215
Query: 423 HWWIKQAVRKSLSDQSRTIRLPV 445
WWI+QA+ ++L+DQ+RTIR+PV
Sbjct: 216 TWWIRQAMSRALADQARTIRVPV 238
>sp|Q8CP24|RPOD_STAES RNA polymerase sigma factor RpoD OS=Staphylococcus epidermidis
(strain ATCC 12228) GN=rpoD PE=3 SV=1
Length = 368
Score = 116 bits (290), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 51/92 (55%), Positives = 70/92 (76%), Gaps = 1/92 (1%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
EL +R+ G + K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ EKFD S
Sbjct: 119 ELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFS 178
Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
KGFKFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPV 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 = 116 bits (290), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 51/92 (55%), Positives = 70/92 (76%), Gaps = 1/92 (1%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
EL +R+ G + K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ EKFD S
Sbjct: 119 ELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFS 178
Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
KGFKFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPV 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 = 115 bits (289), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 49/93 (52%), Positives = 69/93 (74%)
Query: 353 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA 412
+REL G K+ ++ +N+RLV+S+AK Y G GM DL+QEG GL+R EKFD
Sbjct: 261 KRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDY 320
Query: 413 SKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
+KG+KFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 321 TKGYKFSTYATWWIRQAITRAMADQARTIRIPV 353
>sp|P77951|HRDB_STRGR RNA polymerase principal sigma factor HrdB OS=Streptomyces griseus
GN=hrdB PE=1 SV=1
Length = 514
Score = 115 bits (288), Expect = 8e-25, Method: Compositional matrix adjust.
Identities = 49/93 (52%), Positives = 69/93 (74%)
Query: 353 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDA 412
+REL G K+ ++ +N+RLV+S+AK Y G GM DL+QEG GL+R EKFD
Sbjct: 264 KRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDY 323
Query: 413 SKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
+KG+KFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 324 TKGYKFSTYATWWIRQAITRAMADQARTIRIPV 356
>sp|Q99TT5|RPOD_STAAN RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
N315) GN=rpoD PE=1 SV=1
Length = 368
Score = 114 bits (286), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 50/92 (54%), Positives = 70/92 (76%), Gaps = 1/92 (1%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
EL +R+ G + K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ EKFD +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFN 178
Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
KGFKFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|P0A0I9|RPOD_STAAW RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
MW2) GN=rpoD PE=3 SV=1
Length = 368
Score = 114 bits (286), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 50/92 (54%), Positives = 70/92 (76%), Gaps = 1/92 (1%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
EL +R+ G + K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ EKFD +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFN 178
Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
KGFKFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|Q6G905|RPOD_STAAS RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
MSSA476) GN=rpoD PE=3 SV=1
Length = 368
Score = 114 bits (286), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 50/92 (54%), Positives = 70/92 (76%), Gaps = 1/92 (1%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
EL +R+ G + K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ EKFD +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFN 178
Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
KGFKFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|Q6GGD8|RPOD_STAAR RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
MRSA252) GN=rpoD PE=3 SV=1
Length = 368
Score = 114 bits (286), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 50/92 (54%), Positives = 70/92 (76%), Gaps = 1/92 (1%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
EL +R+ G + K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ EKFD +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFN 178
Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
KGFKFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPV 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 = 114 bits (286), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 50/92 (54%), Positives = 70/92 (76%), Gaps = 1/92 (1%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
EL +R+ G + K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ EKFD +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFN 178
Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
KGFKFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>sp|Q5HFJ9|RPOD_STAAC RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
COL) GN=rpoD PE=3 SV=1
Length = 368
Score = 114 bits (286), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 50/92 (54%), Positives = 70/92 (76%), Gaps = 1/92 (1%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
EL +R+ G + K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ EKFD +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFN 178
Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
KGFKFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPV 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 = 114 bits (286), Expect = 1e-24, Method: Compositional matrix adjust.
