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= 003180
(842 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 = 1141 bits (2951), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 544/862 (63%), Positives = 660/862 (76%), Gaps = 34/862 (3%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
+LPH+ T + ET+KA++ GY+IHR+LLCAL RR DDRDH+G KRLDLAGPLL LFRM
Sbjct: 346 LLPHITTMEGFETRKAFFLGYMIHRMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRM 405
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWG-QANAAGTRAGV 119
LFRK+TRDV Y+QKCV+ ++ NL A+K+ IT+GL+YSLATGNWG Q + R GV
Sbjct: 406 LFRKMTRDVYKYMQKCVETNREFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGV 465
Query: 120 SQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNL 179
SQVLNR T+ASTLSHLRR N+PIGR+GKLAKPRQLHN+ WGM+CPAETPEGQACGLVKNL
Sbjct: 466 SQVLNRYTFASTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNL 525
Query: 180 ALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKT 239
+LM Y++VGS + PI+EFLEEWG E E+ +P+ P ATK+FVNG W+G+HRDP L +T
Sbjct: 526 SLMSYVSVGSPSAPIIEFLEEWGLETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTET 585
Query: 240 XXXXXXXVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEKQ-------RLLIKKRDI 292
+D++ EV +VRDIR KELR++TD GR RPLFIV+ L I+K I
Sbjct: 586 LRSLRRRLDISAEVSIVRDIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHI 645
Query: 293 IALQQRES-----PEDG-GWHDLVAKGFXXXXXXXXXXXXXXXXXXNDL----------- 335
L + + PE GW LV+ G DL
Sbjct: 646 QQLIEDKDRYDIDPEQRFGWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYE 705
Query: 336 VQARLHPEE-------AYADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQ 388
V+ L P + + +THCEIHP++ILG+ ASIIPFPDHNQSPRNTYQSAMGKQ
Sbjct: 706 VKEELDPAQRVKPAPNPHVHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQ 765
Query: 389 AMGIYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQE 448
AMG+Y+TNYQ RMDT+A +LYYPQKPL TTR+ME+L FR+LPAG NAIVAI CYSGYNQE
Sbjct: 766 AMGVYLTNYQVRMDTMANILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQE 825
Query: 449 DSVIMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDD 508
DS+IMNQ+SIDRG FRS+F+R+Y D+EKK+G V E+F RP RS T+ M+HG+YDKL+DD
Sbjct: 826 DSIIMNQASIDRGLFRSIFYRTYTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDD 885
Query: 509 GLAPPGTRVSGEDVIIGKTTPISQD-EAQGQASR-YTRRDHSISLRHSETGMVDQVLLTT 566
GL PGTRVSGED+IIGKT PI D E GQ ++ + +RD S LR +E+G+VDQV++TT
Sbjct: 886 GLIAPGTRVSGEDIIIGKTAPIPLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTT 945
Query: 567 NADGLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHA 626
N +GL+FVKVR+RS RIPQIGDKF+SRHGQKGT+GMTY EDMP++ +GI PDII+NPHA
Sbjct: 946 NQEGLKFVKVRMRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHA 1005
Query: 627 IPSRMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGH 686
IPSRMT+ L+EC + KV+A G EGDATPFTDVTV+ +SK L G+Q RGFE MY+GH
Sbjct: 1006 IPSRMTVAHLVECQLSKVSALSGFEGDATPFTDVTVEAVSKLLRSHGFQSRGFEVMYHGH 1065
Query: 687 TGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERD 746
TGR+L A +FLGPTYYQRLKH+VDDKIH+R RGPVQILTRQP EGRSRDGGLRFGEMERD
Sbjct: 1066 TGRKLVAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERD 1125
Query: 747 CMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIP 806
C I+HG S L+ERLFD SDAYRV VC+ CGLIAIA+ KK+S+ECR C+N+T QV++P
