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= 001021
(1186 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 1520 bits (3935), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 731/1193 (61%), Positives = 906/1193 (75%), Gaps = 52/1193 (4%)
Query: 29 WAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQ-------QS 81
W VIS++FEE L RQQL SFDEF+QNTMQEIVD+ + + + +QH Q +
Sbjct: 18 WTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRYEI 77
Query: 82 DFAEIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQ 141
+F +IYLS+P MTE+DG T T+FP+ ARLRNLTYS+PLYVD+ K+V+ + E +
Sbjct: 78 NFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGEEE 137
Query: 142 DF--------TKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVL 193
+KVFIGK+PIMLRS++C L S+ +L +L ECPYDQGGYFIINGSEKV+
Sbjct: 138 WLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIINGSEKVI 197
Query: 194 IAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQY 253
IAQE+ + N V VFKK P+ AYVAE+RS E +R S+M +++++R + +SGQ
Sbjct: 198 IAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTE---NSGQT 254
Query: 254 IRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQ 313
IRATLPYIR++IPI+IVFRALG V D+DILEHICYD D QM+E+++P +EEAFVIQ++
Sbjct: 255 IRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFVIQDKD 314
Query: 314 VALDYIGKRGATVGVTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLC 373
+ALDYIGKRG+T GVTR+KR++YA +ILQKE+LPH+ T + ET+KA++ GY+IHR+LLC
Sbjct: 315 IALDYIGKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRMLLC 374
Query: 374 ALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAI 433
AL RR DDRDH+G KRLDLAGPLL LFRMLFRK+TRDV Y+QKCV+ ++ NL A+
Sbjct: 375 ALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNREFNLTLAV 434
Query: 434 KAKTITSGLKYSLATGNWG-QANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKL 492
K+ IT+GL+YSLATGNWG Q + R GVSQVLNR T+ASTLSHLRR N+PIGR+GKL
Sbjct: 435 KSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNTPIGRDGKL 494
Query: 493 AKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEE 552
AKPRQLHN+ WGM+CPAETPEGQACGLVKNL+LM Y++VGS + PI+EFLEEWG E E+
Sbjct: 495 AKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLETLED 554
Query: 553 ISPAVIPQATKIFVNGCWVGIHRDPEMLVKTXXXXXXXVDVNTEVGVVRDIRLKELRIYT 612
+P+ P ATK+FVNG W+G+HRDP L +T +D++ EV +VRDIR KELR++T
Sbjct: 555 YNPSASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDIREKELRLFT 614
Query: 613 DYGRCSRPLFIVEKQ-------RLLIKKRDIIALQQRES-----PEDG-GWHDLVAKGFX 659
D GR RPLFIV+ L I+K I L + + PE GW LV+ G
Sbjct: 615 DAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPEQRFGWTALVSSGLI 674
Query: 660 XXXXXXXXXXXXXXXXXNDL-----------VQARLHPEE-------AYADTYTHCEIHP 701
DL V+ L P + + +THCEIHP
Sbjct: 675 EYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAPNPHVHAWTHCEIHP 734
Query: 702 SLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVT 761
++ILG+ ASIIPFPDHNQSPRNTYQSAMGKQAMG+Y+TNYQ RMDT+A +LYYPQKPL T
Sbjct: 735 AMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKPLAT 794
Query: 762 TRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKK 821
TR+ME+L FR+LPAG NAIVAI CYSGYNQEDS+IMNQ+SIDRG FRS+F+R+Y D+EKK
Sbjct: 795 TRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQEKK 854
Query: 822 MGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQD-EAQ 880
+G V E+F RP RS T+ M+HG+YDKL+DDGL PGTRVSGED+IIGKT PI D E
Sbjct: 855 IGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDHEEL 914
Query: 881 GQASR-YTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHG 939
GQ ++ + +RD S LR +E+G+VDQV++TTN +GL+FVKVR+RS RIPQIGDKF+SRHG
Sbjct: 915 GQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFASRHG 974
Query: 940 QKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDAT 999
QKGT+GMTY EDMP++ +GI PDII+NPHAIPSRMT+ L+EC + KV+A G EGDAT
Sbjct: 975 QKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEGDAT 1034
Query: 1000 PFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHS 1059
PFTDVTV+ +SK L G+Q RGFE MY+GHTGR+L A +FLGPTYYQRLKH+VDDKIH+
Sbjct: 1035 PFTDVTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDKIHA 1094
Query: 1060 RGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEH 1119
R RGPVQILTRQP EGRSRDGGLRFGEMERDC I+HG S L+ERLFD SDAYRV VC+
Sbjct: 1095 RARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSDAYRVIVCDI 1154
Query: 1120 CGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTK 1172
CGLIAIA+ KK+S+ECR C+N+T QV++PYA KLLFQELM+M IAPR+ TK
Sbjct: 1155 CGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNIAPRLFTK 1207
>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 = 1471 bits (3807), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 715/1193 (59%), Positives = 887/1193 (74%), Gaps = 53/1193 (4%)
Query: 28 AWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQS------ 81
+WAVISA+F EKGLV QQLDSF++F+ T+Q+I+ E + + + +QH +
Sbjct: 30 SWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYE 89
Query: 82 -DFAEIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRV----------IKK 130
F +IY++KPM+ ESDG T L+P+ ARLRNLTYS+ L+VDV KR +K
Sbjct: 90 ISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKY 149
Query: 131 GHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSE 190
EE + + KVFIG++PIMLRS C L + +E DL +L ECP+D GGYFIINGSE
