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= 000996
(1195 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 = 1530 bits (3961), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 737/1196 (61%), Positives = 911/1196 (76%), Gaps = 47/1196 (3%)
Query: 28 AWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETI 87
W VIS++FEE L RQQL SFDEF+QNTMQEIVD+ + + + +QH G Q D
Sbjct: 17 CWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHT-GAQGDVTRR- 74
Query: 88 YKISFGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVT 147
Y+I+FGQIYLS+P MTE+DG T T+FP+ ARLRNLTYS+PLYVD+ K+V+ +
Sbjct: 75 YEINFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIG 134
Query: 148 ETQDF--------TKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSE 199
E + +KVFIGK+PIMLRS++C L S+ +L +L ECPYDQGGYFIINGSE
Sbjct: 135 EEEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIINGSE 194
Query: 200 KVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSS 259
KV+IAQE+ + N V VFKK P+ AYVAE+RS E +R S+M +++++R + +S
Sbjct: 195 KVIIAQERSAANIVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTE---NS 251
Query: 260 GQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQ 319
GQ IRATLPYIR++IPI+IVFRALG V D+DILEHICYD D QM+E+++P +EEAFVIQ
Sbjct: 252 GQTIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEAFVIQ 311
Query: 320 NQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRL 379
++ +ALDYIGKRG+T GVTR+KR++YA +ILQKE+LPH+ T + ET+KA++ GY+IHR+
Sbjct: 312 DKDIALDYIGKRGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRM 371
Query: 380 LLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQ 439
LLCAL RR DDRDH+G KRLDLAGPLL LFRMLFRK+TRDV Y+QKCV+ ++ NL
Sbjct: 372 LLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNREFNLT 431
Query: 440 FAIKAKTITSGLKYSLATGNWG-QANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGRE 498
A+K+ IT+GL+YSLATGNWG Q + R GVSQVLNR T+ASTLSHLRR N+PIGR+
Sbjct: 432 LAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTNTPIGRD 491
Query: 499 GKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTEN 558
GKLAKPRQLHN+ WGM+CPAETPEGQACGLVKNL+LM Y++VGS + PI+EFLEEWG E
Sbjct: 492 GKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLEEWGLET 551
Query: 559 FEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTXXXXXXXVDVNTEVGVVRDIRLKELR 618
E+ +P+ P ATK+FVNG W+G+HRDP L +T +D++ EV +VRDIR KELR
Sbjct: 552 LEDYNPSASPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVRDIREKELR 611
Query: 619 IYTDYGRCSRPLFIVEKQ-------RLLIKKRDIIALQQRES-----PEDG-GWHDLVAK 665
++TD GR RPLFIV+ L I+K I L + + PE GW LV+
Sbjct: 612 LFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPEQRFGWTALVSS 671
Query: 666 GFXXXXXXXXXXXXXXXXXXNDL-----------VQARLHPEE-------AYADTYTHCE 707
G DL V+ L P + + +THCE
Sbjct: 672 GLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAPNPHVHAWTHCE 731
Query: 708 IHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKP 767
IHP++ILG+ ASIIPFPDHNQSPRNTYQSAMGKQAMG+Y+TNYQ RMDT+A +LYYPQKP
Sbjct: 732 IHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYYPQKP 791
Query: 768 LVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDE 827
L TTR+ME+L FR+LPAG NAIVAI CYSGYNQEDS+IMNQ+SIDRG FRS+F+R+Y D+
Sbjct: 792 LATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQ 851
Query: 828 EKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQD- 886
EKK+G V E+F RP RS T+ M+HG+YDKL+DDGL PGTRVSGED+IIGKT PI D
Sbjct: 852 EKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDH 911
Query: 887 EAQGQASR-YTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSS 945
E GQ ++ + +RD S LR +E+G+VDQV++TTN +GL+FVKVR+RS RIPQIGDKF+S
Sbjct: 912 EELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRSTRIPQIGDKFAS 971
Query: 946 RHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEG 1005
RHGQKGT+GMTY EDMP++ +GI PDII+NPHAIPSRMT+ L+EC + KV+A G EG
Sbjct: 972 RHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALSGFEG 1031
Query: 1006 DATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDK 1065
DATPFTDVTV+ +SK L G+Q RGFE MY+GHTGR+L A +FLGPTYYQRLKH+VDDK
Sbjct: 1032 DATPFTDVTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKLVAQVFLGPTYYQRLKHLVDDK 1091
Query: 1066 IHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHV 1125
IH+R RGPVQILTRQP EGRSRDGGLRFGEMERDC I+HG S L+ERLFD SDAYRV V
Sbjct: 1092 IHARARGPVQILTRQPVEGRSRDGGLRFGEMERDCQISHGCSSVLRERLFDCSDAYRVIV 1151
Query: 1126 CEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTK 1181
C+ CGLIAIA+ KK+S+ECR C+N+T QV++PYA KLLFQELM+M IAPR+ TK
Sbjct: 1152 CDICGLIAIASYKKDSYECRSCQNRTRFSQVYLPYAAKLLFQELMSMNIAPRLFTK 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 = 1484 bits (3842), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 721/1195 (60%), Positives = 894/1195 (74%), Gaps = 48/1195 (4%)
Query: 28 AWAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETI 87
+WAVISA+F EKGLV QQLDSF++F+ T+Q+I+ E + + + +QH +SD
Sbjct: 30 SWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHT--TESDNISRK 87
Query: 88 YKISFGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRV----------I 137
Y+ISFG+IY++KPM+ ESDG T L+P+ ARLRNLTYS+ L+VDV KR +
Sbjct: 88 YEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGREL 147
Query: 138 KKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIING 197
K EE + + KVFIG++PIMLRS C L + +E DL +L ECP+D GGYFIING
