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= 046825
(1208 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 323 bits (827), Expect = 5e-88, Method: Compositional matrix adjust.
Identities = 243/768 (31%), Positives = 366/768 (47%), Gaps = 144/768 (18%)
Query: 298 SKGGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKV-IVARWMNLQQSVNVLFDGKN 356
S G S E T LS +++AN AN + + A IV+ + L Q +
Sbjct: 257 SVDGTSRGEDDLTHKLSDIIKAN---ANVRRCEQEGAPAHIVSEYEQLLQFHVATYMDNE 313
Query: 357 AAGQ--------RDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVNEIGI 408
AGQ R + S I L+ KEG R LMGKRV+++ R+VI+ DP L+++E+G+
Sbjct: 314 IAGQPQALQKSGRPLKS-IRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDELGV 372
Query: 409 PPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRISIGR 468
P A LTYPE VTP+N+ +L++ + NG + HPGA + + G
Sbjct: 373 PRSIAKTLTYPETVTPYNIYQLQELVRNGPDEHPGAKYIIR---------------DTGE 417
Query: 469 KLDTSRGAIVQPGKDSDNEFE-GKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGE 527
++D + + D G V RH++DGDVV+ NRQP+LHK S+M H +RV+
Sbjct: 418 RID-----LRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMP-Y 471
Query: 528 KTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRSLIQ 587
T R++ + S YNADFDGDEMN+H PQ E +RAE I Q V P + P+ ++Q
Sbjct: 472 STFRLNLSVTSPYNADFDGDEMNMHVPQSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQ 531
Query: 588 DHIVSAALLTKKDTFLNRDEFCQXXXXXXXXXXXXXXFTGKPGQRVLISRSEQEVLPLLP 647
D + + +D FL R+ +L +LP P
Sbjct: 532 DTLAGVRKFSLRDNFLTRNAVMNI---------------------MLWVPDWDGILPP-P 569
Query: 648 AIWKPEPLWTGKQVITAVLNHITRGRPPFVVERGGKLPQDFFKTRFNADKQSDRKKNDKG 707
I KP+ LWTGKQ+++ ++ +G L +D DKQS D G
Sbjct: 570 VILKPKVLWTGKQILS------------LIIPKGINLIRD-------DDKQSLSNPTDSG 610
Query: 708 KLSKTNKMHXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIYKNDLVRGVIDKA 767
L I +++ GV+DK
Sbjct: 611 ML--------------------------------------------IENGEIIYGVVDKK 626
Query: 768 QF--ADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERK 825
+ GLVHT+ + G + + R+ +L +GF+ G+ D + D +E
Sbjct: 627 TVGASQGGLVHTIWKEKGPEICKGFFNGIQRVVNYWLLHNGFSIGIGDTIADADTMKEVT 686
Query: 826 NHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNK 885
+ K + E A+ + +LK E +R +A V+ ++ +Q
Sbjct: 687 RTV-------KEARRQVAECIQDAQHN--RLKPEPGMTLRESFEAKVS----RILNQARD 733
Query: 886 HTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMV 945
+ S +E LK + N + M +G+KGS +N Q+S+ +GQQ +EGKR+P
Sbjct: 734 NAGRS------AEHSLKDS--NNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGF 785
Query: 946 SGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQR 1005
+TLP F D +P + GFI + +L GL PQE++FH MAGREGL+DTAVKT+ +GY+QR
Sbjct: 786 KYRTLPHFPKDDDSPESRGFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQR 845
Query: 1006 CLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDAL 1053
L+K +E + + YD +VR+A G I+QF YGEDG+D + FD+L
Sbjct: 846 RLVKAMEDVMVRYDGTVRNAMGDIIQFAYGEDGLDATLVEY-QVFDSL 892
Score = 91.3 bits (225), Expect = 3e-18, Method: Compositional matrix adjust.
Identities = 46/85 (54%), Positives = 63/85 (74%), Gaps = 1/85 (1%)
Query: 1120 NEMAKQDFLKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLG 1179
N++A + + V+ +F ++ PGE VG LA+QS+GEP+TQMTLNTFH AG NVTLG
Sbjct: 1041 NKVAFEWIMGEVEARFQQAVVSPGEMVGTLAAQSIGEPATQMTLNTFHYAGVSSKNVTLG 1100
Query: 1180 IPRLQEILTIASKDIKTPVITCPLL 1204
+PRL+EIL +A K+IKTP +T L+
Sbjct: 1101 VPRLKEILNVA-KNIKTPSLTIYLM 1124
Score = 47.0 bits (110), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 26/48 (54%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPXXXXXXXXXXKRICFFCHHFK 48
C+TCG+ CPGHFGHI+L PV++ + +C+ C K
Sbjct: 69 CQTCGETMADCPGHFGHIELAKPVFHIGFLSKIKKILECVCWNCGKLK 116
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|A Chain A, Rnap At 3.2ang
pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 880
Score = 203 bits (516), Expect = 5e-52, Method: Compositional matrix adjust.