Sbjct: 150 ELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSE 209
Query: 191 KVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSS 250
KVLIAQE+ + N V VFKK P+ ++VAE+RS E +R ST+ V++ R GSS
Sbjct: 210 KVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGRE----GSS 265
Query: 251 GQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQ 310
+ I+ATLPYI+ +IPI+I+FRALG + D +ILEHICYD D QM+E+L+P +E+ FVIQ
Sbjct: 266 ARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQ 325
Query: 311 NQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRL 370
+++ ALD+IG+RG +G+ ++KRI+YAK+ILQKE LPH+ + E++KA++ GY+I+RL
Sbjct: 326 DRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRL 385
Query: 371 LLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQ 430
LLCAL R+ +DDRDH+G KRLDLAGPLL LF+ LF+KLT+D+ Y+Q+ V+ D N++
Sbjct: 386 LLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMK 445
Query: 431 FAIKAKTITSGLKYSLATGNWG-QANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGRE 489
AI AKTITSGLKY+LATGNWG Q A +RAGVSQVLNR TY+STLSHLRR N+PIGR+
Sbjct: 446 LAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRD 505
Query: 490 GKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTEN 549
GKLAKPRQLHN+ WG++CPAETPEGQACGLVKNL+LM I+VG+ PI+ FL EWG E
Sbjct: 506 GKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEP 565
Query: 550 FEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTXXXXXXXVDVNTEVGVVRDIRLKELR 609
E+ P P AT++FVNG W G+HR+P L++T D+N EV ++RDIR KEL+
Sbjct: 566 LEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELK 625
Query: 610 IYTDYGRCSRPLFIVEK------QRLLIKKRDIIALQQRESPE-DGG--------WHDLV 654
I+TD GR RPLFIVE + L ++K I L E + +GG W L+
Sbjct: 626 IFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLL 685
Query: 655 AKGFXXXXXXXXXXXXXXXXXXNDLVQARLHPEEA-------------YADTYTHCEIHP 701
+G DL A + E +A T+THCEIHP
Sbjct: 686 NEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHP 745
Query: 702 SLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVT 761
S+ILGV ASIIPFPDHNQSPRNTYQSAMGKQAMG+++TNY RMDT+A +LYYPQKPL T
Sbjct: 746 SMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGT 805
Query: 762 TRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKK 821
TRAME+L FR+LPAG NAIVAIACYSGYNQEDS+IMNQSSIDRG FRSLFFRSY D+EKK
Sbjct: 806 TRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKK 865
Query: 822 MGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ- 880
G + E F +P R+NT+ M+HG+YDKLDDDGL PG RVSGEDVIIGKTTPIS DE +
Sbjct: 866 YGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEEL 925
Query: 881 GQASRY-TRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHG 939
GQ + Y ++RD S LR +E G+VDQVL+TTN DGL+FVKVRVR+ +IPQIGDKF+SRHG
Sbjct: 926 GQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHG 985
Query: 940 QKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDAT 999
QKGT+G+TY +EDMP+T EGI PD+I+NPHAIPSRMT+ LIEC++ KVAA G EGDA+
Sbjct: 986 QKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDAS 1045
Query: 1000 PFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHS 1059
PFTD+TV+ ISK L + GYQ RGFE MYNGHTG++L A IF GPTYYQRL+HMVDDKIH+
Sbjct: 1046 PFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHA 1105
Query: 1060 RGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEH 1119
R RGP+Q+LTRQP EGRSRDGGLRFGEMERDCMIAHGA+ FLKERL + SDA+RVH+C
Sbjct: 1106 RARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGI 1165
Query: 1120 CGLI-AIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLT 1171
CGL+ IA L N FEC+GC NK DI Q+HIPYA KLLFQELMAM I PR+ T
Sbjct: 1166 CGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYT 1218
>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 = 880 bits (2275), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 491/1162 (42%), Positives = 686/1162 (59%), Gaps = 72/1162 (6%)
Query: 29 WAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYL 88
W VI AYF+ KGLVRQ LDS+++F++N +QEI+DE +I PG + +I +
Sbjct: 14 WKVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEI-----PTEIPGLKVRLGKIRI 68
Query: 89 SKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFI 148
KP + ESD + P ARLRNLTY+APL++ + ++ + E +V+I
Sbjct: 69 GKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIP--VENNIEAEP-------EEVYI 119
Query: 149 GKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFK 208
G +PIML+S+ + Q + L E+GE P D GGYFI+NGSE+V++ QE ++ N V V
Sbjct: 120 GDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLVDT 179
Query: 209 KRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPII 268
+ + + A++ S + + R P T+ K G+ + P + +IP +
Sbjct: 180 GKTGSNITHTAKIIS-STAGYRVPVTI-------ERLKDGT----FHVSFPAVPGKIPFV 227
Query: 269 IVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGV 328
I+ RALG + D+DI+ + D ++ L PSLE+A I N ALD+IG R A +G
Sbjct: 228 ILMRALGILTDRDIVYAVSLD---PEIQNELFPSLEQASSIANVDDALDFIGSRVA-IGQ 283
Query: 329 TRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGN 388
R+ RI+ A++I+ K LPH+GT KKAYY Y I +++ LGRR DD+DHY N
Sbjct: 284 KRENRIEKAQQIIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYAN 343
Query: 389 KRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLAT 448
KRL LAG L LFR+ F+ +D+ ++K G+ + L+ ++ +T ++++LAT
Sbjct: 344 KRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALVRPDIVTERIRHALAT 403
