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= 016077
(395 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 = 320 bits (820), Expect = 1e-86, Method: Compositional matrix adjust.
Identities = 206/372 (55%), Positives = 257/372 (69%), Gaps = 26/372 (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 VISIAKNYQGAG 389
VISIAKNYQGAG
Sbjct: 344 VISIAKNYQGAG 355
>sp|Q9LD95|SIGF_ARATH RNA polymerase sigma factor sigF, chloroplastic OS=Arabidopsis
thaliana GN=SIGF PE=1 SV=1
Length = 547
Score = 89.4 bits (220), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 54/144 (37%), Positives = 80/144 (55%), Gaps = 1/144 (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 CKDKMITSNIRLVISIAKNYQGAG 389
++K+IT+N+RLV+ IAK YQ G
Sbjct: 307 SREKLITANLRLVVHIAKQYQNRG 330
>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 = 80.9 bits (198), Expect = 1e-14, Method: Compositional matrix adjust.
Identities = 50/119 (42%), Positives = 69/119 (57%), Gaps = 2/119 (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 VLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
LSE+ P ++WA A + R RL+ G KDKM+ SN+RLV+SIAK Y G
Sbjct: 119 RLSEKLERDPRDSEWAEAVQLPLPAFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRG 177
>sp|P38023|RPOD1_SYNE7 RNA polymerase sigma factor rpoD1 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD1 PE=3 SV=2
Length = 399
Score = 68.9 bits (167), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 45/98 (45%), Positives = 58/98 (59%)
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 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
E RRRL G KDKM+ SN+RLV+SIAK Y G
Sbjct: 149 PLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRG 186
>sp|O24621|SIGC_ARATH RNA polymerase sigma factor sigC OS=Arabidopsis thaliana GN=SIGC
PE=2 SV=1
Length = 571
Score = 66.2 bits (160), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 51/78 (65%)
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 TSNIRLVISIAKNYQGAG 389
S LV+ +A+NY+G G
Sbjct: 338 KSTRSLVLFLARNYRGLG 355
>sp|Q31QG5|RPOD3_SYNE7 RNA polymerase sigma factor rpoD3 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD3 PE=3 SV=1
Length = 320
Score = 66.2 bits (160), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 43/97 (44%), Positives = 59/97 (60%), Gaps = 3/97 (3%)
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 AGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNY 385
AG+ ELR++ + G K KMI +N+RLV+S+AK Y
Sbjct: 68 AGLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKY 104
>sp|Q31ME3|RPOD2_SYNE7 RNA polymerase sigma factor rpoD2 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD2 PE=1 SV=1
Length = 320
Score = 65.9 bits (159), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 35/82 (42%), Positives = 50/82 (60%)
Query: 305 RLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGI 364
RLLTA EE+ +Q L+ L + L +R G P+ +WAAA ++ +L R++ G
Sbjct: 24 RLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDLNLEDLDRQIEQGQ 83
Query: 365 LCKDKMITSNIRLVISIAKNYQ 386
K KMI +N+RLV+SIAK YQ
Sbjct: 84 RAKRKMIEANLRLVVSIAKKYQ 105
>sp|P52322|RPOD_MICAE RNA polymerase sigma factor rpoD1 OS=Microcystis aeruginosa
GN=rpoD1 PE=3 SV=1
Length = 416
Score = 55.8 bits (133), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 42/137 (30%), Positives = 56/137 (40%), Gaps = 39/137 (28%)
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 SNIRLVISIAKNYQGAG 389
SN+RLV+SIAK Y G
Sbjct: 187 SNLRLVVSIAKKYMNRG 203
>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 = 55.5 bits (132), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 49/81 (60%)
Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
LL+ +E+ + +Q ++ + +E L+E+ PT +WA + + L ++L+ G +
Sbjct: 37 LLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEWADKMQLKEDVLLQQLSQGQI 96
Query: 366 CKDKMITSNIRLVISIAKNYQ 386
K KMI +N+RLV+SIAK YQ
Sbjct: 97 AKQKMIQANLRLVVSIAKKYQ 117
>sp|O24629|SIGA_ARATH RNA polymerase sigma factor sigA OS=Arabidopsis thaliana GN=SIGA
PE=1 SV=1
Length = 502
