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= 001050
(1173 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1I3Q|B Chain B, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|B Chain B, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|B Chain B, Rna Polymerase Ii Elongation Complex
pdb|1K83|B Chain B, Crystal Structure Of Yeast Rna Polymerase Ii Complexed With
The Inhibitor Alpha Amanitin
pdb|1NIK|B Chain B, Wild Type Rna Polymerase Ii
pdb|1NT9|B Chain B, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|B Chain B, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|B Chain B, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|B Chain B, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|B Chain B, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|B Chain B, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|B Chain B, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|B Chain B, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|B Chain B, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|B Chain B, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|B Chain B, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|B Chain B, Complete Rna Polymerase Ii Elongation Complex With Substrate
Analogue Gmpcpp
pdb|1Y1V|B Chain B, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|B Chain B, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|B Chain B, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|B Chain B, 12-Subunit Rna Polymerase Ii
pdb|2E2H|B Chain B, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|B Chain B, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|B Chain B, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|B Chain B, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex A
pdb|2JA6|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex B
pdb|2JA7|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA7|N Chain N, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA8|B Chain B, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex D
pdb|2YU9|B Chain B, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With Utp
pdb|2R7Z|B Chain B, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|B Chain B, Elongation Complex Of Rna Polymerase Ii With Artificial Rdrp
Scaffold
pdb|2R93|B Chain B, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|B Chain B, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|B Chain B, Crystal Structure Of 10 Subunit Rna Polymerase Ii In Complex
With The Inhibitor Alpha-Amanitin
pdb|3FKI|B Chain B, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|B Chain B, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|B Chain B, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|B Chain B, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|B Chain B, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|B Chain B, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|B Chain B, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|B Chain B, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|C Chain C, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|B Chain B, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|N Chain N, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|B Chain B, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iii With A T-U
Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|B Chain B, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|B Chain B, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|B Chain B, Complete Rna Polymerase Ii Elongation Complex Iv With A T-U
Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|B Chain B, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
D
pdb|3I4N|B Chain B, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
E
pdb|3K1F|B Chain B, Crystal Structure Of Rna Polymerase Ii In Complex With Tfiib
pdb|3K7A|B Chain B, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|B Chain B, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|B Chain B, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|B Chain B, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|B Chain B, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|B Chain B, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|B Chain B, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|B Chain B, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|B Chain B, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|B Chain B, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|B Chain B, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|B Chain B, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|B Chain B, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|3J0K|B Chain B, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|B Chain B, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|B Chain B, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|B Chain B, Rna Polymerase Ii Elongation Complex Containing A Cpd Lesion
pdb|4BBR|B Chain B, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|B Chain B, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1224
Score = 600 bits (1546), Expect = e-171, Method: Compositional matrix adjust.
Identities = 418/1258 (33%), Positives = 623/1258 (49%), Gaps = 138/1258 (10%)
Query: 2 DSDDNGFTDPTSLCDLGEEFLKTFCRKAAVS-FFNEYGLVSHQINSYNEFIKNGLQKAFD 60
D D GF D ++ + + A +S FF E GLVS Q++S+N+F+ LQ