Identities = 157/450 (34%), Positives = 233/450 (51%), Gaps = 65/450 (14%)
Query: 228 PSGFKKQKDLFSGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVV 287
P F +++ L PSD+++ +EK+ E++ E+ + + + L V+
Sbjct: 161 PYNFYEERKEGVAKLTPSDIRERLEKVPESDVEILGYDPTTSRPEW--------MILTVL 212
Query: 288 LVPPIKFRLPSKGGDSVM--EHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQ 345
VPPI R PS +S + E T L +++ N L + ++ +I W LQ
Sbjct: 213 PVPPITIR-PSIMIESGIRAEDDLTHKLVDIVRINERLKES-IDAGAPQLIIEDLWDLLQ 270
Query: 346 QSVNVLFD--------GKNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISP 397
V FD K+ +G R + + + Q L+ KEG FR L GKRV+++ R+VISP
Sbjct: 271 YHVATYFDNEIPGLPPSKHRSG-RPLRT-LAQRLKGKEGRFRGNLSGKRVDFSSRTVISP 328
Query: 398 DPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLP 457
DP ++++E+G+P A LT PER+TPWN+ KLR +ING + PGA + +
Sbjct: 329 DPNISIDEVGVPEIIARTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIR-------- 380
Query: 458 PNKKMRISIGRKLDTSRGAIVQPGKDSDNEFE-GKMVYRHLQDGDVVLVNRQPTLHKPSI 516
P+ GR++D V+ K+ + G +V RHL DGDVVL NRQP+LH+ S+
Sbjct: 381 PD-------GRRIDLR---YVKDRKELASTLAPGYVVERHLTDGDVVLFNRQPSLHRISM 430
Query: 517 MAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRP 576
MAH VRVLKG T R++ C YNADFDGDEMN+H PQ E + AEA I+ + + P
Sbjct: 431 MAHRVRVLKG-LTFRLNLLVCPPYNADFDGDEMNLHVPQSEEAIAEAKEIMLVHKNIITP 489
Query: 577 SNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQXXXXXXXXXXXXXXFTGKPGQRVLIS 636
G P+ QD+I A LLT K T L ++E Q ++
Sbjct: 490 RYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQ-----------------------ILG 526
Query: 637 RSEQEVLPLLPAIWKPEPLWTGKQVITAVL 666
++ ++ PAI P +TGKQV++A L
Sbjct: 527 VADVKIDLGEPAILAPREYYTGKQVVSAFL 556
Score = 155 bits (393), Expect = 9e-38, Method: Compositional matrix adjust.
Identities = 97/285 (34%), Positives = 160/285 (56%), Gaps = 26/285 (9%)
Query: 759 LVRGVIDKAQFADY---GLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLL 815
L+ GV DK + ++H + + Y L+ L R+F F+++ GFT ++D+
Sbjct: 593 LLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIRFVELQGFTMRLEDVS 652
Query: 816 ILKDKERERKNHLHGSEEIGKRVHLEAL-ELEDGAEIDPIKLKSEIEKAMRGGGDAAVAY 874
+ D ++E N + + +V ++ L + E++PI ++ +E+++
Sbjct: 653 LGDDVKKEIYNEIDRA-----KVEVDNLIQKYKNGELEPIPGRT-LEESL---------- 696
Query: 875 FDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQ 934
+ + L+K S++ ++ S+ L P N+ +M +GA+GS +N Q+++ LGQQ
Sbjct: 697 -ENYILDTLDKLRSTA--GDIASK-YLDPF--NFAYVMARTGARGSVLNITQMAAMLGQQ 750
Query: 935 ELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTA 994
+ G+R+ R +TLP F P+D +P A GFI F TGL+P E +FH GREGLVDTA
Sbjct: 751 SVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTA 810
Query: 995 VKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGV 1039
V+TS+SGY+QR LI L L+ YD +VR G ++Q YG+DGV
Sbjct: 811 VRTSQSGYMQRRLINALSDLRAEYDGTVRSLYGEVIQVAYGDDGV 855
Score = 50.8 bits (120), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 34/75 (45%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPXXXXXXXXXXKRICFFCHHFKASRREVEKCVRK 60
C TCG CPGHFGHI+LV PV + K C C K S E+EK R
Sbjct: 58 CPTCGNTLGNCPGHFGHIELVRPVIHVGFVKHVYEFLKATCRRCGRVKISEDEIEKYSRI 117
Query: 61 LELIIKGDIIAAKSL 75
I K AA+ L
Sbjct: 118 YNAIKKRWPSAARRL 132
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 880
Score = 201 bits (511), Expect = 2e-51, Method: Compositional matrix adjust.