Sbjct: 1126 CQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLP 1185
Query: 807 YACKLLFQELMAMAIAPRMLTK 828
YA KLLFQELM+M IAPR+ TK
Sbjct: 1186 YAAKLLFQELMSMNIAPRLFTK 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 = 1133 bits (2930), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 545/859 (63%), Positives = 653/859 (76%), Gaps = 32/859 (3%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
LPH+ + E++KA++ GY+I+RLLLCAL R+ +DDRDH+G KRLDLAGPLL LF+
Sbjct: 360 FLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKT 419
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWG-QANAAGTRAGV 119
LF+KLT+D+ Y+Q+ V+ D N++ AI AKTITSGLKY+LATGNWG Q A +RAGV
Sbjct: 420 LFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGV 479
Query: 120 SQVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNL 179
SQVLNR TY+STLSHLRR N+PIGR+GKLAKPRQLHN+ WG++CPAETPEGQACGLVKNL
Sbjct: 480 SQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNL 539
Query: 180 ALMVYITVGSAAYPILEFLEEWGTENFEEISPAVIPQATKIFVNGCWVGIHRDPEMLVKT 239
+LM I+VG+ PI+ FL EWG E E+ P P AT++FVNG W G+HR+P L++T
Sbjct: 540 SLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMET 599
Query: 240 XXXXXXXVDVNTEVGVVRDIRLKELRIYTDYGRCSRPLFIVEK------QRLLIKKRDII 293
D+N EV ++RDIR KEL+I+TD GR RPLFIVE + L ++K I
Sbjct: 600 LRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIA 659
Query: 294 ALQQRESPE-DGG--------WHDLVAKGFXXXXXXXXXXXXXXXXXXNDLVQARLHPEE 344
L E + +GG W L+ +G DL A + E
Sbjct: 660 KLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEEN 719
Query: 345 A-------------YADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMG 391
+A T+THCEIHPS+ILGV ASIIPFPDHNQSPRNTYQSAMGKQAMG
Sbjct: 720 DLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMG 779
Query: 392 IYVTNYQFRMDTLAYVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSV 451
+++TNY RMDT+A +LYYPQKPL TTRAME+L FR+LPAG NAIVAIACYSGYNQEDS+
Sbjct: 780 VFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSM 839
Query: 452 IMNQSSIDRGFFRSLFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKLDDDGLA 511
IMNQSSIDRG FRSLFFRSY D+EKK G + E F +P R+NT+ M+HG+YDKLDDDGL
Sbjct: 840 IMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLI 899
Query: 512 PPGTRVSGEDVIIGKTTPISQDEAQ-GQASRY-TRRDHSISLRHSETGMVDQVLLTTNAD 569
PG RVSGEDVIIGKTTPIS DE + GQ + Y ++RD S LR +E G+VDQVL+TTN D
Sbjct: 900 APGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQD 959
Query: 570 GLRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPS 629
GL+FVKVRVR+ +IPQIGDKF+SRHGQKGT+G+TY +EDMP+T EGI PD+I+NPHAIPS
Sbjct: 960 GLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPS 1019
Query: 630 RMTIGQLIECIMGKVAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGR 689
RMT+ LIEC++ KVAA G EGDA+PFTD+TV+ ISK L + GYQ RGFE MYNGHTG+
Sbjct: 1020 RMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGK 1079
Query: 690 RLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMI 749
+L A IF GPTYYQRL+HMVDDKIH+R RGP+Q+LTRQP EGRSRDGGLRFGEMERDCMI
Sbjct: 1080 KLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMI 1139
Query: 750 AHGASHFLKERLFDQSDAYRVHVCEHCGLI-AIANLKKNSFECRGCKNKTDIVQVHIPYA 808
AHGA+ FLKERL + SDA+RVH+C CGL+ IA L N FEC+GC NK DI Q+HIPYA
Sbjct: 1140 AHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYA 1199