Sbjct: 12 DEDPYGFEDESAPITAEDSW-------AVISAFFREKGLVSQQLDSFNQFVDYTLQDIIC 64
Query: 61 SFGETIVEPGYDPSKKGEGEWRYASMRFGQVTLDKPSFFAGNGGDEHDMFPRHARLQNMT 120
I+E + + + R + FG++ + KP +G H ++P+ ARL+N+T
Sbjct: 65 EDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVT-HALYPQEARLRNLT 123
Query: 121 YSSRMKVKVQFQVYTQKRVTSDKFKTGREQYIQKEVLSD-ETTNIIIGRIPVMVKSDLCW 179
YSS + V V+ + Y V + K + I +E D E+ + IGR+P+M++S C+
Sbjct: 124 YSSGLFVDVKKRTYEAIDVPGRELKY---ELIAEESEDDSESGKVFIGRLPIMLRSKNCY 180
Query: 180 MKGVEKGD------CDFDHGGYFIIKGAEKVFVAQEQICLKRLWVSNSMGWT-VAYKSE- 231
+ + D C FD GGYFII G+EKV +AQE+ + V + +++ +E
Sbjct: 181 LSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEI 240
Query: 232 ----NKRNRLIVRL-VDMSKFEDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNL 286
K +R I L V + E ++ ++ +IPI I+F ALG+ D EI+
Sbjct: 241 RSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEH 300
Query: 287 IDFTCEDCSILNILFASIHDADNKCDEFRKGRNALKYVDKLIKGTTFPPGES-----TEE 341
I + D +L +L + D D AL ++ + +GT + ++
Sbjct: 301 ICYDVNDWQMLEMLKPCVEDGFVIQDR----ETALDFIGR--RGTALGIKKEKRIQYAKD 354
Query: 342 CMNTYLFP---SLHG-TKQKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKXXXXXXXXXX 397
+ P L G +KA FLGYM+ LL R+ D+RD F K
Sbjct: 355 ILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPL-- 412
Query: 398 XXXKVHIAHARKRMAKALQRDL--YGDRTVRP-----IEYYLDASILTNGLSRAFSTGAW 450
+A K + K L +D+ Y RTV ++ ++A +T+GL A +TG W
Sbjct: 413 ------LAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNW 466
Query: 451 SHPFKRTERISGIVANLGRANPLQTLVDLRRTRQQVQYTGKVGDARYPHPSHWGKICFLS 510
K +G+ L R TL LRRT + GK+ R H +HWG +C
Sbjct: 467 GEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAE 526
Query: 511 TPDGENCGLVKNLGVTGLVSTSI-LEPIFEQLFNSGMEKLADDASYSLGGKFKVFVDGDW 569
TP+G+ CGLVKNL + +S PI L GME L D + +VFV+G W
Sbjct: 527 TPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVW 586
Query: 570 IGVCKDSLSFVSXXXXXXXXXXXPTQVEIKRDELQSEVRIFMDAGRILRPLLVVEN---- 625
GV ++ + +V + RD + E++IF DAGR+ RPL +VE+
Sbjct: 587 HGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESL 646
Query: 626 --------MGKIKSL--------EG-----KNYTFQALLDHGIIELVGTEEEEDCCTAWG 664
G I L EG + YT+ +LL+ G++E + EEEE A
Sbjct: 647 GHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQ 706
Query: 665 IKYLLK---------DIEDKKPIK-------FTHCELDMSFLLGLSCGIIPFANHDHARR 708
+ L D++ K I+ FTHCE+ S +LG++ IIPF +H+ + R
Sbjct: 707 PEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPR 766
Query: 709 VLYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPR 768
YQS QA+G TN ++R+DT+++ L+YPQ+PL T + L
Sbjct: 767 NTYQS-AMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAME-----------YLKF 814
Query: 769 PELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRS 828
EL GQNAIVA+ + GYNQEDS++MN++S++RG+FRS RSY + M + +
Sbjct: 815 RELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITE-T 873
Query: 829 SDDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYA---------------DS 873
+ ++ K G D LDDDG G + D++IGK S
Sbjct: 874 FEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHS 933
Query: 874 GADHSIKLKHTERGMVQKVVLSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFL 933
D S L+ TE G+V +V++++N DG F V +R + P +GDKF+S HGQKG +G
Sbjct: 934 KRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGIT 993
Query: 934 ESQENFPFTIQGIVPDIVINPHAFPSRQTPGQXXXXXXXXXXXXXXXXXCSGLKRYATPF 993
+E+ PFT +GIVPD++INPHA PSR T SG + A+PF
Sbjct: 994 YRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAA------LSGNEGDASPF 1047
Query: 994 ATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRN 1053
+V+ I++ L G+ G E +Y+G TG+ + + IF GPT+YQRL HM +DK+ R
Sbjct: 1048 TDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARA 1107
Query: 1054 TGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCK 1113
GP+ LTRQPV R R GG++FGEMERDC+IAHGAA+ L ERL SD++++HIC C
Sbjct: 1108 RGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGIC- 1166
Query: 1114 NVANVIQXXXXXXXXXXXPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171
+ VI C+ CD+ DI + ++PY AKLL QEL +M IT + T+
Sbjct: 1167 GLMTVIAKLNHNQFE-----CKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTD 1219
>pdb|3H0G|B Chain B, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|N Chain N, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1210
Score = 592 bits (1526), Expect = e-169, Method: Compositional matrix adjust.
Identities = 410/1239 (33%), Positives = 616/1239 (49%), Gaps = 127/1239 (10%)
Query: 19 EEFLKTFCRKAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVEPGYDPSKKGE 78
E + C SFF E L Q+ S++EF++N +Q+ D T+ Y +
Sbjct: 10 ETLTQEDCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDD-DSTLTLDQYAQHTGAQ 68
Query: 79 GE-WRYASMRFGQVTLDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQK 137
G+ R + FGQ+ L +P+ +G MFP+ ARL+N+TYSS + V ++ +V
Sbjct: 69 GDVTRRYEINFGQIYLSRPTMTEADGSTT-TMFPQEARLRNLTYSSPLYVDMRKKVM--- 124
Query: 138 RVTSDKFKTGREQYIQKEVLSDETTNIIIGRIPVMVKSDLCWMKGV------EKGDCDFD 191
V +D E+ E +E + + IG+IP+M++S C + GV + +C +D
Sbjct: 125 -VAADSNVPIGEEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYD 183
Query: 192 HGGYFIIKGAEKVFVAQEQICLKRLWV-SNSMGWTVAYKSE-----NKRNRLI--VRLVD 243
GGYFII G+EKV +AQE+ + V + +AY +E + +RLI +++
Sbjct: 184 QGGYFIINGSEKVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKL 243
Query: 244 MSKFEDIKGGEKVLSVYFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFAS 303
M++ + G ++ ++ ++IPI I+F ALGV D++I+ I + D +L ++
Sbjct: 244 MARNTENSGQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPC 303