Query: 449 GNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCP 508
GNW G R GVSQ+L+R + S LSHLRR+ S + R + R LH +QWG MCP
Sbjct: 404 GNW-----VGGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCP 458
Query: 509 AETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIP--------- 559
ETPEG GLVKNLALM I VG + + L E G EE+ V
Sbjct: 459 FETPEGPNSGLVKNLALMAQIAVGINEKIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYL 518
Query: 560 QATKIFVNGCWVGIHRDPEMLVKTXXXXXXXVDVNTEVGV---VRDIRLKELRIYTDYGR 616
+ +K+ +NG VG +RD E L K +++ EV V V D + E+ + D GR
Sbjct: 519 KWSKVILNGRLVGYYRDGEELAKKIRERRRKGEISDEVNVGHIVTDF-INEVHVNCDSGR 577
Query: 617 CSRPLFIVEKQRLLIKKRDIIALQQRESPEDGG---WHDLVAKGFXXXXXXXXXXXXXXX 673
RPL IV L+ + DI L D G + DLV +G
Sbjct: 578 VRRPLIIVSNGNPLVTREDIEKL-------DSGSITFDDLVRQGKIEYLDAEEEENAYVA 630
Query: 674 XXXNDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQA 733
+DL PE +TH EI ILG+ ASIIP+P+HNQSPRNTYQSAM KQA
Sbjct: 631 LEPSDLT-----PE------HTHLEIWSPAILGITASIIPYPEHNQSPRNTYQSAMAKQA 679
Query: 734 MGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQED 793
+G+Y NYQ R DT A++L+YPQ+PLV TRA++ + + PAG NAI+A+ ++GYN ED
Sbjct: 680 LGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVISFTGYNMED 739
Query: 794 SVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKL-DDD 852
S+IMN+SS++RG +RS FFR Y EE K ++ P+ G + Y +L +D+
Sbjct: 740 SIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPE-PGVRGYKGKEYYRLLEDN 798
Query: 853 GLAPPGTRVSGEDVIIGKTTPIS-QDEAQGQASRYTRRDHSISLRHSETGMVDQVLLTTN 911
G+ P V G DV+IGK +P E + + +RD SI RH E G+VD VL+T
Sbjct: 799 GVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGIVDLVLITET 858
Query: 912 ADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAI 971
A+G + VKVRVR +RIP IGDKF+SRHGQKG +GM Q DMP+TV+G+ PD+I+NPHA+
Sbjct: 859 AEGNKLVKVRVRDLRIPSIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHAL 918
Query: 972 PSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHT 1031
PSRMT+GQ++E I GK AA G DATPF ++ + + K GY E Y+G T
Sbjct: 919 PSRMTLGQIMEGIAGKYAALSGNIVDATPFYKTPIEQLQNEILKYGYLPDATEVTYDGRT 978
Query: 1032 GRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDC 1091
G+++ + I+ G YYQ+L HMV DKIH+R RGPVQILTRQP EGR+R+GGLRFGEMERDC
Sbjct: 979 GQKIKSRIYFGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDC 1038
Query: 1092 MIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPY 1151
+I G + LK+RL D SD ++VC+ CG I + KN + C +K+++ V + Y
Sbjct: 1039 LIGFGTAMLLKDRLLDNSDRTTIYVCDQCGYIGWYDKNKNKYVCPIHGDKSNLFPVTVSY 1098
Query: 1152 ACKLLFQELMAMAIAPRMLTKE 1173
A KLL QELM+M I+PR++ ++
Sbjct: 1099 AFKLLIQELMSMIISPRLILED 1120
>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 = 871 bits (2251), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 486/1161 (41%), Positives = 685/1161 (59%), Gaps = 70/1161 (6%)
Query: 29 WAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYL 88
W VI AYF+ KGLVRQ LDS+++F++N +QEI+DE +I PG + +I +
Sbjct: 11 WRVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEI-----PTEIPGLKVRLGKIRI 65
Query: 89 SKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFI 148
KP + ESD + P ARLRNLTY+APL++ + ++ + E +V+I
Sbjct: 66 GKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIP--VENNIEAEP-------EEVYI 116
Query: 149 GKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFK 208
G +PIML+S+ + Q + L E+GE P D GGYFI+NGSE+V++ QE ++ N V V
Sbjct: 117 GDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLVDT 176
Query: 209 KRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPII 268
+ + + A++ S + + R P T+ K G+ + P + +IP +
Sbjct: 177 GKTGSNITHTAKIIS-STAGYRVPVTI-------ERLKDGT----FHVSFPAVPGKIPFV 224
Query: 269 IVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYIGKRGATVGV 328
I+ RALG + D+DI+ + D ++ L PSLE+A I N ALD+IG R A +G
Sbjct: 225 ILMRALGILTDRDIVYAVSLD---PEVQNELFPSLEQASSIANVDDALDFIGSRVA-IGQ 280
Query: 329 TRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGN 388
R+ RI+ A++I+ K LPH+GT KKAYY Y I +++ LGRR DD+DHY N
Sbjct: 281 KRENRIEKAQQIIDKYFLPHLGTSAEDRKKKAYYLAYAISKVIELYLGRREPDDKDHYAN 340
Query: 389 KRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLAT 448
KRL LAG L LFR+ F+ +D+ ++K G+ + L+ ++ +T ++++LAT
Sbjct: 341 KRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALVRPDIVTERIRHALAT 400
Query: 449 GNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCP 508
GNW G R GVSQ+L+R + S LSHLRR+ S + R + R LH +QWG MCP
Sbjct: 401 GNW-----VGGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCP 455
Query: 509 AETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIP--------- 559
ETPEG GLVKNLALM I VG + + L E G EE+ V
Sbjct: 456 FETPEGPNSGLVKNLALMAQIAVGINERIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYL 515
Query: 560 QATKIFVNGCWVGIHRDPEMLVKTXXXXXXXVDVNTEVGV---VRDIRLKELRIYTDYGR 616
+ +K+ +NG +G ++D L +++ EV V V D + E+ + D GR
Sbjct: 516 KWSKVILNGRLIGYYQDGGELANKIRERRRKGEISDEVNVGHIVTDF-INEVHVNCDSGR 574
Query: 617 CSRPLFIVEKQRLLIKKRDIIALQQRESPEDGG--WHDLVAKGFXXXXXXXXXXXXXXXX 674
RPL IV L+ DI E E G + DLV +G
Sbjct: 575 VRRPLIIVSNGNPLVTIEDI------EKLESGAITFDDLVRQGKIEYLDAEEEENAYVAL 628
Query: 675 XXNDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAM 734
NDL P+ +TH EI ILG+ ASIIP+P+HNQSPRNTYQSAM KQA+
Sbjct: 629 EPNDLT-----PD------HTHLEIWSPAILGITASIIPYPEHNQSPRNTYQSAMAKQAL 677