Identities = 155/450 (34%), Positives = 233/450 (51%), Gaps = 65/450 (14%)
Query: 228 PSGFKKQKDLFSGPLLPSDVKDIIEKLWENEFELCSFISDMQQQGFGKKAGHSIFFLGVV 287
P F +++ L PSD+++ +EK+ +++ E+ + + + L V+
Sbjct: 161 PYNFYEERKEGVAKLTPSDIRERLEKIPDSDVEILGYDPTTSRPEW--------MILTVL 212
Query: 288 LVPPIKFRLPSKGGDSVM--EHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQ 345
VPPI R PS +S + E T L +++ N L + ++ +I W LQ
Sbjct: 213 PVPPITIR-PSIMIESGIRAEDDLTHKLVDIVRINERLKES-IDAGAPQLIIEDLWDLLQ 270
Query: 346 QSVNVLFD--------GKNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISP 397
V FD K+ +G R + + + Q L+ KEG FR L GKRV+++ R+VISP
Sbjct: 271 YHVATYFDNEIPGLPPSKHRSG-RPLRT-LAQRLKGKEGRFRGNLSGKRVDFSSRTVISP 328
Query: 398 DPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLP 457
DP ++++E+G+P A LT PER+TPWN+ KLR +ING + PGA + +
Sbjct: 329 DPNISIDEVGVPEIIAKTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIR-------- 380
Query: 458 PNKKMRISIGRKLDTSRGAIVQPGKDSDNEFE-GKMVYRHLQDGDVVLVNRQPTLHKPSI 516
P+ GR++D V+ K+ + G ++ RHL DGD+VL NRQP+LH+ S+
Sbjct: 381 PD-------GRRIDLR---YVKDRKELASTLAPGYIIERHLIDGDIVLFNRQPSLHRISM 430
Query: 517 MAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRP 576
MAH VRVLKG T R++ C YNADFDGDEMN+H PQ E + AEA I+ + + P
Sbjct: 431 MAHRVRVLKG-LTFRLNLLVCPPYNADFDGDEMNLHVPQSEEAIAEAKEIMLVHKNIITP 489
Query: 577 SNGDPLRSLIQDHIVSAALLTKKDTFLNRDEFCQXXXXXXXXXXXXXXFTGKPGQRVLIS 636
G P+ QD+I A LLT K T L ++E Q ++
Sbjct: 490 RYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQ-----------------------ILG 526
Query: 637 RSEQEVLPLLPAIWKPEPLWTGKQVITAVL 666
++ ++ PAI P +TGKQVI+A L
Sbjct: 527 VADVKIDLGEPAILAPREYYTGKQVISAFL 556
Score = 156 bits (394), Expect = 7e-38, Method: Compositional matrix adjust.
Identities = 98/285 (34%), Positives = 160/285 (56%), Gaps = 26/285 (9%)
Query: 759 LVRGVIDKAQFADY---GLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLL 815
L+ GV DK + ++H + + Y L+ L R+F F+++ GFT ++D+
Sbjct: 593 LLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIRFVELQGFTMRLEDVS 652
Query: 816 ILKDKERERKNHLHGSEEIGKRVHLEAL-ELEDGAEIDPIKLKSEIEKAMRGGGDAAVAY 874
+ D ++E N + + +V ++ L + E++PI ++ +E+++
Sbjct: 653 LGDDVKKEIYNEIDRA-----KVEVDNLIQKYKNGELEPIPGRT-LEESL---------- 696
Query: 875 FDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQ 934
+ + L+K S++ ++ S+ L P N+ +M +GA+GS +N Q+++ LGQQ
Sbjct: 697 -ENYILDTLDKLRSTA--GDIASK-YLDPF--NFAYVMARTGARGSVLNITQMAAMLGQQ 750
Query: 935 ELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTA 994
+ G+R+ R +TLP F P+D +P A GFI F TGL+P E +FH GREGLVDTA
Sbjct: 751 SVRGERIKRGYMTRTLPHFKPYDISPEARGFIYSSFRTGLKPTELFFHAAGGREGLVDTA 810
Query: 995 VKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGV 1039
V+TS+SGY+QR LI L L+ YD +VR G +VQ YG+DGV
Sbjct: 811 VRTSQSGYMQRRLINALSDLRAEYDGTVRSLYGEVVQVAYGDDGV 855
Score = 50.8 bits (120), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 34/75 (45%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPXXXXXXXXXXKRICFFCHHFKASRREVEKCVRK 60
C TCG CPGHFGHI+LV PV + K C C K S E+EK R
Sbjct: 58 CPTCGNTLGNCPGHFGHIELVRPVIHVGLVKHIYEFLKATCRRCGRVKISEDEIEKYSRI 117
Query: 61 LELIIKGDIIAAKSL 75
I K AA+ L
Sbjct: 118 YNAIKKRWPSAARRL 132
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
With The Inhibitor Alpha Amanitin
pdb|1NIK|A Chain A, Wild Type Rna Polymerase Ii
pdb|1NT9|A Chain A, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|A Chain A, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|A Chain A, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|A Chain A, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|A Chain A, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|A Chain A, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|A Chain A, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|A Chain A, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|A Chain A, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|A Chain A, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|A Chain A, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|A Chain A, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|A Chain A, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|A Chain A, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|A Chain A, 12-Subunit Rna Polymerase Ii
pdb|2E2H|A Chain A, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|A Chain A, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|A Chain A, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|M Chain M, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2YU9|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Utp
pdb|2R7Z|A Chain A, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|A Chain A, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|A Chain A, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|A Chain A, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|A Chain A, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
Complex With The Inhibitor Alpha-Amanitin
pdb|3FKI|A Chain A, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|A Chain A, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|A Chain A, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|A Chain A, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|A Chain A, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|A Chain A, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|A Chain A, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|B Chain B, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|A Chain A, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|M Chain M, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|A Chain A, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|A Chain A, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|A Chain A, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|A Chain A, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3K7A|A Chain A, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|A Chain A, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|A Chain A, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|A Chain A, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|A Chain A, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|A Chain A, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|A Chain A, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|A Chain A, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|A Chain A, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|A Chain A, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4BBR|A Chain A, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|A Chain A, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1733
Score = 180 bits (456), Expect = 5e-45, Method: Compositional matrix adjust.