Query: 304 IHDADNKCDEFRKGRNALKYVDKLIKGTTFPPGESTE-------ECMNTYLFPSLHGTK- 355
I +A D+ AL Y+ K +G+T G + E + + L P + +
Sbjct: 304 IEEAFVIQDK----DIALDYIGK--RGST--TGVTREKRLRYAHDILQKELLPHITTMEG 355
Query: 356 ---QKARFLGYMVKCLLQAYSGRRKCDNRDDFRNKXXXXXXXXXXXXXKVHIAHARKRMA 412
+KA FLGYM+ +L RR+ D+RD F K ++ + +
Sbjct: 356 FETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVY 415
Query: 413 KALQRDLYGDRTVRPIEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANP 472
K +Q+ + +R + + ++I+TNGL + +TG W + G+ L R
Sbjct: 416 KYMQKCVETNREFN-LTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTF 474
Query: 473 LQTLVDLRRTRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVST- 531
TL LRRT + GK+ R H +HWG +C TP+G+ CGLVKNL + VS
Sbjct: 475 ASTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVG 534
Query: 532 SILEPIFEQLFNSGMEKLADDASYSLGGKFKVFVDGDWIGVCKDSLSFVSXXXXXXXXXX 591
S PI E L G+E L D + KVFV+G W+GV +D
Sbjct: 535 SPSAPIIEFLEEWGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLD 594
Query: 592 XPTQVEIKRDELQSEVRIFMDAGRILRPLLVVEN------MGKI--------KSLEGKN- 636
+V I RD + E+R+F DAGRI RPL +V+N G++ + +E K+
Sbjct: 595 ISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDR 654
Query: 637 --------YTFQALLDHGIIELVGTEEEEDCCTA---------------WGIKYLLKDIE 673
+ + AL+ G+IE + EEEE A + +K L +
Sbjct: 655 YDIDPEQRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQ 714
Query: 674 DKKPI------KFTHCELDMSFLLGLSCGIIPFANHDHARRVLYQSQKHSSQAIGFPTTN 727
KP +THCE+ + +LG+ IIPF +H+ + R YQS QA+G TN
Sbjct: 715 RVKPAPNPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQS-AMGKQAMGVYLTN 773
Query: 728 PSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPELYNGQNAIVAVNVHLGY 787
+R+DT+++ L+YPQ+PL T + L EL GQNAIVA+ + GY
Sbjct: 774 YQVRMDTMANILYYPQKPLATTRSME-----------YLKFRELPAGQNAIVAILCYSGY 822
Query: 788 NQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMVNFGKIQSKIGRVDS 847
NQEDS++MN+AS++RG+FRS R+Y + M V + V ++ K G D
Sbjct: 823 NQEDSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVME-EFERPVRSTTLRMKHGTYDK 881
Query: 848 LDDDGFPFIGANLQSGDIVIGKYADSGADH---------------SIKLKHTERGMVQKV 892
L+DDG G + DI+IGK A DH S L+ TE G+V +V
Sbjct: 882 LEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQV 941
Query: 893 VLSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFLESQENFPFTIQGIVPDIVI 952
++++N +G F V +R R P +GDKF+S HGQKG +G E+ PF+ QGIVPDI+I
Sbjct: 942 MVTTNQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIII 1001
Query: 953 NPHAFPSRQTPGQXXXXXXXXXXXXXXXXXCSGLKRYATPFATPSVDAITEQLHRAGFSK 1012
NPHA PSR T SG + ATPF +V+A+++ L GF
Sbjct: 1002 NPHAIPSRMTVAHLVECQLSKVSA------LSGFEGDATPFTDVTVEAVSKLLRSHGFQS 1055
Query: 1013 WGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQPVADRKRFG 1072
G E +Y G TG + + +F+GPT+YQRL H+ +DK+ R GPV LTRQPV R R G
Sbjct: 1056 RGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDG 1115
Query: 1073 GIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQXXXXXXXXXXXP 1132
G++FGEMERDC I+HG ++ L ERLF SD+Y++ +C C +A
Sbjct: 1116 GLRFGEMERDCQISHGCSSVLRERLFDCSDAYRVIVCDICGLIA-------IASYKKDSY 1168
Query: 1133 YCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171
CR C + + +PY AKLL QEL SM I + T+
Sbjct: 1169 ECRSCQNRTRFSQVYLPYAAKLLFQELMSMNIAPRLFTK 1207
>pdb|2PMZ|B Chain B, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|R Chain R, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|B Chain B, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|J Chain J, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 1124
Score = 483 bits (1242), Expect = e-136, Method: Compositional matrix adjust.
Identities = 365/1198 (30%), Positives = 562/1198 (46%), Gaps = 155/1198 (12%)
Query: 32 SFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVE-PGYDPSKKGEGEWRYASMRFGQ 90
++F GLV ++SYN+F++N LQ+ D GE E PG +R G+
Sbjct: 16 AYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTEIPGL-------------KVRLGK 62
Query: 91 VTLDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQ 150
+ + KP + G E ++ P ARL+N+TY++ + + T V ++
Sbjct: 63 IRIGKPRVRESDRG-EREISPMEARLRNLTYAAPLWL-------TMIPVENN-------- 106
Query: 151 YIQKEVLSDETTNIIIGRIPVMVKSDL------CWMKGVEKGDCDFDHGGYFIIKGAEKV 204
+ E + IG +P+M+KS + K +E G+ D GGYFI+ G+E+V
Sbjct: 107 ------IEAEPEEVYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERV 160
Query: 205 FVAQEQICLKRLWV-----SNSMGWTVAYKSENKRNRLIVRLVDMSKFEDIKGGEKVLSV 259
V QE + R+ V +++ T S R+ V + E +K G +S
Sbjct: 161 IVTQEDLAPNRVLVDTGKTGSNITHTAKIISSTAGYRVPVTI------ERLKDGTFHVSF 214
Query: 260 YFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGRN 319
+ +IP IL ALG+ +D++IV + D + N LF S+ A + + +
Sbjct: 215 PAVPGKIPFVILMRALGILTDRDIVYAVSL---DPEVQNELFPSLEQASSIANV----DD 267
Query: 320 ALKYVDKLIKGTTFPPG-------ESTEECMNTYLFPSLHGT----KQKARFLGYMVKCL 368
AL ++ G+ G E ++ ++ Y P L + K+KA +L Y + +
Sbjct: 268 ALDFI-----GSRVAIGQKRENRIEKAQQIIDKYFLPHLGTSAEDRKKKAYYLAYAISKV 322
Query: 369 LQAYSGRRKCDNRDDFRNKXXXXXXXXXXXXXKVHIAHARKRMAKALQRDLYGDRTVRPI 428
++ Y GRR+ D++D + NK +V K + L++ R + +
Sbjct: 323 IELYLGRREPDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKL-AL 381
Query: 429 EYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTRQQVQY 488
+ + I+T + A +TG W RT G+ L R N L L LRR +
Sbjct: 382 KALVRPDIVTERIRHALATGNWVG--GRT----GVSQLLDRTNWLSMLSHLRRVISSLAR 435
Query: 489 TGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSILEPIFEQ-LFNSGME 547
+AR H + WG++C TP+G N GLVKNL + ++ I E I E+ L+ G+