Sbjct: 148 KYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIING 207
Query: 198 SEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGG 257
SEKVLIAQE+ + N V VFKK P+ ++VAE+RS E +R ST+ V++ R G
Sbjct: 208 SEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGRE----G 263
Query: 258 SSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFV 317
SS + I+ATLPYI+ +IPI+I+FRALG + D +ILEHICYD D QM+E+L+P +E+ FV
Sbjct: 264 SSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFV 323
Query: 318 IQNQQVALDYIGKRGATVGVTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIH 377
IQ+++ ALD+IG+RG +G+ ++KRI+YAK+ILQKE LPH+ + E++KA++ GY+I+
Sbjct: 324 IQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMIN 383
Query: 378 RLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVN 437
RLLLCAL R+ +DDRDH+G KRLDLAGPLL LF+ LF+KLT+D+ Y+Q+ V+ D N
Sbjct: 384 RLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFN 443
Query: 438 LQFAIKAKTITSGLKYSLATGNWG-QANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIG 496
++ AI AKTITSGLKY+LATGNWG Q A +RAGVSQVLNR TY+STLSHLRR N+PIG
Sbjct: 444 MKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIG 503
Query: 497 REGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGT 556
R+GKLAKPRQLHN+ WG++CPAETPEGQACGLVKNL+LM I+VG+ PI+ FL EWG
Sbjct: 504 RDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGM 563
Query: 557 ENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKTXXXXXXXVDVNTEVGVVRDIRLKE 616
E E+ P P AT++FVNG W G+HR+P L++T D+N EV ++RDIR KE
Sbjct: 564 EPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKE 623
Query: 617 LRIYTDYGRCSRPLFIVEK------QRLLIKKRDIIALQQRESPE-DGG--------WHD 661
L+I+TD GR RPLFIVE + L ++K I L E + +GG W
Sbjct: 624 LKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSS 683
Query: 662 LVAKGFXXXXXXXXXXXXXXXXXXNDLVQARLHPEEA-------------YADTYTHCEI 708
L+ +G DL A + E +A T+THCEI
Sbjct: 684 LLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEI 743
Query: 709 HPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPL 768
HPS+ILGV ASIIPFPDHNQSPRNTYQSAMGKQAMG+++TNY RMDT+A +LYYPQKPL
Sbjct: 744 HPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPL 803
Query: 769 VTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEE 828
TTRAME+L FR+LPAG NAIVAIACYSGYNQEDS+IMNQSSIDRG FRSLFFRSY D+E
Sbjct: 804 GTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQE 863
Query: 829 KKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEA 888
KK G + E F +P R+NT+ M+HG+YDKLDDDGL PG RVSGEDVIIGKTTPIS DE
Sbjct: 864 KKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEE 923
Query: 889 Q-GQASRY-TRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSR 946
+ GQ + Y ++RD S LR +E G+VDQVL+TTN DGL+FVKVRVR+ +IPQIGDKF+SR
Sbjct: 924 ELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASR 983
Query: 947 HGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGD 1006
HGQKGT+G+TY +EDMP+T EGI PD+I+NPHAIPSRMT+ LIEC++ KVAA G EGD
Sbjct: 984 HGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGD 1043
Query: 1007 ATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKI 1066
A+PFTD+TV+ ISK L + GYQ RGFE MYNGHTG++L A IF GPTYYQRL+HMVDDKI
Sbjct: 1044 ASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKI 1103
Query: 1067 HSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVC 1126
H+R RGP+Q+LTRQP EGRSRDGGLRFGEMERDCMIAHGA+ FLKERL + SDA+RVH+C
Sbjct: 1104 HARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHIC 1163
Query: 1127 EHCGLI-AIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLT 1180
CGL+ IA L N FEC+GC NK DI Q+HIPYA KLLFQELMAM I PR+ T
Sbjct: 1164 GICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYT 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 = 879 bits (2270), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 493/1171 (42%), Positives = 688/1171 (58%), Gaps = 81/1171 (6%)
Query: 29 WAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETIY 88
W VI AYF+ KGLVRQ LDS+++F++N +QEI+DE +I PG
Sbjct: 14 WKVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEI-----PTEIPG---------L 59
Query: 89 KISFGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTE 148
K+ G+I + KP + ESD + P ARLRNLTY+APL++ + ++ + E
Sbjct: 60 KVRLGKIRIGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIP--VENNIEAEP--- 114
Query: 149 TQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKM 208
+V+IG +PIML+S+ + Q + L E+GE P D GGYFI+NGSE+V++ QE +
Sbjct: 115 ----EEVYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDL 170
Query: 209 STNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLP 268
+ N V V + + + A++ S + + R P T+ K G+ + P
Sbjct: 171 APNRVLVDTGKTGSNITHTAKIIS-STAGYRVPVTI-------ERLKDGT----FHVSFP 218
Query: 269 YIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYI 328
+ +IP +I+ RALG + D+DI+ + D ++ L PSLE+A I N ALD+I
Sbjct: 219 AVPGKIPFVILMRALGILTDRDIVYAVSLD---PEIQNELFPSLEQASSIANVDDALDFI 275
Query: 329 GKRGATVGVTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRA 388
G R A +G R+ RI+ A++I+ K LPH+GT KKAYY Y I +++ LGRR
Sbjct: 276 GSRVA-IGQKRENRIEKAQQIIDKYFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRRE 334
Query: 389 EDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTIT 448
DD+DHY NKRL LAG L LFR+ F+ +D+ ++K G+ + L+ ++ +T
Sbjct: 335 PDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALVRPDIVT 394