Query: 809 CKLLFQELMAMAIAPRMLT 827
KLLFQELMAM I PR+ T
Sbjct: 1200 AKLLFQELMAMNITPRLYT 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 = 696 bits (1796), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 376/846 (44%), Positives = 508/846 (60%), Gaps = 42/846 (4%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
LPH+GT KKAYY Y I +++ LGRR DD+DHY NKRL LAG L LFR+
Sbjct: 300 FLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFASLFRV 359
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVS 120
F+ +D+ ++K G+ + L+ ++ +T ++++LATGNW G R GVS
Sbjct: 360 AFKAFVKDLTYQLEKSKVRGRKLALKALVRPDIVTERIRHALATGNW-----VGGRTGVS 414
Query: 121 QVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 180
Q+L+R + S LSHLRR+ S + R + R LH +QWG MCP ETPEG GLVKNLA
Sbjct: 415 QLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLA 474
Query: 181 LMVYITVGSAAYPILEFLEEWGTENFEEISPAVIP---------QATKIFVNGCWVGIHR 231
LM I VG + + L E G EE+ V + +K+ +NG VG +R
Sbjct: 475 LMAQIAVGINEKIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLVGYYR 534
Query: 232 DPEMLVKTXXXXXXXVDVNTEVGV---VRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIK 288
D E L K +++ EV V V D + E+ + D GR RPL IV L+
Sbjct: 535 DGEELAKKIRERRRKGEISDEVNVGHIVTDF-INEVHVNCDSGRVRRPLIIVSNGNPLVT 593
Query: 289 KRDIIALQQRESPEDGG---WHDLVAKGFXXXXXXXXXXXXXXXXXXNDLVQARLHPEEA 345
+ DI L D G + DLV +G +DL PE
Sbjct: 594 REDIEKL-------DSGSITFDDLVRQGKIEYLDAEEEENAYVALEPSDLT-----PE-- 639
Query: 346 YADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLA 405
+TH EI ILG+ ASIIP+P+HNQSPRNTYQSAM KQA+G+Y NYQ R DT A
Sbjct: 640 ----HTHLEIWSPAILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRA 695
Query: 406 YVLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRS 465
++L+YPQ+PLV TRA++ + + PAG NAI+A+ ++GYN EDS+IMN+SS++RG +RS
Sbjct: 696 HLLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYRS 755
Query: 466 LFFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKL-DDDGLAPPGTRVSGEDVII 524
FFR Y EE K ++ P+ G + Y +L +D+G+ P V G DV+I
Sbjct: 756 TFFRLYSTEEVKYPGGQEDKIVMPE-PGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLI 814
Query: 525 GKTTPIS-QDEAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRI 583
GK +P E + + +RD SI RH E G+VD VL+T A+G + VKVRVR +RI
Sbjct: 815 GKVSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRI 874
Query: 584 PQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGK 643
P IGDKF+SRHGQKG +GM Q DMP+TV+G+ PD+I+NPHA+PSRMT+GQ++E I GK
Sbjct: 875 PSIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGK 934
Query: 644 VAAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQ 703
AA G DATPF ++ + + K GY E Y+G TG+++ + I+ G YYQ
Sbjct: 935 YAALSGNIVDATPFYKTPIEQLQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQ 994
Query: 704 RLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFD 763
+L HMV DKIH+R RGPVQILTRQP EGR+R+GGLRFGEMERDC+I G + LK+RL D
Sbjct: 995 KLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLD 1054
Query: 764 QSDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAP 823
SD ++VC+ CG I + KN + C +K+++ V + YA KLL QELM+M I+P
Sbjct: 1055 NSDRTTIYVCDQCGYIGWYDKNKNKYVCPIHGDKSNLFPVTVSYAFKLLIQELMSMIISP 1114
Query: 824 RMLTKE 829
R++ ++