Sbjct: 436 GQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGINERIVEKTLYEMGVV 495
Query: 548 KLADDA-SYSLGGK--------FKVFVDGDWIGVCKDSLSFVSXXXXXXXXXXXPTQVEI 598
+ + + GG+ KV ++G IG +D + +V +
Sbjct: 496 PVEEVIRRVTEGGEDQNEYLKWSKVILNGRLIGYYQDGGELANKIRERRRKGEISDEVNV 555
Query: 599 KR--DELQSEVRIFMDAGRILRPLLVVEN------MGKIKSLEGKNYTFQALLDHGIIEL 650
+ +EV + D+GR+ RPL++V N + I+ LE TF L+ G IE
Sbjct: 556 GHIVTDFINEVHVNCDSGRVRRPLIIVSNGNPLVTIEDIEKLESGAITFDDLVRQGKIEY 615
Query: 651 VGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRVL 710
+ EEEE+ A L D TH E+ +LG++ IIP+ H+ + R
Sbjct: 616 LDAEEEENAYVALEPNDLTPD--------HTHLEIWSPAILGITASIIPYPEHNQSPRNT 667
Query: 711 YQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRPE 770
YQS + QA+G N +R DT +H L YPQRPL +T D +G RP
Sbjct: 668 YQS-AMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTN--------RPA 718
Query: 771 LYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSD 830
G NAI+AV GYN EDS++MNR+S+ERGM+RS R Y E E++ D
Sbjct: 719 ---GNNAILAVMSFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTE----EVKYPGGQED 771
Query: 831 DMV-NFGKIQSKIGR--VDSLDDDGFPFIGANLQSGDIVIGKYA--------------DS 873
+V ++ G+ L+D+G ++ GD++IGK + +
Sbjct: 772 KIVMPEAGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQA 831
Query: 874 GADHSIKLKHTERGMVQKVVLSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQKGVLGFL 933
D SI +H E G+V V+++ +G V +R +R P +GDKF+S HGQKGV+G L
Sbjct: 832 KRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIPTIGDKFASRHGQKGVIGML 891
Query: 934 ESQENFPFTIQGIVPDIVINPHAFPSRQTPGQXXXXXXXXXXXXXXXXXCSGLKRYATPF 993
Q + P+T++G+VPDI++NPHA PSR T GQ SG ATPF
Sbjct: 892 IPQVDMPYTVKGVVPDIILNPHALPSRMTLGQ------IMEGIAGKYAALSGNIVDATPF 945
Query: 994 ATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRN 1053
++ + ++ R G+ TE +YDGRTG+ ++S I+ G +YQ+L HM DK+ R
Sbjct: 946 YKTPIEQLQNEILRYGYLPDATEVVYDGRTGQKIKSRIYFGVVYYQKLHHMVADKLHARA 1005
Query: 1054 TGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCK 1113
GPV LTRQP R R GG++FGEMERDCLI G A L +RL SD +++C +C
Sbjct: 1006 RGPVQILTRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSDRTMIYVCDQCG 1065
Query: 1114 NVANVIQXXXXXXXXXXXPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLKFDTE 1171
+ + C I ++ V Y KLL QEL SM I+ + E
Sbjct: 1066 YIGWYDKNKNKYV-------CPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPRLVLE 1116
>pdb|2WAQ|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|B Chain B, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|R Chain R, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|B Chain B, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|R Chain R, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|B Chain B, Rnap At 3.2ang
pdb|4B1O|B Chain B, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|R Chain R, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 1131
Score = 479 bits (1232), Expect = e-135, Method: Compositional matrix adjust.
Identities = 363/1204 (30%), Positives = 565/1204 (46%), Gaps = 159/1204 (13%)
Query: 28 KAAVSFFNEYGLVSHQINSYNEFIKNGLQKAFDSFGETIVE-PGYDPSKKGEGEWRYASM 86
K ++F GLV ++SYN+F++N LQ+ D GE E PG +
Sbjct: 15 KVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTEIPGL-------------KV 61
Query: 87 RFGQVTLDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKT 146
R G++ + KP + G E ++ P ARL+N+TY++ + + T V ++
Sbjct: 62 RLGKIRIGKPRVRESDRG-EREISPMEARLRNLTYAAPLWL-------TMIPVENN---- 109
Query: 147 GREQYIQKEVLSDETTNIIIGRIPVMVKSDL------CWMKGVEKGDCDFDHGGYFIIKG 200
+ E + IG +P+M+KS + K +E G+ D GGYFI+ G
Sbjct: 110 ----------IEAEPEEVYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNG 159
Query: 201 AEKVFVAQEQICLKRLWV-SNSMGWTVAYKSENKRNRLIVRLVDMSKFEDIKGGEKVLSV 259
+E+V V QE + R+ V + G + + ++ + R+ E +K G +S
Sbjct: 160 SERVIVTQEDLAPNRVLVDTGKTGSNITHTAKIISSTAGYRV--PVTIERLKDGTFHVSF 217
Query: 260 YFLSTEIPIWILFFALGVSSDKEIVNLIDFTCEDCSILNILFASIHDADNKCDEFRKGRN 319
+ +IP IL ALG+ +D++IV + D I N LF S+ A + + +
Sbjct: 218 PAVPGKIPFVILMRALGILTDRDIVYAVSL---DPEIQNELFPSLEQASSIANV----DD 270
Query: 320 ALKYVDKLIKGTTFPPG-------ESTEECMNTYLFPSLHGT-----KQKARFLGYMVKC 367
AL ++ G+ G E ++ ++ Y P L GT ++KA +L Y +
Sbjct: 271 ALDFI-----GSRVAIGQKRENRIEKAQQIIDKYFLPHL-GTSADDRRKKAYYLAYAISK 324
Query: 368 LLQAYSGRRKCDNRDDFRNKXXXXXXXXXXXXXKVHIAHARKRMAKALQRDLYGDRTVRP 427
+++ Y GRR+ D++D + NK +V K + L++ R +
Sbjct: 325 VIELYLGRREPDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKL-A 383
Query: 428 IEYYLDASILTNGLSRAFSTGAWSHPFKRTERISGIVANLGRANPLQTLVDLRRTRQQVQ 487
++ + I+T + A +TG W RT G+ L R N L L LRR +
Sbjct: 384 LKALVRPDIVTERIRHALATGNWVG--GRT----GVSQLLDRTNWLSMLSHLRRVISSLA 437
Query: 488 YTGKVGDARYPHPSHWGKICFLSTPDGENCGLVKNLGVTGLVSTSILEPIFEQ-LFNSGM 546
+AR H + WG++C TP+G N GLVKNL + ++ I E I E+ L+ G+
Sbjct: 438 RGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGINEKIVEKTLYEMGV 497
Query: 547 EKLADDA-SYSLGGK--------FKVFVDGDWIGVCKDSLSFVSXXXXXXXXXXXPTQVE 597
+ + + GG+ KV ++G +G +D +V
Sbjct: 498 VPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLVGYYRDGEELAKKIRERRRKGEISDEVN 557
Query: 598 IKR--DELQSEVRIFMDAGRILRPLLVVENMGK------IKSLEGKNYTFQALLDHGIIE 649
+ + +EV + D+GR+ RPL++V N I+ L+ + TF L+ G IE
Sbjct: 558 VGHIVTDFINEVHVNCDSGRVRRPLIIVSNGNPLVTREDIEKLDSGSITFDDLVRQGKIE 617
Query: 650 LVGTEEEEDCCTAWGIKYLLKDIEDKKPIKFTHCELDMSFLLGLSCGIIPFANHDHARRV 709
+ EEEE+ Y+ + D P + TH E+ +LG++ IIP+ H+ + R
Sbjct: 618 YLDAEEEENA-------YVALEPSDLTP-EHTHLEIWSPAILGITASIIPYPEHNQSPRN 669
Query: 710 LYQSQKHSSQAIGFPTTNPSIRVDTLSHQLFYPQRPLFRTMISDCLGKPGYGHNHILPRP 769