Identities = 50/92 (54%), Positives = 70/92 (76%), Gaps = 1/92 (1%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDAS 413
EL +R+ G + K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ EKFD +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFN 178
Query: 414 KGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
KGFKFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 179 KGFKFSTYATWWIRQAITRAIADQARTIRIPV 210
>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 = 114 bits (284), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 47/82 (57%), Positives = 64/82 (78%)
Query: 364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAH 423
I K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ +KFD SKGFKFSTYA
Sbjct: 129 IEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYAT 188
Query: 424 WWIKQAVRKSLSDQSRTIRLPV 445
WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 189 WWIRQAITRAIADQARTIRIPV 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 = 114 bits (284), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 47/82 (57%), Positives = 64/82 (78%)
Query: 364 ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAH 423
I K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ +KFD SKGFKFSTYA
Sbjct: 129 IEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYAT 188
Query: 424 WWIKQAVRKSLSDQSRTIRLPV 445
WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 189 WWIRQAITRAIADQARTIRIPV 210
>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 = 113 bits (283), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 47/85 (55%), Positives = 65/85 (76%)
Query: 361 NYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFST 420
N + K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ +KFD SKGFKFST
Sbjct: 128 NGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFST 187
Query: 421 YAHWWIKQAVRKSLSDQSRTIRLPV 445
YA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 188 YATWWIRQAITRAIADQARTIRIPV 212
>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 = 113 bits (283), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 50/91 (54%), Positives = 69/91 (75%), Gaps = 1/91 (1%)
Query: 356 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASK 414
L +R+ G I K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ EKFD +K
Sbjct: 126 LAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDFNK 185
Query: 415 GFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
GFKFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 186 GFKFSTYATWWIRQAITRAIADQARTIRIPV 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 = 113 bits (283), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 50/91 (54%), Positives = 69/91 (75%), Gaps = 1/91 (1%)
Query: 356 LRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASK 414
L +R+ G I K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ EKFD +K
Sbjct: 126 LAKRIEAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDFNK 185
Query: 415 GFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
GFKFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 186 GFKFSTYATWWIRQAITRAIADQARTIRIPV 216
>sp|P52328|RPSD2_BACSP RNA polymerase sigma factor RpoD OS=Bacillus sp. GN=sigA PE=3 SV=1
Length = 377
Score = 113 bits (283), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 51/95 (53%), Positives = 71/95 (74%), Gaps = 1/95 (1%)
Query: 352 DQRELRRRLNYGIL-CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKF 410
D+ EL +R+ G K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ EKF
Sbjct: 125 DEVELAKRIMNGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKF 184
Query: 411 DASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
D +KGFKFSTYA WWI+QA+ ++++DQ+RTIR+PV
Sbjct: 185 DHNKGFKFSTYATWWIRQAITRAIADQARTIRIPV 219
>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 = 113 bits (282), Expect = 3e-24, Method: Compositional matrix adjust.
Identities = 60/140 (42%), Positives = 87/140 (62%), Gaps = 9/140 (6%)
Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
LLTA +E++L+ I+ ++ RE L G P A +R L ++ G
Sbjct: 51 LLTAEDEVRLATRIEAGVRA---REELETADTGEP------APTPRRRRTLEETVHDGQE 101
Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
KD M+ +N+RLV+S+AK + G+ L D++QEG GL+R EKFD +KGFKFSTYA WW
Sbjct: 102 AKDHMVRANLRLVVSMAKRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKGFKFSTYATWW 161
Query: 426 IKQAVRKSLSDQSRTIRLPV 445
I+QA+ + L+ +RT+RLPV
Sbjct: 162 IRQAIERGLATHARTVRLPV 181
>sp|P52323|RPOD_BORBU RNA polymerase sigma factor RpoD OS=Borrelia burgdorferi (strain
ATCC 35210 / B31 / CIP 102532 / DSM 4680) GN=rpoD PE=3
SV=2
Length = 631
Score = 113 bits (282), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 47/80 (58%), Positives = 64/80 (80%)
Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
KD++I +N+RLV+SIAK Y G++ DLVQEG GL++ EKF+ +GFKFSTYA WW
Sbjct: 391 AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEKFEYKRGFKFSTYATWW 450
Query: 426 IKQAVRKSLSDQSRTIRLPV 445
I+QA+ +S+SDQ+RTIR+PV
Sbjct: 451 IRQAITRSISDQARTIRVPV 470
>sp|O83506|RPOD_TREPA RNA polymerase sigma factor RpoD OS=Treponema pallidum (strain
Nichols) GN=rpoD PE=3 SV=1
Length = 611
Score = 112 bits (281), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 48/79 (60%), Positives = 63/79 (79%)
Query: 367 KDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWWI 426
KDK+I +N+RLV+SIAK Y G+ DLVQEG GL++ EKF+ KG+KFSTYA WWI
Sbjct: 374 KDKLINANLRLVVSIAKKYTNRGLLFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATWWI 433
Query: 427 KQAVRKSLSDQSRTIRLPV 445
+QA+ +S+SDQ+RTIR+PV
Sbjct: 434 RQAITRSISDQARTIRVPV 452
>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 = 112 bits (281), Expect = 4e-24, Method: Compositional matrix adjust.
Identities = 46/80 (57%), Positives = 63/80 (78%)
Query: 366 CKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 425
K ++ +N+RLV+SIAK Y G GM DL+QEG GL++ EKFD +KGFKFSTYA WW
Sbjct: 135 AKRRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYNKGFKFSTYATWW 194
Query: 426 IKQAVRKSLSDQSRTIRLPV 445
I+QA+ ++++DQ+RTIR+PV
Sbjct: 195 IRQAITRAIADQARTIRIPV 214
>sp|Q9Z7F0|RPOD_CHLPN RNA polymerase sigma factor RpoD OS=Chlamydia pneumoniae GN=rpoD
PE=3 SV=1
Length = 572
Score = 112 bits (280), Expect = 6e-24, Method: Compositional matrix adjust.