Query: 449 SGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLH 508
++++LATGNW G R GVSQ+L+R + S LSHLRR+ S + R + R LH
Sbjct: 395 ERIRHALATGNW-----VGGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLH 449
Query: 509 NSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIP 568
+QWG MCP ETPEG GLVKNLALM I VG + + L E G EE+ V
Sbjct: 450 GTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGINEKIVEKTLYEMGVVPVEEVIRRVTE 509
Query: 569 ---------QATKIFVNGCWVGIHRDPEMLVKTXXXXXXXVDVNTEVGV---VRDIRLKE 616
+ +K+ +NG VG +RD E L K +++ EV V V D + E
Sbjct: 510 GGEDQNEYLKWSKVILNGRLVGYYRDGEELAKKIRERRRKGEISDEVNVGHIVTDF-INE 568
Query: 617 LRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGG---WHDLVAKGFXXXXXX 673
+ + D GR RPL IV L+ + DI L D G + DLV +G
Sbjct: 569 VHVNCDSGRVRRPLIIVSNGNPLVTREDIEKL-------DSGSITFDDLVRQGKIEYLDA 621
Query: 674 XXXXXXXXXXXXNDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNT 733
+DL PE +TH EI ILG+ ASIIP+P+HNQSPRNT
Sbjct: 622 EEEENAYVALEPSDLT-----PE------HTHLEIWSPAILGITASIIPYPEHNQSPRNT 670
Query: 734 YQSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIA 793
YQSAM KQA+G+Y NYQ R DT A++L+YPQ+PLV TRA++ + + PAG NAI+A+
Sbjct: 671 YQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVI 730
Query: 794 CYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHG 853
++GYN EDS+IMN+SS++RG +RS FFR Y EE K ++ P+ G +
Sbjct: 731 SFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPE-PGVRGYKGK 789
Query: 854 SYDKL-DDDGLAPPGTRVSGEDVIIGKTTPIS-QDEAQGQASRYTRRDHSISLRHSETGM 911
Y +L +D+G+ P V G DV+IGK +P E + + +RD SI RH E G+
Sbjct: 790 EYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGI 849
Query: 912 VDQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITP 971
VD VL+T A+G + VKVRVR +RIP IGDKF+SRHGQKG +GM Q DMP+TV+G+ P
Sbjct: 850 VDLVLITETAEGNKLVKVRVRDLRIPSIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVP 909
Query: 972 DIIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRG 1031
D+I+NPHA+PSRMT+GQ++E I GK AA G DATPF ++ + + K GY
Sbjct: 910 DVILNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKTPIEQLQNEILKYGYLPDA 969
Query: 1032 FETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGL 1091
E Y+G TG+++ + I+ G YYQ+L HMV DKIH+R RGPVQILTRQP EGR+R+GGL
Sbjct: 970 TEVTYDGRTGQKIKSRIYFGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGL 1029
Query: 1092 RFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKT 1151
RFGEMERDC+I G + LK+RL D SD ++VC+ CG I + KN + C +K+
Sbjct: 1030 RFGEMERDCLIGFGTAMLLKDRLLDNSDRTTIYVCDQCGYIGWYDKNKNKYVCPIHGDKS 1089
Query: 1152 DIVQVHIPYACKLLFQELMAMAIAPRMLTKE 1182
++ V + YA KLL QELM+M I+PR++ ++
Sbjct: 1090 NLFPVTVSYAFKLLIQELMSMIISPRLILED 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 = 869 bits (2246), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 488/1170 (41%), Positives = 687/1170 (58%), Gaps = 79/1170 (6%)
Query: 29 WAVISAYFEEKGLVRQQLDSFDEFIQNTMQEIVDESADIEIRPESQHNPGQQSDFAETIY 88
W VI AYF+ KGLVRQ LDS+++F++N +QEI+DE +I PG
Sbjct: 11 WRVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEI-----PTEIPG---------L 56
Query: 89 KISFGQIYLSKPMMTESDGETATLFPKAARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTE 148
K+ G+I + KP + ESD + P ARLRNLTY+APL++ + ++ + E
Sbjct: 57 KVRLGKIRIGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIP--VENNIEAEP--- 111
Query: 149 TQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGECPYDQGGYFIINGSEKVLIAQEKM 208
+V+IG +PIML+S+ + Q + L E+GE P D GGYFI+NGSE+V++ QE +
Sbjct: 112 ----EEVYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDL 167
Query: 209 STNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLP 268
+ N V V + + + A++ S + + R P T+ K G+ + P
Sbjct: 168 APNRVLVDTGKTGSNITHTAKIIS-STAGYRVPVTI-------ERLKDGT----FHVSFP 215
Query: 269 YIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQMMELLRPSLEEAFVIQNQQVALDYI 328
+ +IP +I+ RALG + D+DI+ + D ++ L PSLE+A I N ALD+I
Sbjct: 216 AVPGKIPFVILMRALGILTDRDIVYAVSLD---PEVQNELFPSLEQASSIANVDDALDFI 272
Query: 329 GKRGATVGVTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRA 388
G R A +G R+ RI+ A++I+ K LPH+GT KKAYY Y I +++ LGRR
Sbjct: 273 GSRVA-IGQKRENRIEKAQQIIDKYFLPHLGTSAEDRKKKAYYLAYAISKVIELYLGRRE 331
Query: 389 EDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTIT 448
DD+DHY NKRL LAG L LFR+ F+ +D+ ++K G+ + L+ ++ +T
Sbjct: 332 PDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKSKVRGRKLALKALVRPDIVT 391
Query: 449 SGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLH 508
++++LATGNW G R GVSQ+L+R + S LSHLRR+ S + R + R LH
Sbjct: 392 ERIRHALATGNW-----VGGRTGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLH 446
Query: 509 NSQWGMMCPAETPEGQACGLVKNLALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIP 568
+QWG MCP ETPEG GLVKNLALM I VG + + L E G EE+ V
Sbjct: 447 GTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGINERIVEKTLYEMGVVPVEEVIRRVTE 506
Query: 569 ---------QATKIFVNGCWVGIHRDPEMLVKTXXXXXXXVDVNTEVGV---VRDIRLKE 616
+ +K+ +NG +G ++D L +++ EV V V D + E
Sbjct: 507 GGEDQNEYLKWSKVILNGRLIGYYQDGGELANKIRERRRKGEISDEVNVGHIVTDF-INE 565
Query: 617 LRIYTDYGRCSRPLFIVEKQRLLIKKRDIIALQQRESPEDGG--WHDLVAKGFXXXXXXX 674
+ + D GR RPL IV L+ DI E E G + DLV +G
Sbjct: 566 VHVNCDSGRVRRPLIIVSNGNPLVTIEDI------EKLESGAITFDDLVRQGKIEYLDAE 619
Query: 675 XXXXXXXXXXXNDLVQARLHPEEAYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTY 734