Score = 48.5 bits (114), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 40/135 (29%), Positives = 67/135 (49%), Gaps = 12/135 (8%)
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 IRLVISIAKNYQGAG 389
+RLV+SIA+ Y G
Sbjct: 268 VRLVMSIAQRYDNLG 282
>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 = 45.4 bits (106), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 34/117 (29%), Positives = 52/117 (44%), Gaps = 27/117 (23%)
Query: 295 RYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQ- 353
RYL+ R++ AN Q L L ++E L+ G P+ +WAA AG++
Sbjct: 89 RYLKL-----RIVLANAVKQGDEVATPYLHLIEVQERLASELGHRPSLERWAATAGINLC 143
Query: 354 ---------------------RELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
EL + + G+ K+ MI +N+RLV+S+AK YQ G
Sbjct: 144 DLKPILSEGKRRWAEIAKMTVEELEKMQSQGLQSKEHMIKANLRLVVSVAKKYQNRG 200
>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 = 43.5 bits (101), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/45 (46%), Positives = 26/45 (57%)
Query: 345 WAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
WA AG+ EL GI K MI +N+RLV+S+AK YQ G
Sbjct: 144 WAELAGLTVEELENIEKQGITAKAHMIKANLRLVVSVAKKYQNRG 188
>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 = 42.0 bits (97), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 22/38 (57%), Positives = 27/38 (71%), Gaps = 1/38 (2%)
Query: 353 QRELRRRLNYG-ILCKDKMITSNIRLVISIAKNYQGAG 389
+REL RR G K+K+ITSN+RLV+SIAK Y G G
Sbjct: 141 ERELARRAQMGDKKAKEKLITSNLRLVVSIAKRYMGRG 178
>sp|P27785|RPOD_STRAU RNA polymerase sigma factor RpoD OS=Streptomyces aureofaciens
GN=rpoD PE=3 SV=1
Length = 317
Score = 40.0 bits (92), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 29/84 (34%), Positives = 43/84 (51%), Gaps = 13/84 (15%)
Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
LLTA EE+ L+ ++ L E E+ GG+ A +L R + G +
Sbjct: 33 LLTAAEEVDLARRVEAGLFAE-------EKLGGAADLDSQLAV------DLDRLVVMGRM 79
Query: 366 CKDKMITSNIRLVISIAKNYQGAG 389
K ++I SN+RLV+S+AK Y G G
Sbjct: 80 AKRRLIESNLRLVVSVAKRYVGRG 103
>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 = 37.7 bits (86), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 15/24 (62%), Positives = 18/24 (75%)
Query: 366 CKDKMITSNIRLVISIAKNYQGAG 389
KDKM+ SN+RLV+SIAK Y G
Sbjct: 189 AKDKMVQSNLRLVVSIAKKYMNRG 212
Score = 35.8 bits (81), Expect = 0.61, 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|Q31QR8|RPOD4_SYNE7 RNA polymerase sigma factor rpoD4 OS=Synechococcus elongatus
(strain PCC 7942) GN=rpoD4 PE=3 SV=1
Length = 311
Score = 37.4 bits (85), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 35/111 (31%), Positives = 51/111 (45%), Gaps = 19/111 (17%)
Query: 279 RRKRPSVQEVDYSDPLRYLRATTSSSRLLTANEEMQLSAGIQDLLKLEGLREVLSERCGG 338
RR + E SD + + ++ LLTA EE++LS +Q ++ L L
Sbjct: 6 RRNLNAAVERHTSDHVSWYLSSIGRIPLLTAEEEVELSRKVQLMMAL------LENPDAE 59
Query: 339 SPTFAQWAAAAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
S + Q AG QR K KM+ +N+RLV+S+AK YQ G
Sbjct: 60 SNSENQAVLQAG--QR-----------AKTKMLKANLRLVVSVAKKYQNQG 97
>sp|P0A602|RPOD_MYCTU RNA polymerase sigma factor RpoD OS=Mycobacterium tuberculosis
GN=rpoD PE=1 SV=1
Length = 528
Score = 37.0 bits (84), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 9/84 (10%)
Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
LL A EE++L+ I+ L L LSER P +R++ G
Sbjct: 240 LLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP---------AAQRRDMMWICRDGDR 290
Query: 366 CKDKMITSNIRLVISIAKNYQGAG 389
K+ ++ +N+RLV+S+AK Y G G
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRG 314
>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 = 37.0 bits (84), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 41/84 (48%), Gaps = 9/84 (10%)
Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
LL A EE++L+ I+ L L LSER P +R++ G
Sbjct: 240 LLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP---------AAQRRDMMWICRDGDR 290
Query: 366 CKDKMITSNIRLVISIAKNYQGAG 389
K+ ++ +N+RLV+S+AK Y G G
Sbjct: 291 AKNHLLEANLRLVVSLAKRYTGRG 314
>sp|Q9ZNX9|SIGE_ARATH RNA polymerase sigma factor sigE, chloroplastic/mitochondrial
OS=Arabidopsis thaliana GN=SIGE PE=1 SV=1
Length = 517