Query: 735 GIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDS 794
G+Y NYQ R DT A++L+YPQ+PLV TRA++ + + PAG NAI+A+ ++GYN EDS
Sbjct: 678 GLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVMSFTGYNMEDS 737
Query: 795 VIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKL-DDDG 853
+IMN+SS++RG +RS FFR Y EE K ++ P+ + G + Y +L +D+G
Sbjct: 738 IIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPE-AGVRGYKGKEYYRLLEDNG 796
Query: 854 LAPPGTRVSGEDVIIGKTTPIS-QDEAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNA 912
+ P V G DV+IGK +P E + + +RD SI RH E G+VD VL+T A
Sbjct: 797 VVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGIVDLVLITETA 856
Query: 913 DGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIP 972
+G + VKVRVR +RIP IGDKF+SRHGQKG +GM Q DMP+TV+G+ PDII+NPHA+P
Sbjct: 857 EGNKLVKVRVRDLRIPTIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDIILNPHALP 916
Query: 973 SRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTG 1032
SRMT+GQ++E I GK AA G DATPF ++ + + + GY E +Y+G TG
Sbjct: 917 SRMTLGQIMEGIAGKYAALSGNIVDATPFYKTPIEQLQNEILRYGYLPDATEVVYDGRTG 976
Query: 1033 RRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCM 1092
+++ + I+ G YYQ+L HMV DK+H+R RGPVQILTRQP EGR+R+GGLRFGEMERDC+
Sbjct: 977 QKIKSRIYFGVVYYQKLHHMVADKLHARARGPVQILTRQPTEGRAREGGLRFGEMERDCL 1036
Query: 1093 IAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYA 1152
I G + LK+RL D SD ++VC+ CG I + KN + C +K+++ V + YA
Sbjct: 1037 IGFGTAMLLKDRLLDNSDRTMIYVCDQCGYIGWYDKNKNKYVCPIHGDKSNLFPVTVSYA 1096
Query: 1153 CKLLFQELMAMAIAPRMLTKE 1173
KLL QELM+M I+PR++ ++
Sbjct: 1097 FKLLIQELMSMIISPRLVLED 1117
>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 = 162 bits (411), Expect = 9e-40, Method: Compositional matrix adjust.
Identities = 126/468 (26%), Positives = 209/468 (44%), Gaps = 91/468 (19%)
Query: 773 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 830
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 717
Query: 831 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 880
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 718 --PERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRS 775
Query: 881 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 930
G+ +R + D S+ + E G+V L D G+R V+V V R Q+
Sbjct: 776 IFGEKARDVK-DTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQV 834
Query: 931 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 990
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 835 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 894
Query: 991 HMGKEGDATPFTDVTVDNISKALHKC------GYQMRGFE-------------------- 1024
+G+ + F T I + L + Q GF
Sbjct: 895 FLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSP 954
Query: 1025 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 1067
+Y+G TG I +G + +L HMV+DK+H+R GP +
Sbjct: 955 GKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1014
Query: 1068 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 1127
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1015 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAII---- 1070
Query: 1128 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 1175
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1071 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1106
Score = 67.8 bits (164), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 114/495 (23%), Positives = 191/495 (38%), Gaps = 109/495 (22%)
Query: 68 EIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFP-------------KAARLRNLT 114
++ PE + N G Q+ F E + P+ G+ + R ++LT
Sbjct: 33 DVPPEKRENVGIQAAFKETF---PIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLT 89
Query: 115 YSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELG 174
Y APLY + ++I K D + E + VF+G +P+M
Sbjct: 90 YQAPLYARL--QLIHK--DTGLIKEDE----VFLGHLPLMT------------------- 122
Query: 175 ECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPST 234
+ G FIING+++V+++Q S + +P +Y + S+ R P
Sbjct: 123 -----EDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRY-----IASIIPLPKRGP-- 170
Query: 235 MFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICY-DFQDT 293
++ + S T+ + + P++++ R LG+ + + E Y D
Sbjct: 171 -WIDLEVEASGV---------VTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQG 220
Query: 294 QMMEL---LRPSLEEAFV----------IQNQQVALDYI------GKRGATVGVTRDKRI 334
+ E +RP EEA V + AL Y+ KR R K
Sbjct: 221 LLDEAVLAMRP--EEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAE 278
Query: 335 KYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLA 394
+ L L G+F + Y+ L + DD DH GN+R+
Sbjct: 279 EKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFA--LTAGVPGHEVDDIDHLGNRRIRTV 336
Query: 395 GPLLGGLFRMLFRKLTRDVRA-YVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQ 453
G L+ FR+ +L R VR V D L + ++ + + L+
Sbjct: 337 GELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLEAALREFF------- 386
Query: 454 ANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQLHNSQWGMMCPA 509
+R+ +SQ + S+L H RR+++ P G RE R +H + +G +CP
Sbjct: 387 -----SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPV 441
Query: 510 ETPEGQACGLVKNLA 524
ETPEG GL+ +LA
Sbjct: 442 ETPEGANIGLITSLA 456
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 162 bits (411), Expect = 9e-40, Method: Compositional matrix adjust.