NDL P+ +TH EI ILG+ ASIIP+P+HNQSPRNTY
Sbjct: 620 EEENAYVALEPNDLT-----PD------HTHLEIWSPAILGITASIIPYPEHNQSPRNTY 668
Query: 735 QSAMGKQAMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIAC 794
QSAM KQA+G+Y NYQ R DT A++L+YPQ+PLV TRA++ + + PAG NAI+A+
Sbjct: 669 QSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVMS 728
Query: 795 YSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGS 854
++GYN EDS+IMN+SS++RG +RS FFR Y EE K ++ P+ + G +
Sbjct: 729 FTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKYPGGQEDKIVMPE-AGVRGYKGKE 787
Query: 855 YDKL-DDDGLAPPGTRVSGEDVIIGKTTPIS-QDEAQGQASRYTRRDHSISLRHSETGMV 912
Y +L +D+G+ P V G DV+IGK +P E + + +RD SI RH E G+V
Sbjct: 788 YYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGIV 847
Query: 913 DQVLLTTNADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPD 972
D VL+T A+G + VKVRVR +RIP IGDKF+SRHGQKG +GM Q DMP+TV+G+ PD
Sbjct: 848 DLVLITETAEGNKLVKVRVRDLRIPTIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPD 907
Query: 973 IIVNPHAIPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGF 1032
II+NPHA+PSRMT+GQ++E I GK AA G DATPF ++ + + + GY
Sbjct: 908 IILNPHALPSRMTLGQIMEGIAGKYAALSGNIVDATPFYKTPIEQLQNEILRYGYLPDAT 967
Query: 1033 ETMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLR 1092
E +Y+G TG+++ + I+ G YYQ+L HMV DK+H+R RGPVQILTRQP EGR+R+GGLR
Sbjct: 968 EVVYDGRTGQKIKSRIYFGVVYYQKLHHMVADKLHARARGPVQILTRQPTEGRAREGGLR 1027
Query: 1093 FGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTD 1152
FGEMERDC+I G + LK+RL D SD ++VC+ CG I + KN + C +K++
Sbjct: 1028 FGEMERDCLIGFGTAMLLKDRLLDNSDRTMIYVCDQCGYIGWYDKNKNKYVCPIHGDKSN 1087
Query: 1153 IVQVHIPYACKLLFQELMAMAIAPRMLTKE 1182
+ V + YA KLL QELM+M I+PR++ ++
Sbjct: 1088 LFPVTVSYAFKLLIQELMSMIISPRLVLED 1117
>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 = 163 bits (412), Expect = 7e-40, Method: Compositional matrix adjust.
Identities = 126/468 (26%), Positives = 209/468 (44%), Gaps = 91/468 (19%)
Query: 782 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 839
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 718
Query: 840 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 889
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 719 --PERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRS 776
Query: 890 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 939
G+ +R + D S+ + E G+V L D G+R V+V V R Q+
Sbjct: 777 IFGEKARDVK-DTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQV 835
Query: 940 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 999
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 836 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 895
Query: 1000 HMGKEGDATPFTDVTVDNISKALHKC------GYQMRGFE-------------------- 1033
+G+ + F T I + L + Q GF
Sbjct: 896 FLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSP 955
Query: 1034 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 1076
+Y+G TG I +G + +L HMV+DK+H+R GP +
Sbjct: 956 GKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1015
Query: 1077 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 1136
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1016 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAII---- 1071
Query: 1137 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 1184
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1072 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1107
Score = 69.7 bits (169), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 115/502 (22%), Positives = 194/502 (38%), Gaps = 114/502 (22%)
Query: 68 EIRPESQHNPGQQSDFAETI-----------YKISFGQIYLSKPMMTESDGETATLFPKA 116
++ PE + N G Q+ F ET + F + + P ++ +
Sbjct: 33 DVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDE---------- 82
Query: 117 ARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSE 176
R ++LTY APLY + ++I K D + E + VF+G +P+M
Sbjct: 83 CREKDLTYQAPLYARL--QLIHK--DTGLIKEDE----VFLGHLPLMT------------ 122
Query: 177 KDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAES 236
+ G FIING+++V+++Q S + +P +Y + S+
Sbjct: 123 ------------EDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRY-----IASIIPL 165
Query: 237 QNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHIC 296
R P ++ + S T+ + + P++++ R LG+ + + E
Sbjct: 166 PKRGP---WIDLEVEASGV---------VTMKVNKRKFPLVLLLRVLGYDQETLVRELSA 213
Query: 297 Y-DFQDTQMMEL---LRPSLEEAFV----------IQNQQVALDYI------GKRGATVG 336
Y D + E +RP EEA V + AL Y+ KR
Sbjct: 214 YGDLVQGLLDEAVLAMRP--EEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGE 271
Query: 337 VTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYG 396
R K + L L G+F + Y+ L + DD DH G
Sbjct: 272 AGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFA--LTAGVPGHEVDDIDHLG 329
Query: 397 NKRLDLAGPLLGGLFRMLFRKLTRDVRA-YVQKCVDNGKDVNLQFAIKAKTITSGLKYSL 455
N+R+ G L+ FR+ +L R VR V D L + ++ + + L+
Sbjct: 330 NRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLEAALREFF 386
Query: 456 ATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQLHNSQ 511
+R+ +SQ + S+L H RR+++ P G RE R +H +
Sbjct: 387 ------------SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTH 434
Query: 512 WGMMCPAETPEGQACGLVKNLA 533
+G +CP ETPEG GL+ +LA
Sbjct: 435 YGRICPVETPEGANIGLITSLA 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 (411), Expect = 7e-40, Method: Compositional matrix adjust.