Identities = 131/382 (34%), Positives = 187/382 (48%), Gaps = 56/382 (14%)
Query: 292 IKFRLPSKGGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVL 351
I F +G D + T L+ +L+ANI L N + + A + LQ V
Sbjct: 250 ISFNESQRGEDDL-----TFKLADILKANISLETLEHNGAPHHAIEEAESL-LQFHVATY 303
Query: 352 FDGKNAAGQRDM-------ASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVN 404
D + AGQ I L+ KEG R LMGKRV+++ R+VIS DP L ++
Sbjct: 304 MD-NDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELD 362
Query: 405 EIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRI 464
++G+P A LTYPE VTP+N+ +L + NG HPGA Y+ + S R+ +R
Sbjct: 363 QVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGA-KYVIRDSGDRI----DLRY 417
Query: 465 SIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVL 524
S R +Q G V RH+ D D VL NRQP+LHK S+MAH V+V+
Sbjct: 418 S-------KRAGDIQLQY-------GWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVI 463
Query: 525 KGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRS 584
T R++ + S YNADFDGDEMN+H PQ E +RAE + Q V P + P
Sbjct: 464 P-YSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMG 522
Query: 585 LIQDHIVSAALLTKKDTFLNRDEFCQXXXXXXXXXXXXXXFTGKPGQRVLISRSEQEVLP 644
++QD + LT +DTF+ D+ +L + + +
Sbjct: 523 IVQDTLCGIRKLTLRDTFIELDQVLN----------------------MLYWVPDWDGVI 560
Query: 645 LLPAIWKPEPLWTGKQVITAVL 666
PAI KP+PLW+GKQ+++ +
Sbjct: 561 PTPAIIKPKPLWSGKQILSVAI 582
Score = 152 bits (383), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 94/289 (32%), Positives = 155/289 (53%), Gaps = 23/289 (7%)
Query: 754 IYKNDLVRGVIDKAQF--ADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGV 811
I ++ GV++K ++ GL+H V G L + ++ +L +GF+ G+
Sbjct: 607 IIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGI 666
Query: 812 DDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAA 871
D + RE + E K+V L++ A+ + + K + +R +
Sbjct: 667 GDTIADGPTMREITETI---AEAKKKV----LDVTKEAQANLLTAKHGM--TLRESFEDN 717
Query: 872 VAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHL 931
V F + + + L+E LK N + M +G+KGS +N Q+S+ +
Sbjct: 718 VVRFLNEARDKAGR----------LAEVNLKDL--NNVKQMVMAGSKGSFINIAQMSACV 765
Query: 932 GQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLV 991
GQQ +EGKR+ +TLP F D++P + GF+ + +L GL PQE++FH M GREGL+
Sbjct: 766 GQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLI 825
Query: 992 DTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVD 1040
DTAVKT+ +GY+QR L+K LE + + YD + R++ G+++QF YGEDG+D
Sbjct: 826 DTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMD 874
Score = 87.4 bits (215), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 46/88 (52%), Positives = 62/88 (70%), Gaps = 4/88 (4%)
Query: 1122 MAKQDF---LKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTL 1178
+ KQ F L ++ +F+ S+ PGE VG+LA+QS+GEP+TQMTLNTFH AG VT
Sbjct: 1037 LTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTS 1096
Query: 1179 GIPRLQEILTIASKDIKTPVITCPLLVG 1206
G+PRL+EIL +A K++KTP +T L G
Sbjct: 1097 GVPRLKEILNVA-KNMKTPSLTVYLEPG 1123
Score = 43.9 bits (102), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 23/44 (52%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPXXXXXXXXXXKRICFFC 44
C+TC + CPGHFGHIDL PV++ + +C C
Sbjct: 67 CQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHC 110
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|A Chain A, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|A Chain A, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
Length = 1732
Score = 180 bits (456), Expect = 5e-45, Method: Compositional matrix adjust.