YQS + QA+G N +R DT +H L YPQRPL +T D +G RP
Sbjct: 670 TYQS-AMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTN--------RP 720
Query: 770 ELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSS 829
G NAI+AV GYN EDS++MNR+S+ERGM+RS R Y E E++
Sbjct: 721 A---GNNAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTE----EVKYPGGQE 773
Query: 830 DDMVN--------FGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYA---------- 871
D +V GK ++ L+D+G ++ GD++IGK +
Sbjct: 774 DKIVMPEPGVRGYKGKEYYRL-----LEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKE 828
Query: 872 ----DSGADHSIKLKHTERGMVQKVVLSSNDDGKNFSVVSLRQVRSPCLGDKFSSMHGQK 927
+ D SI +H E G+V V+++ +G V +R +R P +GDKF+S HGQK
Sbjct: 829 LSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIPSIGDKFASRHGQK 888
Query: 928 GVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQXXXXXXXXXXXXXXXXXCSGLK 987
GV+G L Q + P+T++G+VPD+++NPHA PSR T GQ SG
Sbjct: 889 GVIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQ------IMEGIAGKYAALSGNI 942
Query: 988 RYATPFATPSVDAITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLIHMSED 1047
ATPF ++ + ++ + G+ TE YDGRTG+ ++S I+ G +YQ+L HM D
Sbjct: 943 VDATPFYKTPIEQLQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQKLHHMVAD 1002
Query: 1048 KVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMH 1107
K+ R GPV LTRQP R R GG++FGEMERDCLI G A L +RL SD ++
Sbjct: 1003 KIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDNSDRTTIY 1062
Query: 1108 ICRKCKNVANVIQXXXXXXXXXXXPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLK 1167
+C +C + + C I ++ V Y KLL QEL SM I+ +
Sbjct: 1063 VCDQCGYIGWYDKNKNKYV-------CPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPR 1115
Query: 1168 FDTE 1171
E
Sbjct: 1116 LILE 1119
>pdb|1IW7|C Chain C, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|M Chain M, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|C Chain C, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|M Chain M, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|C Chain C, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|M Chain M, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|2A68|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|C Chain C, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|M Chain M, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|C Chain C, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|M Chain M, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|C Chain C, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|M Chain M, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|C Chain C, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|H Chain H, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|M Chain M, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|C Chain C, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|M Chain M, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4GZY|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|C Chain C, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1119
Score = 138 bits (348), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 123/468 (26%), Positives = 198/468 (42%), Gaps = 110/468 (23%)
Query: 774 GQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSDDMV 833
GQN +VA+ GYN ED++V++ L+R + S HI Y+ E + ++ +R + D+
Sbjct: 669 GQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPER-ITRDIP 727
Query: 834 NFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADSGA------------------ 875
+ + + LD++G IGA ++ GDI++G+ + G
Sbjct: 728 HLSEAALR-----DLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKA 782
Query: 876 ----DHSIKLKHTERGMVQKVV-LSSNDDG-------KNFSVVSLRQVRSPCLGDKFSSM 923
D S+++ E G+V + V L D G + V + Q R +GDK ++
Sbjct: 783 RDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANR 842
Query: 924 HGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQXXXXXXXXXXXXXXXXXC 983
HG KGV+ + E+ P G D+++NP PSR GQ
Sbjct: 843 HGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLG---- 898
Query: 984 SGLKRYATPF----ATPSVDAITEQLHRAGFSK-----WGTER----------------- 1017
+RY +P P + + Q F K +G ++
Sbjct: 899 ---QRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTP 955
Query: 1018 ------------------LYDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHP 1059
LYDGRTGE + I +G F +L HM EDK+ R+TGP
Sbjct: 956 GKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1015
Query: 1060 LTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVI 1119
+T+QP+ + +FGG +FGEME L A+GAA L E L SD + +N A
Sbjct: 1016 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIE------GRNAA--- 1066
Query: 1120 QXXXXXXXXXXXPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLK 1167
Y I G+D+ + +VP ++L +EL ++ + ++
Sbjct: 1067 -------------YEAII-KGEDVPEPSVPESFRVLVKELQALALDVQ 1100
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 34/68 (50%), Gaps = 14/68 (20%)
Query: 471 NPLQTLVDLRR---------TRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVK 521
NPL +L RR TR++ + D R H +H+G+IC + TP+G N GL+
Sbjct: 399 NPLSSLRHKRRISALGPGGLTRERAGF-----DVRDVHRTHYGRICPVETPEGANIGLIT 453
Query: 522 NLGVTGLV 529
+L V
Sbjct: 454 SLAAYARV 461
>pdb|1L9U|C Chain C, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|L Chain L, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|C Chain C, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
Length = 1118
Score = 134 bits (336), Expect = 4e-31, Method: Compositional matrix adjust.