Identities = 126/468 (26%), Positives = 209/468 (44%), Gaps = 91/468 (19%)
Query: 782 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 839
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 718
Query: 840 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 889
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 719 --PERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRS 776
Query: 890 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 939
G+ +R + D S+ + E G+V L D G+R V+V V R Q+
Sbjct: 777 IFGEKARDVK-DTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQV 835
Query: 940 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 999
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 836 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 895
Query: 1000 HMGKEGDATPFTDVTVDNISKALHKC------GYQMRGFE-------------------- 1033
+G+ + F T I + L + Q GF
Sbjct: 896 FLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSP 955
Query: 1034 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 1076
+Y+G TG I +G + +L HMV+DK+H+R GP +
Sbjct: 956 GKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1015
Query: 1077 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 1136
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1016 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAII---- 1071
Query: 1137 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 1184
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1072 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1107
Score = 69.7 bits (169), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 115/502 (22%), Positives = 194/502 (38%), Gaps = 114/502 (22%)
Query: 68 EIRPESQHNPGQQSDFAETI-----------YKISFGQIYLSKPMMTESDGETATLFPKA 116
++ PE + N G Q+ F ET + F + + P ++ +
Sbjct: 33 DVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDE---------- 82
Query: 117 ARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSE 176
R ++LTY APLY + ++I K D + E + VF+G +P+M
Sbjct: 83 CREKDLTYQAPLYARL--QLIHK--DTGLIKEDE----VFLGHLPLMT------------ 122
Query: 177 KDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAES 236
+ G FIING+++V+++Q S + +P +Y + S+
Sbjct: 123 ------------EDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRY-----IASIIPL 165
Query: 237 QNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHIC 296
R P ++ + S T+ + + P++++ R LG+ + + E
Sbjct: 166 PKRGP---WIDLEVEASGV---------VTMKVNKRKFPLVLLLRVLGYDQETLVRELSA 213
Query: 297 Y-DFQDTQMMEL---LRPSLEEAFV----------IQNQQVALDYI------GKRGATVG 336
Y D + E +RP EEA V + AL Y+ KR
Sbjct: 214 YGDLVQGLLDEAVLAMRP--EEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGE 271
Query: 337 VTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYG 396
R K + L L G+F + Y+ L + DD DH G
Sbjct: 272 AGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFA--LTAGVPGHEVDDIDHLG 329
Query: 397 NKRLDLAGPLLGGLFRMLFRKLTRDVRA-YVQKCVDNGKDVNLQFAIKAKTITSGLKYSL 455
N+R+ G L+ FR+ +L R VR V D L + ++ + + L+
Sbjct: 330 NRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLEAALREFF 386
Query: 456 ATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQLHNSQ 511
+R+ +SQ + S+L H RR+++ P G RE R +H +
Sbjct: 387 ------------SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTH 434
Query: 512 WGMMCPAETPEGQACGLVKNLA 533
+G +CP ETPEG GL+ +LA
Sbjct: 435 YGRICPVETPEGANIGLITSLA 456
>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 = 7e-40, Method: Compositional matrix adjust.