Identities = 131/382 (34%), Positives = 187/382 (48%), Gaps = 56/382 (14%)
Query: 292 IKFRLPSKGGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVL 351
I F +G D + T L+ +L+ANI L N + + A + LQ V
Sbjct: 250 ISFNESQRGEDDL-----TFKLADILKANISLETLEHNGAPHHAIEEAESL-LQFHVATY 303
Query: 352 FDGKNAAGQRDM-------ASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVN 404
D + AGQ I L+ KEG R LMGKRV+++ R+VIS DP L ++
Sbjct: 304 MD-NDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELD 362
Query: 405 EIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRI 464
++G+P A LTYPE VTP+N+ +L + NG HPGA Y+ + S R+ +R
Sbjct: 363 QVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGA-KYVIRDSGDRI----DLRY 417
Query: 465 SIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVL 524
S R +Q G V RH+ D D VL NRQP+LHK S+MAH V+V+
Sbjct: 418 S-------KRAGDIQLQY-------GWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVI 463
Query: 525 KGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRS 584
T R++ + S YNADFDGDEMN+H PQ E +RAE + Q V P + P
Sbjct: 464 P-YSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMG 522
Query: 585 LIQDHIVSAALLTKKDTFLNRDEFCQXXXXXXXXXXXXXXFTGKPGQRVLISRSEQEVLP 644
++QD + LT +DTF+ D+ +L + + +
Sbjct: 523 IVQDTLCGIRKLTLRDTFIELDQVLN----------------------MLYWVPDWDGVI 560
Query: 645 LLPAIWKPEPLWTGKQVITAVL 666
PAI KP+PLW+GKQ+++ +
Sbjct: 561 PTPAIIKPKPLWSGKQILSVAI 582
Score = 152 bits (383), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 94/289 (32%), Positives = 155/289 (53%), Gaps = 23/289 (7%)
Query: 754 IYKNDLVRGVIDKAQF--ADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGV 811
I ++ GV++K ++ GL+H V G L + ++ +L +GF+ G+
Sbjct: 607 IIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGI 666
Query: 812 DDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAA 871
D + RE + E K+V L++ A+ + + K + +R +
Sbjct: 667 GDTIADGPTMREITETI---AEAKKKV----LDVTKEAQANLLTAKHGM--TLRESFEDN 717
Query: 872 VAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHL 931
V F + + + L+E LK N + M +G+KGS +N Q+S+ +
Sbjct: 718 VVRFLNEARDKAGR----------LAEVNLKDL--NNVKQMVMAGSKGSFINIAQMSACV 765
Query: 932 GQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLV 991
GQQ +EGKR+ +TLP F D++P + GF+ + +L GL PQE++FH M GREGL+
Sbjct: 766 GQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLI 825
Query: 992 DTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVD 1040
DTAVKT+ +GY+QR L+K LE + + YD + R++ G+++QF YGEDG+D
Sbjct: 826 DTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMD 874
Score = 87.4 bits (215), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 46/88 (52%), Positives = 62/88 (70%), Gaps = 4/88 (4%)
Query: 1122 MAKQDF---LKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTL 1178
+ KQ F L ++ +F+ S+ PGE VG+LA+QS+GEP+TQMTLNTFH AG VT
Sbjct: 1037 LTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTS 1096
Query: 1179 GIPRLQEILTIASKDIKTPVITCPLLVG 1206
G+PRL+EIL +A K++KTP +T L G
Sbjct: 1097 GVPRLKEILNVA-KNMKTPSLTVYLEPG 1123
Score = 43.9 bits (102), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 23/44 (52%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPXXXXXXXXXXKRICFFC 44
C+TC + CPGHFGHIDL PV++ + +C C
Sbjct: 67 CQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHC 110
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 179 bits (453), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 131/382 (34%), Positives = 187/382 (48%), Gaps = 56/382 (14%)
Query: 292 IKFRLPSKGGDSVMEHPQTVLLSKVLQANIYLANAYVNQPDNAKVIVARWMNLQQSVNVL 351
I F +G D + T L+ +L+ANI L N + + A + LQ V
Sbjct: 250 ISFNESQRGEDDL-----TFKLADILKANISLETLEHNGAPHHAIEEAESL-LQFHVATY 303
Query: 352 FDGKNAAGQRDM-------ASGICQLLEKKEGLFRQKLMGKRVNYACRSVISPDPYLAVN 404
D + AGQ I L+ KEG R LMGKRV+++ R+VIS DP L ++
Sbjct: 304 MDN-DIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELD 362
Query: 405 EIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLPPNKKMRI 464
++G+P A LTYPE VTP+N+ +L + NG HPGA Y+ + S R+ +R
Sbjct: 363 QVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGA-KYVIRDSGDRI----DLRY 417
Query: 465 SIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVL 524
S R +Q G V RH+ D D VL NRQP+LHK S+MAH V+V+
Sbjct: 418 S-------KRAGDIQLQY-------GWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVI 463
Query: 525 KGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPSNGDPLRS 584
T R++ + S YNADFDGDEMN+H PQ E +RAE + Q V P + P
Sbjct: 464 P-YSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMG 522
Query: 585 LIQDHIVSAALLTKKDTFLNRDEFCQXXXXXXXXXXXXXXFTGKPGQRVLISRSEQEVLP 644
++QD + LT +DTF+ D+ +L + + +
Sbjct: 523 IVQDTLCGIRKLTLRDTFIELDQVLN----------------------MLYWVPDWDGVI 560
Query: 645 LLPAIWKPEPLWTGKQVITAVL 666
PAI KP+PLW+GKQ+++ +
Sbjct: 561 PTPAIIKPKPLWSGKQILSVAI 582
Score = 152 bits (383), Expect = 1e-36, Method: Compositional matrix adjust.