Identities = 126/468 (26%), Positives = 209/468 (44%), Gaps = 91/468 (19%)
Query: 773 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 830
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 717
Query: 831 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 880
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 718 --PERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRS 775
Query: 881 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 930
G+ +R + D S+ + E G+V L D G+R V+V V R Q+
Sbjct: 776 IFGEKARDVK-DTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQV 834
Query: 931 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 990
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 835 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 894
Query: 991 HMGKEGDATPFTDVTVDNISKALHKC------GYQMRGFE-------------------- 1024
+G+ + F T I + L + Q GF
Sbjct: 895 FLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSP 954
Query: 1025 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 1067
+Y+G TG I +G + +L HMV+DK+H+R GP +
Sbjct: 955 GKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1014
Query: 1068 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 1127
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1015 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAII---- 1070
Query: 1128 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 1175
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1071 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1106
Score = 67.8 bits (164), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 114/495 (23%), Positives = 191/495 (38%), Gaps = 109/495 (22%)
Query: 68 EIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFP-------------KAARLRNLT 114
++ PE + N G Q+ F E + P+ G+ + R ++LT
Sbjct: 33 DVPPEKRENVGIQAAFKETF---PIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLT 89
Query: 115 YSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELG 174
Y APLY + ++I K D + E + VF+G +P+M
Sbjct: 90 YQAPLYARL--QLIHK--DTGLIKEDE----VFLGHLPLMT------------------- 122
Query: 175 ECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPST 234
+ G FIING+++V+++Q S + +P +Y + S+ R P
Sbjct: 123 -----EDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRY-----IASIIPLPKRGP-- 170
Query: 235 MFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICY-DFQDT 293
++ + S T+ + + P++++ R LG+ + + E Y D
Sbjct: 171 -WIDLEVEASGV---------VTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQG 220
Query: 294 QMMEL---LRPSLEEAFV----------IQNQQVALDYI------GKRGATVGVTRDKRI 334
+ E +RP EEA V + AL Y+ KR R K
Sbjct: 221 LLDEAVLAMRP--EEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAE 278
Query: 335 KYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLA 394
+ L L G+F + Y+ L + DD DH GN+R+
Sbjct: 279 EKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFA--LTAGVPGHEVDDIDHLGNRRIRTV 336
Query: 395 GPLLGGLFRMLFRKLTRDVRA-YVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQ 453
G L+ FR+ +L R VR V D L + ++ + + L+
Sbjct: 337 GELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLEAALREFF------- 386
Query: 454 ANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQLHNSQWGMMCPA 509
+R+ +SQ + S+L H RR+++ P G RE R +H + +G +CP
Sbjct: 387 -----SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPV 441
Query: 510 ETPEGQACGLVKNLA 524
ETPEG GL+ +LA
Sbjct: 442 ETPEGANIGLITSLA 456
>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 = 162 bits (410), Expect = 9e-40, Method: Compositional matrix adjust.
Identities = 126/468 (26%), Positives = 209/468 (44%), Gaps = 91/468 (19%)
Query: 773 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 830
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 718
Query: 831 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 880
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 719 --PERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRS 776
Query: 881 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 930
G+ +R + D S+ + E G+V L D G+R V+V V R Q+
Sbjct: 777 IFGEKARDVK-DTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQV 835
Query: 931 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 990
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 836 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 895
Query: 991 HMGKEGDATPFTDVTVDNISKALHKC------GYQMRGFE-------------------- 1024
+G+ + F T I + L + Q GF
Sbjct: 896 FLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSP 955
Query: 1025 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 1067
+Y+G TG I +G + +L HMV+DK+H+R GP +
Sbjct: 956 GKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1015
Query: 1068 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 1127
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1016 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAII---- 1071
Query: 1128 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 1175
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1072 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1107
Score = 67.8 bits (164), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 114/495 (23%), Positives = 191/495 (38%), Gaps = 109/495 (22%)
Query: 68 EIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFP-------------KAARLRNLT 114
++ PE + N G Q+ F E + P+ G+ + R ++LT
Sbjct: 33 DVPPEKRENVGIQAAFKETF---PIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLT 89
Query: 115 YSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELG 174
Y APLY + ++I K D + E + VF+G +P+M
Sbjct: 90 YQAPLYARL--QLIHK--DTGLIKEDE----VFLGHLPLMT------------------- 122
Query: 175 ECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPST 234
+ G FIING+++V+++Q S + +P +Y + S+ R P
Sbjct: 123 -----EDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRY-----IASIIPLPKRGP-- 170
Query: 235 MFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICY-DFQDT 293
++ + S T+ + + P++++ R LG+ + + E Y D
Sbjct: 171 -WIDLEVEASGV---------VTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQG 220
Query: 294 QMMEL---LRPSLEEAFV----------IQNQQVALDYI------GKRGATVGVTRDKRI 334
+ E +RP EEA V + AL Y+ KR R K
Sbjct: 221 LLDEAVLAMRP--EEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAE 278
Query: 335 KYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLA 394
+ L L G+F + Y+ L + DD DH GN+R+
Sbjct: 279 EKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFA--LTAGVPGHEVDDIDHLGNRRIRTV 336
Query: 395 GPLLGGLFRMLFRKLTRDVRA-YVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQ 453
G L+ FR+ +L R VR V D L + ++ + + L+
Sbjct: 337 GELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLEAALREFF------- 386
Query: 454 ANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQLHNSQWGMMCPA 509
+R+ +SQ + S+L H RR+++ P G RE R +H + +G +CP
Sbjct: 387 -----SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPV 441
Query: 510 ETPEGQACGLVKNLA 524
ETPEG GL+ +LA
Sbjct: 442 ETPEGANIGLITSLA 456
>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 = 162 bits (410), Expect = 9e-40, Method: Compositional matrix adjust.