Identities = 126/468 (26%), Positives = 209/468 (44%), Gaps = 91/468 (19%)
Query: 782 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 839
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 717
Query: 840 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 889
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 718 --PERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRS 775
Query: 890 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 939
G+ +R + D S+ + E G+V L D G+R V+V V R Q+
Sbjct: 776 IFGEKARDVK-DTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQV 834
Query: 940 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 999
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 835 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 894
Query: 1000 HMGKEGDATPFTDVTVDNISKALHKC------GYQMRGFE-------------------- 1033
+G+ + F T I + L + Q GF
Sbjct: 895 FLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSP 954
Query: 1034 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 1076
+Y+G TG I +G + +L HMV+DK+H+R GP +
Sbjct: 955 GKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1014
Query: 1077 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 1136
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1015 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAII---- 1070
Query: 1137 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 1184
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1071 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1106
Score = 69.7 bits (169), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 114/506 (22%), Positives = 198/506 (39%), Gaps = 122/506 (24%)
Query: 68 EIRPESQHNPGQQSDFAETI-----------YKISFGQIYLSKPMMTESDGETATLFPKA 116
++ PE + N G Q+ F ET + F + + P ++ +
Sbjct: 33 DVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDE---------- 82
Query: 117 ARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSE 176
R ++LTY APLY + ++I K D + E + VF+G +P+M
Sbjct: 83 CREKDLTYQAPLYARL--QLIHK--DTGLIKEDE----VFLGHLPLMT------------ 122
Query: 177 KDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAES 236
+ G FIING+++V+++Q S + +P +Y + S+
Sbjct: 123 ------------EDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRY-----IASIIPL 165
Query: 237 QNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHIC 296
R P ++ + S T+ + + P++++ R LG+ + + E
Sbjct: 166 PKRGP---WIDLEVEASGV---------VTMKVNKRKFPLVLLLRVLGYDQETLVRELSA 213
Query: 297 Y-DFQDTQMMEL---LRPSLEEAFV----------IQNQQVALDYIGKRGATVGVTRDKR 342
Y D + E +RP EEA V + AL Y+ G+ D +
Sbjct: 214 YGDLVQGLLDEAVLAMRP--EEAMVRLFTLLRPGDPPKKDKALAYL------FGLLADPK 265
Query: 343 IKYAKEILQKEMLPHVGTG---------DFCETKKAYYFGYIIHRLLLCA-LGRRAEDDR 392
E + + +G G + E K + + + L A + DD
Sbjct: 266 RYDLGEAGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDI 325
Query: 393 DHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRA-YVQKCVDNGKDVNLQFAIKAKTITSGL 451
DH GN+R+ G L+ FR+ +L R VR V D L + ++ + + L
Sbjct: 326 DHLGNRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLEAAL 382
Query: 452 KYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQL 507
+ +R+ +SQ + S+L H RR+++ P G RE R +
Sbjct: 383 REFF------------SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDV 430
Query: 508 HNSQWGMMCPAETPEGQACGLVKNLA 533
H + +G +CP ETPEG GL+ +LA
Sbjct: 431 HRTHYGRICPVETPEGANIGLITSLA 456
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 162 bits (411), Expect = 8e-40, Method: Compositional matrix adjust.
Identities = 126/468 (26%), Positives = 209/468 (44%), Gaps = 91/468 (19%)
Query: 782 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 839
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 717
Query: 840 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 889
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 718 --PERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRS 775
Query: 890 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 939
G+ +R + D S+ + E G+V L D G+R V+V V R Q+
Sbjct: 776 IFGEKARDVK-DTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQV 834
Query: 940 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 999
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 835 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 894
Query: 1000 HMGKEGDATPFTDVTVDNISKALHKC------GYQMRGFE-------------------- 1033
+G+ + F T I + L + Q GF
Sbjct: 895 FLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSP 954
Query: 1034 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 1076
+Y+G TG I +G + +L HMV+DK+H+R GP +
Sbjct: 955 GKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1014
Query: 1077 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 1136
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1015 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAII---- 1070
Query: 1137 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 1184
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1071 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1106
Score = 69.3 bits (168), Expect = 1e-11, Method: Compositional matrix adjust.
Identities = 115/502 (22%), Positives = 194/502 (38%), Gaps = 114/502 (22%)
Query: 68 EIRPESQHNPGQQSDFAETI-----------YKISFGQIYLSKPMMTESDGETATLFPKA 116
++ PE + N G Q+ F ET + F + + P ++ +
Sbjct: 33 DVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDE---------- 82
Query: 117 ARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSE 176
R ++LTY APLY + ++I K D + E + VF+G +P+M
Sbjct: 83 CREKDLTYQAPLYARL--QLIHK--DTGLIKEDE----VFLGHLPLMT------------ 122
Query: 177 KDLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAES 236
+ G FIING+++V+++Q S + +P +Y + S+
Sbjct: 123 ------------EDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRY-----IASIIPL 165
Query: 237 QNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHIC 296
R P ++ + S T+ + + P++++ R LG+ + + E
Sbjct: 166 PKRGP---WIDLEVEASGV---------VTMKVNKRKFPLVLLLRVLGYDQETLVRELSA 213