Score = 37.0 bits (84), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 42/80 (52%)
Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
+L++ E L +Q + L +++VL + G P A+ A + E+++++ G
Sbjct: 219 VLSSTEHAWLFKLMQPMKALLEVKDVLQKSLGREPREAEIAGEINMTAGEVKKKIEIGRA 278
Query: 366 CKDKMITSNIRLVISIAKNY 385
++K+I N+RLV+ + Y
Sbjct: 279 ARNKLIKHNLRLVLFVMNKY 298
>sp|P0CZ15|RPOD_RHOCA RNA polymerase sigma factor rpoD OS=Rhodobacter capsulatus GN=rpoD
PE=2 SV=1
Length = 674
Score = 36.2 bits (82), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 342 FAQWAAAAGVDQRELRRRLNY-------GILCKDKMITSNIRLVISIAKNYQGAG 389
AQ GVD E RR +N K +M+ +N+RLVISIAK Y G
Sbjct: 405 MAQVGQYVGVDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRG 459
>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 = 35.8 bits (81), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 27/55 (49%), Gaps = 7/55 (12%)
Query: 342 FAQWAAAAGVDQRELRRRLNY-------GILCKDKMITSNIRLVISIAKNYQGAG 389
AQ GVD E RR +N K +M+ +N+RLVISIAK Y G
Sbjct: 405 MAQVGQYVGVDISEFRRIVNQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRG 459
>sp|Q9Z7F0|RPOD_CHLPN RNA polymerase sigma factor RpoD OS=Chlamydia pneumoniae GN=rpoD
PE=3 SV=1
Length = 572
Score = 35.4 bits (80), Expect = 0.70, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%)
Query: 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
D R L+R ++ K +M+ SN+RLVISIAK Y G
Sbjct: 303 DVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRG 340
>sp|P56835|RPOD_CHLMU RNA polymerase sigma factor RpoD OS=Chlamydia muridarum (strain
MoPn / Nigg) GN=rpoD PE=3 SV=1
Length = 571
Score = 35.4 bits (80), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%)
Query: 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
D R L+R ++ K +M+ SN+RLVISIAK Y G
Sbjct: 303 DVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRG 340
>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 = 35.0 bits (79), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 18/38 (47%), Positives = 24/38 (63%)
Query: 352 DQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
D R L+R ++ K +M+ SN+RLVISIAK Y G
Sbjct: 303 DVRMLQRWMDKSQEAKKEMVESNLRLVISIAKKYTNRG 340
>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 = 35.0 bits (79), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 14/27 (51%), Positives = 20/27 (74%)
Query: 363 GILCKDKMITSNIRLVISIAKNYQGAG 389
G L K ++I +N+RLV+S+AK Y G G
Sbjct: 156 GRLAKRRLIEANLRLVVSVAKRYVGRG 182
>sp|O83506|RPOD_TREPA RNA polymerase sigma factor RpoD OS=Treponema pallidum (strain
Nichols) GN=rpoD PE=3 SV=1
Length = 611
Score = 35.0 bits (79), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/23 (60%), Positives = 18/23 (78%)
Query: 367 KDKMITSNIRLVISIAKNYQGAG 389
KDK+I +N+RLV+SIAK Y G
Sbjct: 374 KDKLINANLRLVVSIAKKYTNRG 396
>sp|Q9PDM9|RPOD_XYLFA RNA polymerase sigma factor RpoD OS=Xylella fastidiosa (strain
9a5c) GN=rpoD PE=3 SV=1
Length = 618
Score = 34.7 bits (78), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 4/42 (9%)
Query: 352 DQRELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAG 389
D +E+ R + YG K +M+ +N+RLVISIAK Y G
Sbjct: 361 DIKEINRMMVYGEAKASKAKKEMVEANLRLVISIAKKYTNRG 402
>sp|Q87DT7|RPOD_XYLFT RNA polymerase sigma factor RpoD OS=Xylella fastidiosa (strain
Temecula1 / ATCC 700964) GN=rpoD PE=3 SV=1
Length = 618
Score = 34.7 bits (78), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 4/42 (9%)
Query: 352 DQRELRRRLNYGIL----CKDKMITSNIRLVISIAKNYQGAG 389
D +E+ R + YG K +M+ +N+RLVISIAK Y G
Sbjct: 361 DIKEINRMMVYGEAKASKAKKEMVEANLRLVISIAKKYTNRG 402
>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 = 33.5 bits (75), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 43/84 (51%), Gaps = 9/84 (10%)
Query: 306 LLTANEEMQLSAGIQDLLKLEGLREVLSERCGGSPTFAQWAAAAGVDQRELRRRLNYGIL 365
LLTA +E++L+ I+ ++ RE L G P A +R L ++ G
Sbjct: 51 LLTAEDEVRLATRIEAGVRA---REELETADTGEP------APTPRRRRTLEETVHDGQE 101
Query: 366 CKDKMITSNIRLVISIAKNYQGAG 389
KD M+ +N+RLV+S+AK + G
Sbjct: 102 AKDHMVRANLRLVVSMAKRHAHRG 125
>sp|Q8CP24|RPOD_STAES RNA polymerase sigma factor RpoD OS=Staphylococcus epidermidis