Sbjct: 1115 RLILED 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 = 689 bits (1778), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 371/845 (43%), Positives = 507/845 (60%), Gaps = 40/845 (4%)
Query: 1 MLPHVGTGDFCETKKAYYFGYIIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRM 60
LPH+GT KKAYY Y I +++ LGRR DD+DHY NKRL LAG L LFR+
Sbjct: 297 FLPHLGTSAEDRKKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFASLFRV 356
Query: 61 LFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVS 120
F+ +D+ ++K G+ + L+ ++ +T ++++LATGNW G R GVS
Sbjct: 357 AFKAFVKDLTYQLEKSKVRGRKLALKALVRPDIVTERIRHALATGNW-----VGGRTGVS 411
Query: 121 QVLNRLTYASTLSHLRRLNSPIGREGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLA 180
Q+L+R + S LSHLRR+ S + R + R LH +QWG MCP ETPEG GLVKNLA
Sbjct: 412 QLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLA 471
Query: 181 LMVYITVGSAAYPILEFLEEWGTENFEEISPAVIP---------QATKIFVNGCWVGIHR 231
LM I VG + + L E G EE+ V + +K+ +NG +G ++
Sbjct: 472 LMAQIAVGINERIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLIGYYQ 531
Query: 232 DPEMLVKTXXXXXXXVDVNTEVGV---VRDIRLKELRIYTDYGRCSRPLFIVEKQRLLIK 288
D L +++ EV V V D + E+ + D GR RPL IV L+
Sbjct: 532 DGGELANKIRERRRKGEISDEVNVGHIVTDF-INEVHVNCDSGRVRRPLIIVSNGNPLVT 590
Query: 289 KRDIIALQQRESPEDGG--WHDLVAKGFXXXXXXXXXXXXXXXXXXNDLVQARLHPEEAY 346
DI E E G + DLV +G NDL P+
Sbjct: 591 IEDI------EKLESGAITFDDLVRQGKIEYLDAEEEENAYVALEPNDLT-----PD--- 636
Query: 347 ADTYTHCEIHPSLILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGIYVTNYQFRMDTLAY 406
+TH EI ILG+ ASIIP+P+HNQSPRNTYQSAM KQA+G+Y NYQ R DT A+
Sbjct: 637 ---HTHLEIWSPAILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAH 693
Query: 407 VLYYPQKPLVTTRAMEHLHFRQLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSL 466
+L+YPQ+PLV TRA++ + + PAG NAI+A+ ++GYN EDS+IMN+SS++RG +RS
Sbjct: 694 LLHYPQRPLVQTRALDIIGYTNRPAGNNAILAVMSFTGYNMEDSIIMNRSSVERGMYRST 753
Query: 467 FFRSYRDEEKKMGTLVKEDFGRPDRSNTMGMRHGSYDKL-DDDGLAPPGTRVSGEDVIIG 525
FFR Y EE K ++ P+ + G + Y +L +D+G+ P V G DV+IG
Sbjct: 754 FFRLYSTEEVKYPGGQEDKIVMPE-AGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIG 812
Query: 526 KTTPIS-QDEAQGQASRYTRRDHSISLRHSETGMVDQVLLTTNADGLRFVKVRVRSVRIP 584
K +P E + + +RD SI RH E G+VD VL+T A+G + VKVRVR +RIP
Sbjct: 813 KVSPPRFLQEFKELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRDLRIP 872
Query: 585 QIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKV 644
IGDKF+SRHGQKG +GM Q DMP+TV+G+ PDII+NPHA+PSRMT+GQ++E I GK
Sbjct: 873 TIGDKFASRHGQKGVIGMLIPQVDMPYTVKGVVPDIILNPHALPSRMTLGQIMEGIAGKY 932
Query: 645 AAHMGKEGDATPFTDVTVDNISKALHKCGYQMRGFETMYNGHTGRRLTAMIFLGPTYYQR 704
AA G DATPF ++ + + + GY E +Y+G TG+++ + I+ G YYQ+
Sbjct: 933 AALSGNIVDATPFYKTPIEQLQNEILRYGYLPDATEVVYDGRTGQKIKSRIYFGVVYYQK 992
Query: 705 LKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQ 764
L HMV DK+H+R RGPVQILTRQP EGR+R+GGLRFGEMERDC+I G + LK+RL D
Sbjct: 993 LHHMVADKLHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLIGFGTAMLLKDRLLDN 1052
Query: 765 SDAYRVHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPR 824
SD ++VC+ CG I + KN + C +K+++ V + YA KLL QELM+M I+PR
Sbjct: 1053 SDRTMIYVCDQCGYIGWYDKNKNKYVCPIHGDKSNLFPVTVSYAFKLLIQELMSMIISPR 1112
Query: 825 MLTKE 829
++ ++
Sbjct: 1113 LVLED 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 = 5e-40, Method: Compositional matrix adjust.