Identities = 125/464 (26%), Positives = 196/464 (42%), Gaps = 96/464 (20%)
Query: 771 LYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSD 830
L GQN +VA+ GYN ED++V++ L+R + S HI Y+ E + ++ +R +
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPER-ITR 723
Query: 831 DMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADSGA--------------- 875
D+ + + + LD++G IGA ++ GDI++G+ + G
Sbjct: 724 DIPHLSEAALR-----DLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFG 778
Query: 876 -------DHSIKLKHTERGMV-QKVVLSSNDDG-------KNFSVVSLRQVRSPCLGDKF 920
D S+++ E G+V ++ L D G + V + Q R +GDK
Sbjct: 779 EKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKL 838
Query: 921 SSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQXXXXXXXXXXXXXXX 980
++ HG KGV+ + E+ P G D+++NP PSR GQ
Sbjct: 839 ANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQ 898
Query: 981 XXCSGL----------------------KRYATPFAT----PSVDAITEQLHRAGFSKWG 1014
S + KR F V A E+L K
Sbjct: 899 RYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSP 958
Query: 1015 TERL-----------YDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQ 1063
E+L YDGRTGE I +G F +L HM EDK+ R+TGP +T+Q
Sbjct: 959 EEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQ 1018
Query: 1064 PVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQXXX 1123
P+ + +FGG +FGEME L A+GAA L E L SD + +N A
Sbjct: 1019 PLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIE------GRNAA------- 1065
Query: 1124 XXXXXXXXPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLK 1167
Y I G+D+ + +VP ++L +EL ++ + ++
Sbjct: 1066 ---------YQAII-KGEDVPEPSVPESFRVLVKELQALALDVQ 1099
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 14/70 (20%)
Query: 471 NPLQTLVDLRR---------TRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVK 521
NPL +L RR TR++ + D R H +H+G+IC + TP+G N GL+
Sbjct: 399 NPLSSLRHKRRISALGPGGLTRERAGF-----DVRDVHRTHYGRICPVETPEGANIGLIT 453
Query: 522 NLGVTGLVST 531
+L V
Sbjct: 454 SLAAYARVDA 463
>pdb|1YNJ|C Chain C, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|C Chain C, Taq Rna Polymerase-rifampicin Complex
pdb|2GHO|C Chain C, Recombinant Thermus Aquaticus Rna Polymerase For Structural
Studies
Length = 1119
Score = 134 bits (336), Expect = 4e-31, Method: Compositional matrix adjust.
Identities = 125/464 (26%), Positives = 196/464 (42%), Gaps = 96/464 (20%)
Query: 771 LYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSD 830
L GQN +VA+ GYN ED++V++ L+R + S HI Y+ E + ++ +R +
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPER-ITR 724
Query: 831 DMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADSGA--------------- 875
D+ + + + LD++G IGA ++ GDI++G+ + G
Sbjct: 725 DIPHLSEAALR-----DLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFG 779
Query: 876 -------DHSIKLKHTERGMV-QKVVLSSNDDG-------KNFSVVSLRQVRSPCLGDKF 920
D S+++ E G+V ++ L D G + V + Q R +GDK
Sbjct: 780 EKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKL 839
Query: 921 SSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQXXXXXXXXXXXXXXX 980
++ HG KGV+ + E+ P G D+++NP PSR GQ
Sbjct: 840 ANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQ 899
Query: 981 XXCSGL----------------------KRYATPFAT----PSVDAITEQLHRAGFSKWG 1014
S + KR F V A E+L K
Sbjct: 900 RYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSP 959
Query: 1015 TERL-----------YDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQ 1063
E+L YDGRTGE I +G F +L HM EDK+ R+TGP +T+Q
Sbjct: 960 EEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQ 1019
Query: 1064 PVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQXXX 1123
P+ + +FGG +FGEME L A+GAA L E L SD + +N A
Sbjct: 1020 PLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIE------GRNAA------- 1066
Query: 1124 XXXXXXXXPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLK 1167
Y I G+D+ + +VP ++L +EL ++ + ++
Sbjct: 1067 ---------YQAII-KGEDVPEPSVPESFRVLVKELQALALDVQ 1100
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 14/70 (20%)
Query: 471 NPLQTLVDLRR---------TRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVK 521
NPL +L RR TR++ + D R H +H+G+IC + TP+G N GL+
Sbjct: 399 NPLSSLRHKRRISALGPGGLTRERAGF-----DVRDVHRTHYGRICPVETPEGANIGLIT 453
Query: 522 NLGVTGLVST 531
+L V
Sbjct: 454 SLAAYARVDA 463
>pdb|1HQM|C Chain C, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase-
Includes Complete Structure With Side-Chains (Except For
Disordered Regions)-Further Refined From Original
Deposition-Contains Additional Sequence Information
Length = 1119
Score = 133 bits (335), Expect = 5e-31, Method: Compositional matrix adjust.