(strain ATCC 12228) GN=rpoD PE=3 SV=1
Length = 368
Score = 32.7 bits (73), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGRM 391
EL +R+ G + K ++ +N+RLV+SIAK Y G G +
Sbjct: 119 ELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVGRGML 156
>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 = 32.7 bits (73), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGRM 391
EL +R+ G + K ++ +N+RLV+SIAK Y G G +
Sbjct: 119 ELAKRIEQGDEIAKSRLAEANLRLVVSIAKRYVGRGML 156
>sp|P77951|HRDB_STRGR RNA polymerase principal sigma factor HrdB OS=Streptomyces griseus
GN=hrdB PE=1 SV=1
Length = 514
Score = 32.3 bits (72), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 353 QRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAGRM 391
+REL G K+ ++ +N+RLV+S+AK Y G G +
Sbjct: 264 KRELEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGML 302
>sp|Q99TT5|RPOD_STAAN RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
N315) GN=rpoD PE=1 SV=1
Length = 368
Score = 32.3 bits (72), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGRM 391
EL +R+ G + K ++ +N+RLV+SIAK Y G G +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGML 156
>sp|P0A0I9|RPOD_STAAW RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
MW2) GN=rpoD PE=3 SV=1
Length = 368
Score = 32.3 bits (72), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGRM 391
EL +R+ G + K ++ +N+RLV+SIAK Y G G +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGML 156
>sp|Q6G905|RPOD_STAAS RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
MSSA476) GN=rpoD PE=3 SV=1
Length = 368
Score = 32.3 bits (72), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGRM 391
EL +R+ G + K ++ +N+RLV+SIAK Y G G +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGML 156
>sp|Q6GGD8|RPOD_STAAR RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
MRSA252) GN=rpoD PE=3 SV=1
Length = 368
Score = 32.3 bits (72), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGRM 391
EL +R+ G + K ++ +N+RLV+SIAK Y G G +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGML 156
>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 = 32.3 bits (72), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGRM 391
EL +R+ G + K ++ +N+RLV+SIAK Y G G +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGML 156
>sp|Q5HFJ9|RPOD_STAAC RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
COL) GN=rpoD PE=3 SV=1
Length = 368
Score = 32.3 bits (72), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGRM 391
EL +R+ G + K ++ +N+RLV+SIAK Y G G +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGML 156
>sp|P0A0J0|RPOD_STAA8 RNA polymerase sigma factor RpoD OS=Staphylococcus aureus (strain
NCTC 8325) GN=rpoD PE=3 SV=1
Length = 368
Score = 32.3 bits (72), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 25/38 (65%), Gaps = 1/38 (2%)
Query: 355 ELRRRLNYGI-LCKDKMITSNIRLVISIAKNYQGAGRM 391
EL +R+ G + K ++ +N+RLV+SIAK Y G G +
Sbjct: 119 ELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGML 156
>sp|Q59914|HRDD_STRGR RNA polymerase principal sigma factor HrdD OS=Streptomyces griseus
GN=hrdD PE=3 SV=1
Length = 332
Score = 32.0 bits (71), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 25/42 (59%)
Query: 348 AAGVDQRELRRRLNYGILCKDKMITSNIRLVISIAKNYQGAG 389
+AG + EL + G KD I SN+RLV+++A+ Y +G
Sbjct: 78 SAGASREELEALVAEGERAKDVFIRSNLRLVVAVARRYPRSG 119
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
0.312 0.123 0.339
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 126,269,209
Number of Sequences: 539616
Number of extensions: 4660495
Number of successful extensions: 16921
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 54
Number of HSP's successfully gapped in prelim test: 199
Number of HSP's that attempted gapping in prelim test: 16589
Number of HSP's gapped (non-prelim): 449
length of query: 395
length of database: 191,569,459
effective HSP length: 120
effective length of query: 275
effective length of database: 126,815,539
effective search space: 34874273225
effective search space used: 34874273225
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 62 (28.5 bits)