Identities = 94/289 (32%), Positives = 155/289 (53%), Gaps = 23/289 (7%)
Query: 754 IYKNDLVRGVIDKAQF--ADYGLVHTVQELYGSNTAGTLLSALSRLFTVFLQMHGFTCGV 811
I ++ GV++K ++ GL+H V G L + ++ +L +GF+ G+
Sbjct: 607 IIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGI 666
Query: 812 DDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMRGGGDAA 871
D + RE + E K+V L++ A+ + + K + +R +
Sbjct: 667 GDTIADGPTMREITETI---AEAKKKV----LDVTKEAQANLLTAKHGM--TLRESFEDN 717
Query: 872 VAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGKNWISLMTTSGAKGSKVNFQQISSHL 931
V F + + + L+E LK N + M +G+KGS +N Q+S+ +
Sbjct: 718 VVRFLNEARDKAGR----------LAEVNLKDL--NNVKQMVMAGSKGSFINIAQMSACV 765
Query: 932 GQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIIDRFLTGLRPQEYYFHCMAGREGLV 991
GQQ +EGKR+ +TLP F D++P + GF+ + +L GL PQE++FH M GREGL+
Sbjct: 766 GQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLI 825
Query: 992 DTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFCYGEDGVD 1040
DTAVKT+ +GY+QR L+K LE + + YD + R++ G+++QF YGEDG+D
Sbjct: 826 DTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMD 874
Score = 87.4 bits (215), Expect = 5e-17, Method: Compositional matrix adjust.
Identities = 45/85 (52%), Positives = 61/85 (71%), Gaps = 4/85 (4%)
Query: 1122 MAKQDF---LKLVKHKFVLSLAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTL 1178
+ KQ F L ++ +F+ S+ PGE VG+LA+QS+GEP+TQMTLNTFH AG VT
Sbjct: 1037 LTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTS 1096
Query: 1179 GIPRLQEILTIASKDIKTPVITCPL 1203
G+PRL+EIL +A K++KTP +T L
Sbjct: 1097 GVPRLKEILNVA-KNMKTPSLTVYL 1120
Score = 43.9 bits (102), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 23/44 (52%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPXXXXXXXXXXKRICFFC 44
C+TC + CPGHFGHIDL PV++ + +C C
Sbjct: 67 CQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHC 110
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 103 bits (258), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 79/261 (30%), Positives = 128/261 (49%), Gaps = 50/261 (19%)
Query: 344 LQQSVNVLFD----GKNAAG--QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISP 397
LQ++V+ L D G+ G +R + S + +++ K+G FRQ L+GKRV+Y+ RSVI+
Sbjct: 299 LQEAVDALLDNGRRGRAITGSNKRPLKS-LADMIKGKQGRFRQNLLGKRVDYSGRSVITV 357
Query: 398 DPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLP 457
PYL +++ G+P AL L P I E+ AT
Sbjct: 358 GPYLRLHQCGLPKKMALELFKP-------------FIYGKLELRGLATT----------- 393
Query: 458 PNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIM 517
I +K+ A+V D +++ H VL+NR PTLH+ I
Sbjct: 394 ------IKAAKKMVEREEAVVWDILD-------EVIREH-----PVLLNRAPTLHRLGIQ 435
Query: 518 AHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPS 577
A +++G K +++H C+ YNADFDGD+M VH P ++ EA ++ + N + P+
Sbjct: 436 AFEPVLIEG-KAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPA 494
Query: 578 NGDPLRSLIQDHIVSAALLTK 598
NG+P+ QD ++ +T+
Sbjct: 495 NGEPIIVPSQDVVLGLYYMTR 515
Score = 67.0 bits (162), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 83/382 (21%), Positives = 147/382 (38%), Gaps = 95/382 (24%)
Query: 806 GFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMR 865
G + G+DD++I + K E+ AE + +++ + + +
Sbjct: 636 GASVGIDDMVIPEKKH----------------------EIISEAEAEVAEIQEQFQSGLV 673
Query: 866 GGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGK-------NWISLMTTSGAK 918
G+ D+ + N S ++++ L +E ++ G+ N I +M SGA+
Sbjct: 674 TAGERYNKVIDIWAAA--NDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGAR 731
Query: 919 GSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIID-----RFLTG 973
GS +Q++ G + G II+ F G
Sbjct: 732 GSAAQIRQLAGMRG-------------------------LMAKPDGSIIETPITANFREG 766
Query: 974 LRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFC 1033
L +Y+ R+GL DTA+KT+ SGYL R L+ + L ++ D +
Sbjct: 767 LNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVI 826
Query: 1034 YGEDGVDVHQTSFISKFDALAAXXXXXXXXXNKFCDKGSHTFVMGRNQEMIYKKCSGQLD 1093
G D + + + + A G+ ++ RN + + C
Sbjct: 827 EGGDVKEPLRDRVLGRVTA------------EDVLKPGTADILVPRNTLLHEQWC----- 869
Query: 1094 ASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQ-----PGEPVGL 1148