Identities = 126/468 (26%), Positives = 209/468 (44%), Gaps = 91/468 (19%)
Query: 773 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 830
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 718
Query: 831 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 880
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 719 --PERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRS 776
Query: 881 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 930
G+ +R + D S+ + E G+V L D G+R V+V V R Q+
Sbjct: 777 IFGEKARDVK-DTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQV 835
Query: 931 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 990
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 836 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 895
Query: 991 HMGKEGDATPFTDVTVDNISKALHKC------GYQMRGFE-------------------- 1024
+G+ + F T I + L + Q GF
Sbjct: 896 FLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSP 955
Query: 1025 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 1067
+Y+G TG I +G + +L HMV+DK+H+R GP +
Sbjct: 956 GKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1015
Query: 1068 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 1127
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1016 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAII---- 1071
Query: 1128 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 1175
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1072 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1107
Score = 67.4 bits (163), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 114/495 (23%), Positives = 191/495 (38%), Gaps = 109/495 (22%)
Query: 68 EIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFP-------------KAARLRNLT 114
++ PE + N G Q+ F E + P+ G+ + R ++LT
Sbjct: 33 DVPPEKRENVGIQAAFKETF---PIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLT 89
Query: 115 YSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELG 174
Y APLY + ++I K D + E + VF+G +P+M
Sbjct: 90 YQAPLYARL--QLIHK--DTGLIKEDE----VFLGHLPLMT------------------- 122
Query: 175 ECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPST 234
+ G FIING+++V+++Q S + +P +Y + S+ R P
Sbjct: 123 -----EDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRY-----IASIIPLPKRGP-- 170
Query: 235 MFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICY-DFQDT 293
++ + S T+ + + P++++ R LG+ + + E Y D
Sbjct: 171 -WIDLEVEASGV---------VTMKVNKRKFPLVLLLRVLGYDQETLVRELSAYGDLVQG 220
Query: 294 QMMEL---LRPSLEEAFV----------IQNQQVALDYI------GKRGATVGVTRDKRI 334
+ E +RP EEA V + AL Y+ KR R K
Sbjct: 221 LLDEAVLAMRP--EEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGEAGRYKAE 278
Query: 335 KYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLA 394
+ L L G+F + Y+ L + DD DH GN+R+
Sbjct: 279 EKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFA--LTAGVPGHEVDDIDHLGNRRIRTV 336
Query: 395 GPLLGGLFRMLFRKLTRDVRA-YVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQ 453
G L+ FR+ +L R VR V D L + ++ + + L+
Sbjct: 337 GELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLEAALREFF------- 386
Query: 454 ANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQLHNSQWGMMCPA 509
+R+ +SQ + S+L H RR+++ P G RE R +H + +G +CP
Sbjct: 387 -----SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPV 441
Query: 510 ETPEGQACGLVKNLA 524
ETPEG GL+ +LA
Sbjct: 442 ETPEGANIGLITSLA 456
>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 = 162 bits (409), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 123/468 (26%), Positives = 212/468 (45%), Gaps = 91/468 (19%)
Query: 773 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 830
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 718
Query: 831 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 880
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 719 --PERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRS 776
Query: 881 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 930
G+ +R + D S+ + E G+V + + D G+R V+V V R Q+
Sbjct: 777 IFGEKARDVK-DTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQV 835
Query: 931 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 990
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 836 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 895
Query: 991 HMGKEGDATPFTDVTVDNISKALHKC-----------GYQ-------------------- 1019
+G+ + F I + L + G+
Sbjct: 896 FLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTP 955
Query: 1020 ------------MRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 1067
++G +Y+G TG + I +G + +L HMV+DK+H+R GP +
Sbjct: 956 GKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1015
Query: 1068 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 1127
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1016 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAII---- 1071
Query: 1128 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 1175
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1072 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1107
Score = 68.6 bits (166), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 109/494 (22%), Positives = 196/494 (39%), Gaps = 107/494 (21%)