Identities = 125/464 (26%), Positives = 196/464 (42%), Gaps = 96/464 (20%)
Query: 771 LYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSD 830
L GQN +VA+ GYN ED++V++ L+R + S HI Y+ E + ++ +R +
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPER-ITR 724
Query: 831 DMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADSGA--------------- 875
D+ + + + LD++G IGA ++ GDI++G+ + G
Sbjct: 725 DIPHLSEAALR-----DLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFG 779
Query: 876 -------DHSIKLKHTERGMV-QKVVLSSNDDG-------KNFSVVSLRQVRSPCLGDKF 920
D S+++ E G+V ++ L D G + V + Q R +GDK
Sbjct: 780 EKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKL 839
Query: 921 SSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQXXXXXXXXXXXXXXX 980
++ HG KGV+ + E+ P G D+++NP PSR GQ
Sbjct: 840 ANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQ 899
Query: 981 XXCSGL----------------------KRYATPFAT----PSVDAITEQLHRAGFSKWG 1014
S + KR F V A E+L K
Sbjct: 900 RYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSP 959
Query: 1015 TERL-----------YDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQ 1063
E+L YDGRTGE I +G F +L HM EDK+ R+TGP +T+Q
Sbjct: 960 EEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQ 1019
Query: 1064 PVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQXXX 1123
P+ + +FGG +FGEME L A+GAA L E L SD + +N A
Sbjct: 1020 PLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIE------GRNAA------- 1066
Query: 1124 XXXXXXXXPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLK 1167
Y I G+D+ + +VP ++L +EL ++ + ++
Sbjct: 1067 ---------YQAII-KGEDVPEPSVPESFRVLVKELQALALDVQ 1100
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 14/70 (20%)
Query: 471 NPLQTLVDLRR---------TRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVK 521
NPL +L RR TR++ + D R H +H+G+IC + TP+G N GL+
Sbjct: 399 NPLSSLRHKRRISALGPGGLTRERAGF-----DVRDVHRTHYGRICPVETPEGANIGLIT 453
Query: 522 NLGVTGLVST 531
+L V
Sbjct: 454 SLAAYARVDA 463
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 133 bits (335), Expect = 5e-31, Method: Compositional matrix adjust.
Identities = 125/464 (26%), Positives = 195/464 (42%), Gaps = 96/464 (20%)
Query: 771 LYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSSD 830
L GQN +VA+ GYN ED++V++ L+R + S HI Y+ E + ++ R +
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG-PERITR 723
Query: 831 DMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADSGA--------------- 875
D+ + + + LD++G IGA ++ GDI++G+ + G
Sbjct: 724 DIPHLSEAALR-----DLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFG 778
Query: 876 -------DHSIKLKHTERGMV-QKVVLSSNDDG-------KNFSVVSLRQVRSPCLGDKF 920
D S+++ E G+V ++ L D G + V + Q R +GDK
Sbjct: 779 EKARDVKDTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDKL 838
Query: 921 SSMHGQKGVLGFLESQENFPFTIQGIVPDIVINPHAFPSRQTPGQXXXXXXXXXXXXXXX 980
++ HG KGV+ + E+ P G D+++NP PSR GQ
Sbjct: 839 ANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQ 898
Query: 981 XXCSGL----------------------KRYATPFAT----PSVDAITEQLHRAGFSKWG 1014
S + KR F V A E+L K
Sbjct: 899 RYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKSP 958
Query: 1015 TERL-----------YDGRTGEMVRSLIFIGPTFYQRLIHMSEDKVKFRNTGPVHPLTRQ 1063
E+L YDGRTGE I +G F +L HM EDK+ R+TGP +T+Q
Sbjct: 959 EEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQ 1018
Query: 1064 PVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSDSYQMHICRKCKNVANVIQXXX 1123
P+ + +FGG +FGEME L A+GAA L E L SD + +N A
Sbjct: 1019 PLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIE------GRNAA------- 1065
Query: 1124 XXXXXXXXPYCRICDSGDDIVKANVPYGAKLLCQELFSMGITLK 1167
Y I G+D+ + +VP ++L +EL ++ + ++
Sbjct: 1066 ---------YQAII-KGEDVPEPSVPESFRVLVKELQALALDVQ 1099
Score = 40.0 bits (92), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 34/70 (48%), Gaps = 14/70 (20%)
Query: 471 NPLQTLVDLRR---------TRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVK 521
NPL +L RR TR++ + D R H +H+G+IC + TP+G N GL+
Sbjct: 399 NPLSSLRHKRRISALGPGGLTRERAGF-----DVRDVHRTHYGRICPVETPEGANIGLIT 453
Query: 522 NLGVTGLVST 531
+L V
Sbjct: 454 SLAAYARVDA 463
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
Length = 1342
Score = 86.7 bits (213), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 58/189 (30%), Positives = 88/189 (46%), Gaps = 28/189 (14%)
Query: 988 RYATPFATPSVDA-----ITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLI 1042
R P ATP D I E L G RLYDGRTGE + +G + +L
Sbjct: 1177 RKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLN 1236
Query: 1043 HMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSD 1102
H+ +DK+ R+TG +T+QP+ + +FGG +FGEME L A+GAA L E L SD
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1296
Query: 1103 SYQMHICRKCKNVANVIQXXXXXXXXXXXPYCRICDSGDDIVKANVPYGAKLLCQELFSM 1162
+ + K N++ G+ ++ +P +L +E+ S+
Sbjct: 1297 D----VNGRTKMYKNIV-------------------DGNHQMEPGMPESFNVLLKEIRSL 1333
Query: 1163 GITLKFDTE 1171
GI ++ + E
Sbjct: 1334 GINIELEDE 1342
Score = 44.3 bits (103), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 53/105 (50%), Gaps = 6/105 (5%)
Query: 770 ELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSS 829
EL GQN VA GYN EDS++++ ++ F + HI+ + ++ + ++
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITA 852
Query: 830 DDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADSG 874
D + N G+ + LD+ G +IGA + GDI++GK G
Sbjct: 853 D-IPNVGE-----AALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891
Score = 43.1 bits (100), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 14/64 (21%)
Query: 471 NPLQTLVDLRR---------TRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVK 521
NPL + RR TR++ + + R HP+H+G++C + TP+G N GL+
Sbjct: 519 NPLSEITHKRRISALGPGGLTRERAGF-----EVRDVHPTHYGRVCPIETPEGPNIGLIN 573
Query: 522 NLGV 525
+L V
Sbjct: 574 SLSV 577
Score = 38.9 bits (89), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 40/176 (22%), Positives = 70/176 (39%), Gaps = 60/176 (34%)
Query: 39 LVSHQINSYNEFIKN------GLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVT 92
L+S Q++S+ +FI+ GL+ AF S S G E +Y S R G+
Sbjct: 27 LLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPI-------QSYSGNSELQYVSYRLGEPV 79
Query: 93 LDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYI 152
D + +++ +TYS+ ++VK++ +Y ++ K +EQ
Sbjct: 80 FDV----------------QECQIRGVTYSAPLRVKLRLVIY-EREAPEGTVKDIKEQ-- 120
Query: 153 QKEVLSDETTNIIIGRIPVMVKSDLCWMKGVEKGDCDFDHGGYFIIKGAEKVFVAQ 208
+ +G IP+M + G F+I G E+V V+Q
Sbjct: 121 ----------EVYMGEIPLMTDN------------------GTFVINGTERVIVSQ 148
>pdb|3IYD|C Chain C, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
pdb|4IGC|C Chain C, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|H Chain H, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1342
Score = 86.7 bits (213), Expect = 7e-17, Method: Compositional matrix adjust.