Identities = 49/94 (52%), Positives = 70/94 (74%)
Query: 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFD 411
D R L+R ++ K +M+ SN+RLVISIAK Y G++ DL+QEG GL++ EKF+
Sbjct: 303 DVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362
Query: 412 ASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
+G+KFSTYA WWI+QAV ++++DQ+RTIR+PV
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPV 396
>sp|Q31QR8|RPOD4_SYNE7 RNA polymerase sigma factor rpoD4 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD4 PE=3 SV=1
Length = 311
Score = 112 bits (279), Expect = 7e-24, Method: Compositional matrix adjust.
Identities = 65/167 (38%), Positives = 95/167 (56%), Gaps = 19/167 (11%)
Query: 279 RRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGG 338
RR + E SD + + ++ LLTA EE++LS +Q ++ L L
Sbjct: 6 RRNLNAAVERHTSDHVSWYLSSIGRIPLLTAEEEVELSRKVQLMMAL------LENPDAE 59
Query: 339 SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQE 398
S + Q AG QR K KM+ +N+RLV+S+AK YQ G+ L DL+QE
Sbjct: 60 SNSENQAVLQAG--QR-----------AKTKMLKANLRLVVSVAKKYQNQGLELLDLIQE 106
Query: 399 GCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
G GL R EKFD + G+KFSTYA+WWI+Q++ +++ + +RTIRLP+
Sbjct: 107 GSLGLERAVEKFDPALGYKFSTYAYWWIRQSMTRAIDNHARTIRLPI 153
>sp|P0CZ15|RPOD_RHOCA RNA polymerase sigma factor rpoD OS=Rhodobacter capsulatus GN=rpoD
PE=2 SV=1
Length = 674
Score = 112 bits (279), Expect = 8e-24, Method: Compositional matrix adjust.
Identities = 52/111 (46%), Positives = 72/111 (64%), Gaps = 7/111 (6%)
Query: 342 FAQWAAAAGVDQRELRRRLNY-------GILCKDKMITSNIRLVISIAKNYQGAGMNLQD 394
AQ GVD E RR +N K +M+ +N+RLVISIAK Y G+ D
Sbjct: 405 MAQVGQYVGVDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLD 464
Query: 395 LVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
L+QEG GL++ +KF+ +G+KFSTYA WWI+QA+ +S++DQ+RTIR+PV
Sbjct: 465 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 515
>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 = 112 bits (279), Expect = 8e-24, Method: Compositional matrix adjust.
Identities = 52/111 (46%), Positives = 72/111 (64%), Gaps = 7/111 (6%)
Query: 342 FAQWAAAAGVDQRELRRRLNY-------GILCKDKMITSNIRLVISIAKNYQGAGMNLQD 394
AQ GVD E RR +N K +M+ +N+RLVISIAK Y G+ D
Sbjct: 405 MAQVGQYVGVDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLD 464
Query: 395 LVQEGCRGLVRGAEKFDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
L+QEG GL++ +KF+ +G+KFSTYA WWI+QA+ +S++DQ+RTIR+PV
Sbjct: 465 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 515
>sp|P56835|RPOD_CHLMU RNA polymerase sigma factor RpoD OS=Chlamydia muridarum (strain
MoPn / Nigg) GN=rpoD PE=3 SV=1
Length = 571
Score = 112 bits (279), Expect = 8e-24, Method: Compositional matrix adjust.
Identities = 49/94 (52%), Positives = 70/94 (74%)
Query: 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFD 411
D R L+R ++ K +M+ SN+RLVISIAK Y G++ DL+QEG GL++ EKF+
Sbjct: 303 DVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362
Query: 412 ASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
+G+KFSTYA WWI+QAV ++++DQ+RTIR+PV
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPV 396
>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 = 111 bits (278), Expect = 1e-23, Method: Compositional matrix adjust.
Identities = 49/94 (52%), Positives = 70/94 (74%)
Query: 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFD 411
D R L+R ++ K +M+ SN+RLVISIAK Y G++ DL+QEG GL++ EKF+
Sbjct: 303 DVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362
Query: 412 ASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPV 445
+G+KFSTYA WWI+QAV ++++DQ+RTIR+PV
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPV 396
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
0.313 0.124 0.346
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 149,139,407
Number of Sequences: 539616
Number of extensions: 5624036
Number of successful extensions: 18486
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 166
Number of HSP's successfully gapped in prelim test: 155
Number of HSP's that attempted gapping in prelim test: 18079
Number of HSP's gapped (non-prelim): 484
length of query: 458
length of database: 191,569,459
effective HSP length: 121
effective length of query: 337
effective length of database: 126,275,923
effective search space: 42554986051
effective search space used: 42554986051
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 63 (28.9 bits)