Identities = 126/468 (26%), Positives = 209/468 (44%), Gaps = 91/468 (19%)
Query: 429 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 486
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 717
Query: 487 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 536
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 718 --PERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRS 775
Query: 537 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 586
G+ +R + D S+ + E G+V L D G+R V+V V R Q+
Sbjct: 776 IFGEKARDVK-DTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQV 834
Query: 587 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 646
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 835 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 894
Query: 647 HMGKEGDATPFTDVTVDNISKALHKC------GYQMRGFE-------------------- 680
+G+ + F T I + L + Q GF
Sbjct: 895 FLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSP 954
Query: 681 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 723
+Y+G TG I +G + +L HMV+DK+H+R GP +
Sbjct: 955 GKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1014
Query: 724 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 783
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1015 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAII---- 1070
Query: 784 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 831
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1071 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1106
Score = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 45/149 (30%), Positives = 70/149 (46%), Gaps = 20/149 (13%)
Query: 37 DDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRA-YVQKCVDNGKDVNLQFAIKAKTIT 95
DD DH GN+R+ G L+ FR+ +L R VR V D L + ++ +
Sbjct: 323 DDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLE 379
Query: 96 SGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKP 151
+ L+ +R+ +SQ + S+L H RR+++ P G RE
Sbjct: 380 AALREFF------------SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDV 427
Query: 152 RQLHNSQWGMMCPAETPEGQACGLVKNLA 180
R +H + +G +CP ETPEG GL+ +LA
Sbjct: 428 RDVHRTHYGRICPVETPEGANIGLITSLA 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 = 5e-40, Method: Compositional matrix adjust.
Identities = 126/468 (26%), Positives = 209/468 (44%), Gaps = 91/468 (19%)
Query: 429 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 486
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 718
Query: 487 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 536
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 719 --PERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRS 776
Query: 537 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 586
G+ +R + D S+ + E G+V L D G+R V+V V R Q+
Sbjct: 777 IFGEKARDVK-DTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQV 835
Query: 587 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 646
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 836 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 895
Query: 647 HMGKEGDATPFTDVTVDNISKALHKC------GYQMRGFE-------------------- 680
+G+ + F T I + L + Q GF
Sbjct: 896 FLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSP 955
Query: 681 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 723
+Y+G TG I +G + +L HMV+DK+H+R GP +
Sbjct: 956 GKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1015
Query: 724 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 783
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1016 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAII---- 1071
Query: 784 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 831
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1072 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1107
Score = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 45/149 (30%), Positives = 70/149 (46%), Gaps = 20/149 (13%)
Query: 37 DDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRA-YVQKCVDNGKDVNLQFAIKAKTIT 95
DD DH GN+R+ G L+ FR+ +L R VR V D L + ++ +
Sbjct: 323 DDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLE 379
Query: 96 SGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKP 151
+ L+ +R+ +SQ + S+L H RR+++ P G RE
Sbjct: 380 AALREFF------------SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDV 427
Query: 152 RQLHNSQWGMMCPAETPEGQACGLVKNLA 180
R +H + +G +CP ETPEG GL+ +LA
Sbjct: 428 RDVHRTHYGRICPVETPEGANIGLITSLA 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 (411), Expect = 6e-40, Method: Compositional matrix adjust.
Identities = 126/468 (26%), Positives = 209/468 (44%), Gaps = 91/468 (19%)
Query: 429 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 486
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 718
Query: 487 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 536
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 719 --PERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRS 776
Query: 537 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 586
G+ +R + D S+ + E G+V L D G+R V+V V R Q+
Sbjct: 777 IFGEKARDVK-DTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQV 835
Query: 587 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 646
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 836 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 895
Query: 647 HMGKEGDATPFTDVTVDNISKALHKC------GYQMRGFE-------------------- 680
+G+ + F T I + L + Q GF
Sbjct: 896 FLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSP 955
Query: 681 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 723
+Y+G TG I +G + +L HMV+DK+H+R GP +
Sbjct: 956 GKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1015
Query: 724 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 783
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1016 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAII---- 1071
Query: 784 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 831
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1072 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1107
Score = 60.1 bits (144), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 45/149 (30%), Positives = 70/149 (46%), Gaps = 20/149 (13%)
Query: 37 DDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRA-YVQKCVDNGKDVNLQFAIKAKTIT 95
DD DH GN+R+ G L+ FR+ +L R VR V D L + ++ +
Sbjct: 323 DDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLE 379
Query: 96 SGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKP 151
+ L+ +R+ +SQ + S+L H RR+++ P G RE
Sbjct: 380 AALREFF------------SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDV 427
Query: 152 RQLHNSQWGMMCPAETPEGQACGLVKNLA 180
R +H + +G +CP ETPEG GL+ +LA
Sbjct: 428 RDVHRTHYGRICPVETPEGANIGLITSLA 456
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 162 bits (411), Expect = 6e-40, Method: Compositional matrix adjust.