Identities = 58/189 (30%), Positives = 88/189 (46%), Gaps = 28/189 (14%)
Query: 988 RYATPFATPSVDA-----ITEQLHRAGFSKWGTERLYDGRTGEMVRSLIFIGPTFYQRLI 1042
R P ATP D I E L G RLYDGRTGE + +G + +L
Sbjct: 1177 RKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLN 1236
Query: 1043 HMSEDKVKFRNTGPVHPLTRQPVADRKRFGGIKFGEMERDCLIAHGAAANLHERLFTLSD 1102
H+ +DK+ R+TG +T+QP+ + +FGG +FGEME L A+GAA L E L SD
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSD 1296
Query: 1103 SYQMHICRKCKNVANVIQXXXXXXXXXXXPYCRICDSGDDIVKANVPYGAKLLCQELFSM 1162
+ + K N++ G+ ++ +P +L +E+ S+
Sbjct: 1297 D----VNGRTKMYKNIV-------------------DGNHQMEPGMPESFNVLLKEIRSL 1333
Query: 1163 GITLKFDTE 1171
GI ++ + E
Sbjct: 1334 GINIELEDE 1342
Score = 44.3 bits (103), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 31/105 (29%), Positives = 53/105 (50%), Gaps = 6/105 (5%)
Query: 770 ELYNGQNAIVAVNVHLGYNQEDSLVMNRASLERGMFRSEHIRSYKAEVDNKEMQVKRRSS 829
EL GQN VA GYN EDS++++ ++ F + HI+ + ++ + ++
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITA 852
Query: 830 DDMVNFGKIQSKIGRVDSLDDDGFPFIGANLQSGDIVIGKYADSG 874
D + N G+ + LD+ G +IGA + GDI++GK G
Sbjct: 853 D-IPNVGE-----AALSKLDESGIVYIGAEVTGGDILVGKVTPKG 891
Score = 43.1 bits (100), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 34/64 (53%), Gaps = 14/64 (21%)
Query: 471 NPLQTLVDLRR---------TRQQVQYTGKVGDARYPHPSHWGKICFLSTPDGENCGLVK 521
NPL + RR TR++ + + R HP+H+G++C + TP+G N GL+
Sbjct: 519 NPLSEITHKRRISALGPGGLTRERAGF-----EVRDVHPTHYGRVCPIETPEGPNIGLIN 573
Query: 522 NLGV 525
+L V
Sbjct: 574 SLSV 577
Score = 38.9 bits (89), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 40/176 (22%), Positives = 70/176 (39%), Gaps = 60/176 (34%)
Query: 39 LVSHQINSYNEFIKN------GLQKAFDSFGETIVEPGYDPSKKGEGEWRYASMRFGQVT 92
L+S Q++S+ +FI+ GL+ AF S S G E +Y S R G+
Sbjct: 27 LLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPI-------QSYSGNSELQYVSYRLGEPV 79
Query: 93 LDKPSFFAGNGGDEHDMFPRHARLQNMTYSSRMKVKVQFQVYTQKRVTSDKFKTGREQYI 152
D + +++ +TYS+ ++VK++ +Y ++ K +EQ
Sbjct: 80 FDV----------------QECQIRGVTYSAPLRVKLRLVIY-EREAPEGTVKDIKEQ-- 120
Query: 153 QKEVLSDETTNIIIGRIPVMVKSDLCWMKGVEKGDCDFDHGGYFIIKGAEKVFVAQ 208
+ +G IP+M + G F+I G E+V V+Q
Sbjct: 121 ----------EVYMGEIPLMTDN------------------GTFVINGTERVIVSQ 148
>pdb|3TBI|B Chain B, Crystal Structure Of T4 Gp33 Bound To E. Coli Rnap
Beta-Flap Domain
Length = 228
Score = 30.0 bits (66), Expect = 7.1, Method: Composition-based stats.
Identities = 12/30 (40%), Positives = 18/30 (60%)
Query: 845 VDSLDDDGFPFIGANLQSGDIVIGKYADSG 874
+ LD+ G +IGA + GDI++GK G
Sbjct: 33 LSKLDESGIVYIGAEVTGGDILVGKVTPKG 62
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.138 0.419
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 34,655,128
Number of Sequences: 62578
Number of extensions: 1466685
Number of successful extensions: 2749
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 2627
Number of HSP's gapped (non-prelim): 49
length of query: 1173
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1063
effective length of database: 8,089,757
effective search space: 8599411691
effective search space used: 8599411691
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (26.6 bits)