Query: 297 Y-DFQDTQMMEL---LRPSLEEAFV----------IQNQQVALDYI------GKRGATVG 336
Y D + E +RP EEA V + AL Y+ KR
Sbjct: 214 YGDLVQGLLDEAVLAMRP--EEAMVRLFTLLRPGDPPKKDKALAYLFGLLADPKRYDLGE 271
Query: 337 VTRDKRIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYG 396
R K + L L G+F + Y+ L + DD DH G
Sbjct: 272 AGRYKAEEKLGVGLSGRTLVRFEDGEFKDEVFLPTLRYLFA--LTAGVPGHEVDDIDHLG 329
Query: 397 NKRLDLAGPLLGGLFRMLFRKLTRDVRA-YVQKCVDNGKDVNLQFAIKAKTITSGLKYSL 455
N+R+ G L+ FR+ +L R VR V D L + ++ + + L+
Sbjct: 330 NRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLEAALREFF 386
Query: 456 ATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQLHNSQ 511
+R+ +SQ + S+L H RR+++ P G RE R +H +
Sbjct: 387 ------------SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTH 434
Query: 512 WGMMCPAETPEGQACGLVKNLA 533
+G +CP ETPEG GL+ +LA
Sbjct: 435 YGRICPVETPEGANIGLITSLA 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 = 124/468 (26%), Positives = 210/468 (44%), Gaps = 91/468 (19%)
Query: 782 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 839
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 718
Query: 840 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 889
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 719 --PERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRS 776
Query: 890 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 939
G+ +R + D S+ + E G+V + + D G+R V+V V R Q+
Sbjct: 777 IFGEKARDVK-DTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQV 835
Query: 940 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 999
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 836 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 895
Query: 1000 HMGKEGDATPFTDVTVDNISKALHKC-------------GYQMRGFE------------- 1033
+G+ + F I + L + G R E
Sbjct: 896 FLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTP 955
Query: 1034 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 1076
+Y+G TG + I +G + +L HMV+DK+H+R GP +
Sbjct: 956 GKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1015
Query: 1077 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 1136
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1016 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAII---- 1071
Query: 1137 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 1184
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1072 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1107
Score = 67.4 bits (163), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 112/493 (22%), Positives = 198/493 (40%), Gaps = 96/493 (19%)
Query: 68 EIRPESQHNPGQQSDFAET--IYKISFGQIYLSKPMMTESDGETATLFPK-AARLRNLTY 124
++ PE + N G Q+ F ET I + G+ L + GE FP+ R ++LTY
Sbjct: 33 DVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPP--FPQDECREKDLTY 90
Query: 125 SAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEKDLTELGE 184
APLY + ++I K D + E + VF+G +P+M
Sbjct: 91 QAPLYARL--QLIHK--DTGLIKEDE----VFLGHIPLM--------------------- 121
Query: 185 CPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKKRQPNKYAYVAEVRSMAESQNRPPSTM 244
+ G FIING+++V+++Q S + +P + Y+A + + P
Sbjct: 122 ---TEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGR--YIASIIPL------PKRGP 170
Query: 245 FVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKDILEHICYDFQDTQM 304
++ + + ++ + + P++++ R LG+ + E Y +
Sbjct: 171 WIDLEVEPNGV---------VSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGL 221
Query: 305 ME----LLRPSLEEAFVIQNQQVALDYIGKRGATV----GVTRDKRI-------KYAKE- 348
M+ +RP EEA + + KR V G+ D R +Y E
Sbjct: 222 MDESVFAMRP--EEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEE 279
Query: 349 ----ILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAG 404
L L G+F + Y+ L + DD DH GN+R+ G
Sbjct: 280 KLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFA--LTAGVPGHEVDDIDHLGNRRIRTVG 337
Query: 405 PLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQAN 464
L+ FR+ +L R VR + + + + + ++ + + ++
Sbjct: 338 ELMTDQFRVGLARLARGVRE--RMLMGSEDSLTPAKLVNSRPLEAAIREFF--------- 386
Query: 465 AAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQLHNSQWGMMCPAET 520
+R+ +SQ + S+L H RR+++ P G RE R +H + +G +CP ET
Sbjct: 387 ---SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVET 443
Query: 521 PEGQACGLVKNLA 533
PEG GL+ +LA
Sbjct: 444 PEGANIGLITSLA 456
>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: 924 LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSR 983
L+ VKV + R Q GDK + RHG KG + EDMP+ G DI++NP +PSR
Sbjct: 1047 LKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSR 1106
Query: 984 MTIGQLIECIMG--------KVAAHMGKEGD----------------------------- 1006
M IGQ++E +G K+ A + ++ +
Sbjct: 1107 MNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSD 1166
Query: 1007 ----------------ATPFTDVTVDNISKALHKCG-YQMRGFETMYNGHTGRRLTAMIF 1049
ATP D + K L K G G +Y+G TG + +
Sbjct: 1167 EEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVT 1226
Query: 1050 LGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHF 1109
+G Y +L H+VDDK+H+R G ++T+QP G+++ GG RFGEME + A+GA++
Sbjct: 1227 VGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1286
Query: 1110 LKERLFDQSD 1119
L+E L +SD
Sbjct: 1287 LQEMLTVKSD 1296
Score = 57.0 bits (136), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 49/197 (24%), Positives = 95/197 (48%), Gaps = 25/197 (12%)
Query: 342 RIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLD 401
R+K+ + +L++E+ G+G + ++ +L+ G+ DD DH GN+R+
Sbjct: 402 RMKFNRSLLREEI---EGSGILSKDD----IIDVMKKLIDIRNGKGEVDDIDHLGNRRIR 454
Query: 402 LAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWG 461
G + FR+ ++ R V+ + + + + Q I AK I++ +K +
Sbjct: 455 SVGEMAENQFRVGLVRVERAVKERL--SLGDLDTLMPQDMINAKPISAAVKEFFGSSQ-- 510
Query: 462 QANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQLHNSQWGMMCP 517
+SQ + + S ++H RR+++ P G RE + R +H + +G +CP
Sbjct: 511 ----------LSQFMVQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCP 560
Query: 518 AETPEGQACGLVKNLAL 534
ETPEG GL+ +L++
Sbjct: 561 IETPEGPNIGLINSLSV 577