Identities = 126/468 (26%), Positives = 209/468 (44%), Gaps = 91/468 (19%)
Query: 429 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 486
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 717
Query: 487 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 536
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 718 --PERITRDIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRS 775
Query: 537 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 586
G+ +R + D S+ + E G+V L D G+R V+V V R Q+
Sbjct: 776 IFGEKARDVK-DTSLRVPPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQV 834
Query: 587 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 646
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 835 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 894
Query: 647 HMGKEGDATPFTDVTVDNISKALHKC------GYQMRGFE-------------------- 680
+G+ + F T I + L + Q GF
Sbjct: 895 FLGQRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSP 954
Query: 681 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 723
+Y+G TG I +G + +L HMV+DK+H+R GP +
Sbjct: 955 GKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1014
Query: 724 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 783
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1015 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAII---- 1070
Query: 784 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 831
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1071 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1106
Score = 60.1 bits (144), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 45/149 (30%), Positives = 70/149 (46%), Gaps = 20/149 (13%)
Query: 37 DDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRA-YVQKCVDNGKDVNLQFAIKAKTIT 95
DD DH GN+R+ G L+ FR+ +L R VR V D L + ++ +
Sbjct: 323 DDIDHLGNRRIRTVGELMADQFRVGLARLARGVRERMVMGSPDTLTPAKL---VNSRPLE 379
Query: 96 SGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKP 151
+ L+ +R+ +SQ + S+L H RR+++ P G RE
Sbjct: 380 AALREFF------------SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDV 427
Query: 152 RQLHNSQWGMMCPAETPEGQACGLVKNLA 180
R +H + +G +CP ETPEG GL+ +LA
Sbjct: 428 RDVHRTHYGRICPVETPEGANIGLITSLA 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: 429 LPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYRDEEK--KMGTLVKEDF 486
L G N +VAI + GYN ED++++++ + R F+ S+ Y E + K+G
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLG------- 718
Query: 487 GRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTPISQDEAQ-------- 536
P+R + + + LD++G+ G V D+++G+T+ + E
Sbjct: 719 --PERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRS 776
Query: 537 --GQASRYTRRDHSISLRHSETGMVDQVLLTTNAD-------GLR-FVKVRVRSVRIPQI 586
G+ +R + D S+ + E G+V + + D G+R V+V V R Q+
Sbjct: 777 IFGEKARDVK-DTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQV 835
Query: 587 GDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSRMTIGQLIECIMGKVAA 646
GDK ++RHG KG V EDMP +G D+I+NP +PSRM +GQ++E +G
Sbjct: 836 GDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGY 895
Query: 647 HMGKEGDATPFTDVTVDNISKALHKC-------------GYQMRGFE------------- 680
+G+ + F I + L + G R E
Sbjct: 896 FLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTP 955
Query: 681 -----------------TMYNGHTGRRLTAMIFLGPTYYQRLKHMVDDKIHSRGRGPVQI 723
+Y+G TG + I +G + +L HMV+DK+H+R GP +
Sbjct: 956 GKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSL 1015
Query: 724 LTRQPAEGRSRDGGLRFGEMERDCMIAHGASHFLKERLFDQSDAYRVHVCEHCGLIAIAN 783
+T+QP G+++ GG RFGEME + A+GA+H L+E L +SD + +I
Sbjct: 1016 ITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAII---- 1071