Query: 68 EIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATL------------FPK-AARLRNLT 114
++ PE + N G Q+ F E + P+ E G+ + FP+ R ++LT
Sbjct: 33 DVPPEKRENVGIQAAFRETF---PIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLT 89
Query: 115 YSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELG 174
Y APLY + ++I K D + E + VF+G +P+M
Sbjct: 90 YQAPLYARL--QLIHK--DTGLIKEDE----VFLGHIPLM-------------------- 121
Query: 175 ECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPST 234
+ G FIING+++V+++Q S + +P + Y+A + + P
Sbjct: 122 ----TEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR--YIASIIPL------PKRG 169
Query: 235 MFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQ 294
++ + + ++ + + P++++ R LG+ + E Y
Sbjct: 170 PWIDLEVEPNGV---------VSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQG 220
Query: 295 MME----LLRPSLEEAFVIQNQQVALDYIGKRGATV----GVTRDKRI-------KYAKE 339
+M+ +RP EEA + + KR V G+ D R +Y E
Sbjct: 221 LMDESVFAMRP--EEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAE 278
Query: 340 -----ILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLA 394
L L G+F + Y+ L + DD DH GN+R+
Sbjct: 279 EKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFA--LTAGVPGHEVDDIDHLGNRRIRTV 336
Query: 395 GPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQA 454
G L+ FR+ +L R VR + + + + + ++ + + ++
Sbjct: 337 GELMTDQFRVGLARLARGVRE--RMLMGSEDSLTPAKLVNSRPLEAAIREFF-------- 386
Query: 455 NAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQLHNSQWGMMCPAE 510
+R+ +SQ + S+L H RR+++ P G RE R +H + +G +CP E
Sbjct: 387 ----SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVE 442
Query: 511 TPEGQACGLVKNLA 524
TPEG GL+ +LA
Sbjct: 443 TPEGANIGLITSLA 456
>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 = 114 bits (286), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 78/250 (31%), Positives = 116/250 (46%), Gaps = 54/250 (21%)
Query: 915 LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSR 974
L+ VKV + R Q GDK + RHG KG + EDMP+ G DI++NP +PSR
Sbjct: 1047 LKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSR 1106
Query: 975 MTIGQLIECIMG--------KVAAHMGKEGD----------------------------- 997
M IGQ++E +G K+ A + ++ +
Sbjct: 1107 MNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSD 1166
Query: 998 ----------------ATPFTDVTVDNISKALHKCG-YQMRGFETMYNGHTGRRLTAMIF 1040
ATP D + K L K G G +Y+G TG + +
Sbjct: 1167 EEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVT 1226
Query: 1041 LGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHF 1100
+G Y +L H+VDDK+H+R G ++T+QP G+++ GG RFGEME + A+GA++
Sbjct: 1227 VGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1286
Query: 1101 LKERLFDQSD 1110
L+E L +SD
Sbjct: 1287 LQEMLTVKSD 1296
Score = 58.5 bits (140), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 49/197 (24%), Positives = 96/197 (48%), Gaps = 25/197 (12%)
Query: 333 RIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLD 392
R+K+ + +L++E+ G+G + ++ +L+ G+ DD DH GN+R+
Sbjct: 402 RMKFNRSLLREEI---EGSGILSKDD----IIDVMKKLIDIRNGKGEVDDIDHLGNRRIR 454
Query: 393 LAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWG 452
G + FR+ ++ R V+ + + + + Q I AK I++ +K +
Sbjct: 455 SVGEMAENQFRVGLVRVERAVKERL--SLGDLDTLMPQDMINAKPISAAVKEFFGSSQ-- 510
Query: 453 QANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQLHNSQWGMMCP 508
+SQ +++ S ++H RR+++ P G RE + R +H + +G +CP
Sbjct: 511 ----------LSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCP 560
Query: 509 AETPEGQACGLVKNLAL 525
ETPEG GL+ +L++
Sbjct: 561 IETPEGPNIGLINSLSV 577
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 58/271 (21%), Positives = 110/271 (40%), Gaps = 67/271 (24%)
Query: 41 LVRQQLDSFDEFI-QNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGE 99
L+ QLDSF +FI Q+ + E+A + P ++ + + L +P+ +
Sbjct: 27 LLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQE-- 84
Query: 100 TATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSY 159
++R +TYSAPL V + + VI + E + +V++G++P+M
Sbjct: 85 --------CQIRGVTYSAPLRVKL-RLVIYEREAPEGTVKDIKEQEVYMGEIPLMT---- 131
Query: 160 CTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKK---RQPNKYA 216
G F+ING+E+V+++Q S + K K
Sbjct: 132 --------------------DNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVL 171
Query: 217 YVAEV----RSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFR 272
Y A + S + + P +FVR+ R ++P I+ R
Sbjct: 172 YNARIIPYRGSWLDFEFDPKDNLFVRIDR--------------------RRKLPATIILR 211
Query: 273 ALGFVADKDI---LEHICYDFQDTQM-MELL 299
AL + ++ + E + ++ +D ++ MEL+
Sbjct: 212 ALNYTTEQILDLFFEKVIFEIRDNKLQMELV 242
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/106 (25%), Positives = 52/106 (49%), Gaps = 13/106 (12%)
Query: 772 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYR--DEEKKMGTLVKED 829
+L G N VA ++GYN EDS+++++ + F ++ + + K+G
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLG------ 846
Query: 830 FGRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 873
P+ ++ + + KLD+ G+ G V+G D+++GK TP
Sbjct: 847 ---PEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
Length = 1342
Score = 114 bits (286), Expect = 2e-25, Method: Compositional matrix adjust.