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: 781 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYR--DEEKKMGTLVKED 838
+L G N VA ++GYN EDS+++++ + F ++ + + K+G
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLG------ 846
Query: 839 FGRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 882
P+ ++ + + KLD+ G+ G V+G D+++GK TP
Sbjct: 847 ---PEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
Score = 38.5 bits (88), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 44/202 (21%), Positives = 83/202 (41%), Gaps = 56/202 (27%)
Query: 118 RLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEK 177
++R +TYSAPL V + + VI + E + +V++G++P+M
Sbjct: 86 QIRGVTYSAPLRVKL-RLVIYEREAPEGTVKDIKEQEVYMGEIPLMT------------- 131
Query: 178 DLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKK---RQPNKYAYVAEV---- 230
G F+ING+E+V+++Q S + K K Y A +
Sbjct: 132 -----------DNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYR 180
Query: 231 RSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKD 290
S + + P +FVR+ R ++P I+ RAL + ++
Sbjct: 181 GSWLDFEFDPKDNLFVRIDR--------------------RRKLPATIILRALNYTTEQI 220
Query: 291 I---LEHICYDFQDTQM-MELL 308
+ E + ++ +D ++ MEL+
Sbjct: 221 LDLFFEKVIFEIRDNKLQMELV 242
>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: 924 LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSR 983
L+ VKV + R Q GDK + RHG KG + EDMP+ G DI++NP +PSR
Sbjct: 1047 LKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSR 1106
Query: 984 MTIGQLIECIMG--------KVAAHMGKEGD----------------------------- 1006
M IGQ++E +G K+ A + ++ +
Sbjct: 1107 MNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSD 1166
Query: 1007 ----------------ATPFTDVTVDNISKALHKCG-YQMRGFETMYNGHTGRRLTAMIF 1049
ATP D + K L K G G +Y+G TG + +
Sbjct: 1167 EEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVT 1226
Query: 1050 LGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHF 1109
+G Y +L H+VDDK+H+R G ++T+QP G+++ GG RFGEME + A+GA++
Sbjct: 1227 VGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1286
Query: 1110 LKERLFDQSD 1119
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: 342 RIKYAKEILQKEMLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLD 401
R+K+ + +L++E+ G+G + ++ +L+ G+ DD DH GN+R+
Sbjct: 402 RMKFNRSLLREEI---EGSGILSKDD----IIDVMKKLIDIRNGKGEVDDIDHLGNRRIR 454
Query: 402 LAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWG 461
G + FR+ ++ R V+ + + + + Q I AK I++ +K +
Sbjct: 455 SVGEMAENQFRVGLVRVERAVKERL--SLGDLDTLMPQDMINAKPISAAVKEFFGSSQ-- 510
Query: 462 QANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPRQLHNSQWGMMCP 517
+SQ +++ S ++H RR+++ P G RE + R +H + +G +CP
Sbjct: 511 ----------LSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCP 560
Query: 518 AETPEGQACGLVKNLAL 534
ETPEG GL+ +L++
Sbjct: 561 IETPEGPNIGLINSLSV 577
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: 781 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYR--DEEKKMGTLVKED 838
+L G N VA ++GYN EDS+++++ + F ++ + + K+G
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLG------ 846
Query: 839 FGRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 882
P+ ++ + + KLD+ G+ G V+G D+++GK TP
Sbjct: 847 ---PEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
Score = 38.5 bits (88), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 44/202 (21%), Positives = 83/202 (41%), Gaps = 56/202 (27%)
Query: 118 RLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSEK 177
++R +TYSAPL V + + VI + E + +V++G++P+M
Sbjct: 86 QIRGVTYSAPLRVKL-RLVIYEREAPEGTVKDIKEQEVYMGEIPLMT------------- 131
Query: 178 DLTELGECPYDQGGYFIINGSEKVLIAQEKMSTNHVYVFKK---RQPNKYAYVAEV---- 230
G F+ING+E+V+++Q S + K K Y A +
Sbjct: 132 -----------DNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYR 180
Query: 231 RSMAESQNRPPSTMFVRMLSRTSAKGGSSGQYIRATLPYIRTEIPIIIVFRALGFVADKD 290
S + + P +FVR+ R ++P I+ RAL + ++
Sbjct: 181 GSWLDFEFDPKDNLFVRIDR--------------------RRKLPATIILRALNYTTEQI 220
Query: 291 I---LEHICYDFQDTQM-MELL 308
+ E + ++ +D ++ MEL+
Sbjct: 221 LDLFFEKVIFEIRDNKLQMELV 242
>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: 1123 VHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 1182
V VCE+CG IA+ + ++ C C + I +V + YA KLL EL AM I P++ E
Sbjct: 5 VWVCENCGHIALEDKRRRRVYCPVCGEEERISKVEMSYAFKLLLDELKAMVIRPKLNLSE 64
Query: 1183 DTK 1185
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 = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 32/92 (34%), Positives = 45/92 (48%), Gaps = 15/92 (16%)
Query: 1049 FLGPTYYQRLKHMVDDKIHSRGRGPV---QILTRQPAEGRSRDGGLRFGEMERDCMIAHG 1105
LGPT+ + ++ D+I+S R P+ QI T+ E RSR G LR R+ ++ G
Sbjct: 105 ILGPTHEETFTELIRDEINSYKRLPLNLYQIQTKYRDEKRSRSGLLR----GREFIMKDG 160
Query: 1106 ASHFLKERLFDQSDAYRVH------VCEHCGL 1131
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 = 34.3 bits (77), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 35/149 (23%), Positives = 62/149 (41%), Gaps = 53/149 (35%)
Query: 68 EIRPESQHNPGQQSDFAETI-----------YKISFGQIYLSKPMMTESDGETATLFPKA 116
++ PE + N G Q+ F ET + F + + P ++ +
Sbjct: 18 DVPPEKRENVGIQAAFKETFPIEEGDKGKGGLVLDFLEYRIGDPPFSQDE---------- 67
Query: 117 ARLRNLTYSAPLYVDVTKRVIKKGHDGEEVTETQDFTKVFIGKVPIMLRSSYCTLYQNSE 176
R ++LTY APLY + ++I K D + E + VF+G +P+M
Sbjct: 68 CREKDLTYQAPLYARL--QLIHK--DTGLIKEDE----VFLGHLPLM------------- 106
Query: 177 KDLTELGECPYDQGGYFIINGSEKVLIAQ 205
+ 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: 857 KLDDDGLAPPGTRVSGEDVIIGKTTP 882
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: 33,722,085
Number of Sequences: 62578
Number of extensions: 1410023
Number of successful extensions: 2796
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2691
Number of HSP's gapped (non-prelim): 57
length of query: 1195
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1085
effective length of database: 8,089,757
effective search space: 8777386345
effective search space used: 8777386345
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)