Query: 784 LKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKEDT 831
D+ + +P + ++L +EL A+A+ + L ++D
Sbjct: 1072 ------------KGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDN 1107
Score = 58.2 bits (139), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 41/148 (27%), Positives = 71/148 (47%), Gaps = 18/148 (12%)
Query: 37 DDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGKDVNLQFAIKAKTITS 96
DD DH GN+R+ G L+ FR+ +L R VR + + + + + ++ + +
Sbjct: 323 DDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRE--RMLMGSEDSLTPAKLVNSRPLEA 380
Query: 97 GLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS--PIG--REGKLAKPR 152
++ +R+ +SQ + S+L H RR+++ P G RE R
Sbjct: 381 AIREFF------------SRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVR 428
Query: 153 QLHNSQWGMMCPAETPEGQACGLVKNLA 180
+H + +G +CP ETPEG GL+ +LA
Sbjct: 429 DVHRTHYGRICPVETPEGANIGLITSLA 456
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
Length = 1342
Score = 115 bits (287), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 78/250 (31%), Positives = 117/250 (46%), Gaps = 54/250 (21%)
Query: 571 LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSR 630
L+ VKV + R Q GDK + RHG KG + EDMP+ G DI++NP +PSR
Sbjct: 1047 LKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSR 1106
Query: 631 MTIGQLIECIMGKVA-------------------------------AHMGKEGDATPFTD 659
M IGQ++E +G A A + ++ D + F+D
Sbjct: 1107 MNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSD 1166
Query: 660 VTVDNIS----------------------KALHKCG-YQMRGFETMYNGHTGRRLTAMIF 696
V ++ K L K G G +Y+G TG + +
Sbjct: 1167 EEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVT 1226
Query: 697 LGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHF 756
+G Y +L H+VDDK+H+R G ++T+QP G+++ GG RFGEME + A+GA++
Sbjct: 1227 VGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1286
Query: 757 LKERLFDQSD 766
L+E L +SD
Sbjct: 1287 LQEMLTVKSD 1296
Score = 56.6 bits (135), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 43/164 (26%), Positives = 80/164 (48%), Gaps = 18/164 (10%)
Query: 22 IIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGK 81
++ +L+ G+ DD DH GN+R+ G + FR+ ++ R V+ + + +
Sbjct: 428 VMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL--SLGDLD 485
Query: 82 DVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS- 140
+ Q I AK I++ +K + +SQ + + S ++H RR+++
Sbjct: 486 TLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMVQNNPLSEITHKRRISAL 533
Query: 141 -PIG--REGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLAL 181
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 = 27/106 (25%), Positives = 52/106 (49%), Gaps = 13/106 (12%)
Query: 428 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYR--DEEKKMGTLVKED 485
+L G N VA ++GYN EDS+++++ + F ++ + + K+G
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLG------ 846
Query: 486 FGRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 529
P+ ++ + + KLD+ G+ G V+G D+++GK TP
Sbjct: 847 ---PEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
>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 = 115 bits (287), Expect = 1e-25, Method: Compositional matrix adjust.
Identities = 78/250 (31%), Positives = 117/250 (46%), Gaps = 54/250 (21%)
Query: 571 LRFVKVRVRSVRIPQIGDKFSSRHGQKGTVGMTYTQEDMPWTVEGITPDIIVNPHAIPSR 630
L+ VKV + R Q GDK + RHG KG + EDMP+ G DI++NP +PSR
Sbjct: 1047 LKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSR 1106
Query: 631 MTIGQLIECIMGKVA-------------------------------AHMGKEGDATPFTD 659
M IGQ++E +G A A + ++ D + F+D