D L++N+ A K S DF + H + LA+ GE +G+
Sbjct: 870 ----------DLLEENSVD-AVKVRSVVSCDTDF-GVCAHCYGRDLARGHIINKGEAIGV 917
Query: 1149 LASQSVGEPSTQMTLNTFHLAG 1170
+A+QS+GEP TQ+T+ TFH+ G
Sbjct: 918 IAAQSIGEPGTQLTMRTFHIGG 939
>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|D Chain D, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|I Chain I, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1407
Score = 103 bits (258), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 79/261 (30%), Positives = 128/261 (49%), Gaps = 50/261 (19%)
Query: 344 LQQSVNVLFD----GKNAAG--QRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVISP 397
LQ++V+ L D G+ G +R + S + +++ K+G FRQ L+GKRV+Y+ RSVI+
Sbjct: 299 LQEAVDALLDNGRRGRAITGSNKRPLKS-LADMIKGKQGRFRQNLLGKRVDYSGRSVITV 357
Query: 398 DPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRLP 457
PYL +++ G+P AL L P I E+ AT
Sbjct: 358 GPYLRLHQCGLPKKMALELFKP-------------FIYGKLELRGLATT----------- 393
Query: 458 PNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQDGDVVLVNRQPTLHKPSIM 517
I +K+ A+V D +++ H VL+NR PTLH+ I
Sbjct: 394 ------IKAAKKMVEREEAVVWDILD-------EVIREH-----PVLLNRAPTLHRLGIQ 435
Query: 518 AHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQYVRPS 577
A +++G K +++H C+ YNADFDGD+M VH P ++ EA ++ + N + P+
Sbjct: 436 AFEPVLIEG-KAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPA 494
Query: 578 NGDPLRSLIQDHIVSAALLTK 598
NG+P+ QD ++ +T+
Sbjct: 495 NGEPIIVPSQDVVLGLYYMTR 515
Score = 67.0 bits (162), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 83/382 (21%), Positives = 147/382 (38%), Gaps = 95/382 (24%)
Query: 806 GFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEALELEDGAEIDPIKLKSEIEKAMR 865
G + G+DD++I + K E+ AE + +++ + + +
Sbjct: 636 GASVGIDDMVIPEKKH----------------------EIISEAEAEVAEIQEQFQSGLV 673
Query: 866 GGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLKPTGK-------NWISLMTTSGAK 918
G+ D+ + N S ++++ L +E ++ G+ N I +M SGA+
Sbjct: 674 TAGERYNKVIDIWAAA--NDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGAR 731
Query: 919 GSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAPRAGGFIID-----RFLTG 973
GS +Q++ G + G II+ F G
Sbjct: 732 GSAAQIRQLAGMRG-------------------------LMAKPDGSIIETPITANFREG 766
Query: 974 LRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDYSVRDADGSIVQFC 1033
L +Y+ R+GL DTA+KT+ SGYL R L+ + L ++ D +
Sbjct: 767 LNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVI 826
Query: 1034 YGEDGVDVHQTSFISKFDALAAXXXXXXXXXNKFCDKGSHTFVMGRNQEMIYKKCSGQLD 1093
G D + + + + A G+ ++ RN + + C
Sbjct: 827 EGGDVKEPLRDRVLGRVTA------------EDVLKPGTADILVPRNTLLHEQWC----- 869
Query: 1094 ASNAYIMELPDALKDNAEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQ-----PGEPVGL 1148
D L++N+ A K S DF + H + LA+ GE +G+
Sbjct: 870 ----------DLLEENSVD-AVKVRSVVSCDTDF-GVCAHCYGRDLARGHIINKGEAIGV 917
Query: 1149 LASQSVGEPSTQMTLNTFHLAG 1170
+A+QS+GEP TQ+T+ TFH+ G
Sbjct: 918 IAAQSIGEPGTQLTMRTFHIGG 939
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1534
Score = 102 bits (253), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 80/265 (30%), Positives = 127/265 (47%), Gaps = 54/265 (20%)
Query: 344 LQQSVNVLFDG-------KNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVIS 396
LQ++V+ L D N R + S + +L K+G FRQ L+GKRV+Y+ RSVI
Sbjct: 574 LQEAVDALLDNGRRGAPVTNPGSDRPLRS-LTDILSGKQGRFRQNLLGKRVDYSGRSVIV 632
Query: 397 PDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRL 456
P L +++ G+P AL L P L K+ +
Sbjct: 633 VGPQLKLHQCGLPKRMALELFKP--------------------------FLLKKMEEKGI 666
Query: 457 PPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQD---GDVVLVNRQPTLHK 513
PN K + R L+ R D +E V+ L++ G VVL+NR PTLH+
Sbjct: 667 APNVK---AARRMLERQR--------DIKDE-----VWDALEEVIHGKVVLLNRAPTLHR 710
Query: 514 PSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQY 573
I A +++G+ ++++H C +NADFDGD+M VH P ++AEA + + +
Sbjct: 711 LGIQAFQPVLVEGQ-SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNL 769
Query: 574 VRPSNGDPLRSLIQDHIVSAALLTK 598
+ P++G+PL +D I+ +T+
Sbjct: 770 LSPASGEPLAKPSRDIILGLYYITQ 794