Identities = 78/250 (31%), Positives = 116/250 (46%), Gaps = 54/250 (21%)
Query: 915 LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSR 974
L+ VKV + R Q GDK + RHG KG + EDMP+ G DI++NP +PSR
Sbjct: 1047 LKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSR 1106
Query: 975 MTIGQLIECIMG--------KVAAHMGKEGD----------------------------- 997
M IGQ++E +G K+ A + ++ +
Sbjct: 1107 MNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSD 1166
Query: 998 ----------------ATPFTDVTVDNISKALHKCG-YQMRGFETMYNGHTGRRLTAMIF 1040
ATP D + K L K G G +Y+G TG + +
Sbjct: 1167 EEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVT 1226
Query: 1041 LGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHF 1100
+G Y +L H+VDDK+H+R G ++T+QP G+++ GG RFGEME + A+GA++
Sbjct: 1227 VGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1286
Query: 1101 LKERLFDQSD 1110
L+E L +SD
Sbjct: 1287 LQEMLTVKSD 1296
Score = 56.6 bits (135), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 43/164 (26%), Positives = 80/164 (48%), Gaps = 18/164 (10%)
Query: 366 IIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGK 425
++ +L+ G+ DD DH GN+R+ G + FR+ ++ R V+ + + +
Sbjct: 428 VMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL--SLGDLD 485
Query: 426 DVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS- 484
+ Q I AK I++ +K + +SQ + + S ++H RR+++
Sbjct: 486 TLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMVQNNPLSEITHKRRISAL 533
Query: 485 -PIG--REGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLAL 525
P G RE + R +H + +G +CP ETPEG GL+ +L++
Sbjct: 534 GPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSV 577
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 58/271 (21%), Positives = 110/271 (40%), Gaps = 67/271 (24%)
Query: 41 LVRQQLDSFDEFI-QNTMQEIVDESADIEIRPESQHNPGQQSDFAEIYLSKPMMTESDGE 99
L+ QLDSF +FI Q+ + E+A + P ++ + + L +P+ +
Sbjct: 27 LLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQE-- 84
Query: 100 TATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSY 159
++R +TYSAPL V + + VI + E + +V++G++P+M
Sbjct: 85 --------CQIRGVTYSAPLRVKL-RLVIYEREAPEGTVKDIKEQEVYMGEIPLMT---- 131
Query: 160 CTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKK---RQPNKYA 216
G F+ING+E+V+++Q S + K K
Sbjct: 132 --------------------DNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVL 171
Query: 217 YVAEV----RSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFR 272
Y A + S + + P +FVR+ R ++P I+ R
Sbjct: 172 YNARIIPYRGSWLDFEFDPKDNLFVRIDR--------------------RRKLPATIILR 211
Query: 273 ALGFVADKDI---LEHICYDFQDTQM-MELL 299
AL + ++ + E + ++ +D ++ MEL+
Sbjct: 212 ALNYTTEQILDLFFEKVIFEIRDNKLQMELV 242
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 27/106 (25%), Positives = 52/106 (49%), Gaps = 13/106 (12%)
Query: 772 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYR--DEEKKMGTLVKED 829
+L G N VA ++GYN EDS+++++ + F ++ + + K+G
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLG------ 846
Query: 830 FGRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 873
P+ ++ + + KLD+ G+ G V+G D+++GK TP
Sbjct: 847 ---PEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP CLAMP
DOMAIN
Length = 436
Score = 48.9 bits (115), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 35/63 (55%)
Query: 1114 VHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 1173
V VCE+CG IA+ + ++ C C + I +V + YA KLL EL AM I P++ E
Sbjct: 5 VWVCENCGHIALEDKRRRRVYCPVCGEEERISKVEMSYAFKLLLDELKAMVIRPKLNLSE 64
Query: 1174 DTK 1176
K
Sbjct: 65 GGK 67
>pdb|2J3L|A Chain A, Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed
With A Prolyl-Adenylate Analogue ('5'-O-(N-(L-Prolyl)-
Sulfamoyl)adenosine)
pdb|2J3L|B Chain B, Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed
With A Prolyl-Adenylate Analogue ('5'-O-(N-(L-Prolyl)-
Sulfamoyl)adenosine)
pdb|2J3M|A Chain A, Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed
With Atp, Manganese And Prolinol
pdb|2J3M|B Chain B, Prolyl-Trna Synthetase From Enterococcus Faecalis Complexed
With Atp, Manganese And Prolinol
Length = 572
Score = 40.0 bits (92), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 32/92 (34%), Positives = 45/92 (48%), Gaps = 15/92 (16%)
Query: 1040 FLGPTYYQRLKHMVDDKIHSRGRGPV---QILTRQPAEGRSRDGGLRFGEMERDCMIAHG 1096
LGPT+ + ++ D+I+S R P+ QI T+ E RSR G LR R+ ++ G
Sbjct: 105 ILGPTHEETFTELIRDEINSYKRLPLNLYQIQTKYRDEKRSRSGLLR----GREFIMKDG 160
Query: 1097 ASHFLKERLFDQSDAYRVH------VCEHCGL 1122
S E DQS YR + + E CGL
Sbjct: 161 YSFHADEASLDQS--YRDYEKAYSRIFERCGL 190
>pdb|3MLQ|A Chain A, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
pdb|3MLQ|B Chain B, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
pdb|3MLQ|C Chain C, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
pdb|3MLQ|D Chain D, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
Length = 188
Score = 32.7 bits (73), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 34/142 (23%), Positives = 59/142 (41%), Gaps = 48/142 (33%)
Query: 68 EIRPESQHNPGQQSDFAEIYLSKPMMTESDGETATLFP-------------KAARLRNLT 114
++ PE + N G Q+ F E + P+ G+ + R ++LT
Sbjct: 18 DVPPEKRENVGIQAAFKETF---PIEEGDKGKGGLVLDFLEYRIGDPPFSQDECREKDLT 74
Query: 115 YSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELG 174
Y APLY + ++I K D + E + VF+G +P+M
Sbjct: 75 YQAPLYARL--QLIHK--DTGLIKEDE----VFLGHLPLM-------------------- 106
Query: 175 ECPYDQGGYFIINGSEKVLIAQ 196
+ G FIING+++V+++Q
Sbjct: 107 ----TEDGSFIINGADRVIVSQ 124
>pdb|3TBI|B Chain B, Crystal Structure Of T4 Gp33 Bound To E. Coli Rnap
Beta-Flap Domain
Length = 228
Score = 31.2 bits (69), Expect = 3.7, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 848 KLDDDGLAPPGTRVSGEDVIIGKTTP 873
KLD+ G+ G V+G D+++GK TP
Sbjct: 35 KLDESGIVYIGAEVTGGDILVGKVTP 60
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 0.136 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 33,487,978
Number of Sequences: 62578
Number of extensions: 1401397
Number of successful extensions: 2794
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 2689
Number of HSP's gapped (non-prelim): 56
length of query: 1186
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1076
effective length of database: 8,089,757
effective search space: 8704578532
effective search space used: 8704578532
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)