Sbjct: 1107 MNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSD 1166
Query: 660 VTVDNIS----------------------KALHKCG-YQMRGFETMYNGHTGRRLTAMIF 696
V ++ K L K G G +Y+G TG + +
Sbjct: 1167 EEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVT 1226
Query: 697 LGPTYYQRLKHMVDDKIHSRGRGPVQILTRQPAEGRSRDGGLRFGEMERDCMIAHGASHF 756
+G Y +L H+VDDK+H+R G ++T+QP G+++ GG RFGEME + A+GA++
Sbjct: 1227 VGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYT 1286
Query: 757 LKERLFDQSD 766
L+E L +SD
Sbjct: 1287 LQEMLTVKSD 1296
Score = 58.2 bits (139), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 43/164 (26%), Positives = 81/164 (49%), Gaps = 18/164 (10%)
Query: 22 IIHRLLLCALGRRAEDDRDHYGNKRLDLAGPLLGGLFRMLFRKLTRDVRAYVQKCVDNGK 81
++ +L+ G+ DD DH GN+R+ G + FR+ ++ R V+ + + +
Sbjct: 428 VMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERL--SLGDLD 485
Query: 82 DVNLQFAIKAKTITSGLKYSLATGNWGQANAAGTRAGVSQVLNRLTYASTLSHLRRLNS- 140
+ Q I AK I++ +K + +SQ +++ S ++H RR+++
Sbjct: 486 TLMPQDMINAKPISAAVKEFFGSSQ------------LSQFMDQNNPLSEITHKRRISAL 533
Query: 141 -PIG--REGKLAKPRQLHNSQWGMMCPAETPEGQACGLVKNLAL 181
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 = 27/106 (25%), Positives = 52/106 (49%), Gaps = 13/106 (12%)
Query: 428 QLPAGINAIVAIACYSGYNQEDSVIMNQSSIDRGFFRSLFFRSYR--DEEKKMGTLVKED 485
+L G N VA ++GYN EDS+++++ + F ++ + + K+G
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLG------ 846
Query: 486 FGRPDR--SNTMGMRHGSYDKLDDDGLAPPGTRVSGEDVIIGKTTP 529
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 = 1e-05, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 35/63 (55%)
Query: 770 VHVCEHCGLIAIANLKKNSFECRGCKNKTDIVQVHIPYACKLLFQELMAMAIAPRMLTKE 829
V VCE+CG IA+ + ++ C C + I +V + YA KLL EL AM I P++ E
Sbjct: 5 VWVCENCGHIALEDKRRRRVYCPVCGEEERISKVEMSYAFKLLLDELKAMVIRPKLNLSE 64
Query: 830 DTK 832
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 = 0.005, Method: Compositional matrix adjust.
Identities = 32/92 (34%), Positives = 45/92 (48%), Gaps = 15/92 (16%)
Query: 696 FLGPTYYQRLKHMVDDKIHSRGRGPV---QILTRQPAEGRSRDGGLRFGEMERDCMIAHG 752
LGPT+ + ++ D+I+S R P+ QI T+ E RSR G LR R+ ++ G
Sbjct: 105 ILGPTHEETFTELIRDEINSYKRLPLNLYQIQTKYRDEKRSRSGLLR----GREFIMKDG 160
Query: 753 ASHFLKERLFDQSDAYRVH------VCEHCGL 778
S E DQS YR + + E CGL
Sbjct: 161 YSFHADEASLDQS--YRDYEKAYSRIFERCGL 190
>pdb|3TBI|B Chain B, Crystal Structure Of T4 Gp33 Bound To E. Coli Rnap
Beta-Flap Domain
Length = 228
Score = 31.6 bits (70), Expect = 2.1, Method: Composition-based stats.
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 504 KLDDDGLAPPGTRVSGEDVIIGKTTP 529
KLD+ G+ G V+G D+++GK TP
Sbjct: 35 KLDESGIVYIGAEVTGGDILVGKVTP 60
>pdb|1ITX|A Chain A, Catalytic Domain Of Chitinase A1 From Bacillus Circulans
Wl-12
Length = 419
Score = 30.0 bits (66), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 21/48 (43%), Gaps = 4/48 (8%)
Query: 191 AYPILEFLEEWG----TENFEEISPAVIPQATKIFVNGCWVGIHRDPE 234
+Y I+ + W N +I P + F + CW GIH +P+
Sbjct: 11 SYKIVGYYPSWAAYGRNYNVADIDPTKVTHINYAFADICWNGIHGNPD 58
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
0.322 0.137 0.417
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 24,688,751
Number of Sequences: 62578
Number of extensions: 1023551
Number of successful extensions: 1954
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: 1882
Number of HSP's gapped (non-prelim): 39
length of query: 842
length of database: 14,973,337
effective HSP length: 107
effective length of query: 735
effective length of database: 8,277,491
effective search space: 6083955885
effective search space used: 6083955885
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)