Score = 77.4 bits (189), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 102/417 (24%), Positives = 176/417 (42%), Gaps = 88/417 (21%)
Query: 783 GSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEA 842
G LL AL F G T G+DD +I E+K +L EE +++
Sbjct: 923 GMEKTARLLDALKYYGFTFSTTSGITIGIDDAVI----PEEKKQYL---EEADRKL---- 971
Query: 843 LELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLK 902
L++E E+ + + ++ + QL T+ V ++ + K
Sbjct: 972 LQIEQAYEMGFLTDRERYDQIL-----------------QLWTETTEKV-----TQAVFK 1009
Query: 903 PTGKNW----ISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDW 958
+N+ + +M SGA+G N QQI G + L K PS ++
Sbjct: 1010 NFEENYPFNPLYVMAQSGARG---NPQQIRQLCGLRGLMQK-----------PSGETFEV 1055
Query: 959 APRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISY 1018
R+ F GL EY+ R+G DTA++T+ SGYL R L+ +++
Sbjct: 1056 PVRSS------FREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVD------VTH 1103
Query: 1019 DYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAAXXXXXXXXXNKFCDKGSHTFVMG 1078
+ VR+AD + V + Q +++ L + G + V+
Sbjct: 1104 EIVVREADCGTTNYI----SVPLFQPDEVTRSLRLRKRAD---------IEAGLYGRVLA 1150
Query: 1079 RNQEMIYKKCSGQLDASNAYIMELPDALKDNAE--KFADKFLSNEMAKQDFLKLVK--HK 1134
R E++ +L+ M+ L AE + + + + + Q + + +
Sbjct: 1151 REVEVL----GVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYG 1206
Query: 1135 FVLSLAQP---GEPVGLLASQSVGEPSTQMTLNTFHLAG-RGEMNVTLGIPRLQEIL 1187
+ LS+A+P GE VG++A+QS+GEP TQ+T+ TFH G G ++T G+PR+ E+
Sbjct: 1207 YDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELF 1263
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|D Chain D, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|N Chain N, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|D Chain D, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|N Chain N, Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Streptolydigin
pdb|2A68|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 1524
Score = 102 bits (253), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 80/265 (30%), Positives = 127/265 (47%), Gaps = 54/265 (20%)
Query: 344 LQQSVNVLFDG-------KNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVIS 396
LQ++V+ L D N R + S + +L K+G FRQ L+GKRV+Y+ RSVI
Sbjct: 574 LQEAVDALLDNGRRGAPVTNPGSDRPLRS-LTDILSGKQGRFRQNLLGKRVDYSGRSVIV 632
Query: 397 PDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRL 456
P L +++ G+P AL L P L K+ +
Sbjct: 633 VGPQLKLHQCGLPKRMALELFKP--------------------------FLLKKMEEKGI 666
Query: 457 PPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQD---GDVVLVNRQPTLHK 513
PN K + R L+ R D +E V+ L++ G VVL+NR PTLH+
Sbjct: 667 APNVK---AARRMLERQR--------DIKDE-----VWDALEEVIHGKVVLLNRAPTLHR 710
Query: 514 PSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQY 573
I A +++G+ ++++H C +NADFDGD+M VH P ++AEA + + +
Sbjct: 711 LGIQAFQPVLVEGQ-SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNL 769
Query: 574 VRPSNGDPLRSLIQDHIVSAALLTK 598
+ P++G+PL +D I+ +T+
Sbjct: 770 LSPASGEPLAKPSRDIILGLYYITQ 794
Score = 77.4 bits (189), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 102/417 (24%), Positives = 176/417 (42%), Gaps = 88/417 (21%)
Query: 783 GSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEA 842
G LL AL F G T G+DD +I E+K +L EE +++
Sbjct: 923 GMEKTARLLDALKYYGFTFSTTSGITIGIDDAVI----PEEKKQYL---EEADRKL---- 971
Query: 843 LELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLK 902
L++E E+ + + ++ + QL T+ V ++ + K
Sbjct: 972 LQIEQAYEMGFLTDRERYDQIL-----------------QLWTETTEKV-----TQAVFK 1009
Query: 903 PTGKNW----ISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDW 958
+N+ + +M SGA+G N QQI G + L K PS ++
Sbjct: 1010 NFEENYPFNPLYVMAQSGARG---NPQQIRQLCGLRGLMQK-----------PSGETFEV 1055
Query: 959 APRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISY 1018
R+ F GL EY+ R+G DTA++T+ SGYL R L+ +++
Sbjct: 1056 PVRSS------FREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVD------VTH 1103
Query: 1019 DYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAAXXXXXXXXXNKFCDKGSHTFVMG 1078
+ VR+AD + V + Q +++ L + G + V+
Sbjct: 1104 EIVVREADCGTTNYI----SVPLFQPDEVTRSLRLRKRAD---------IEAGLYGRVLA 1150
Query: 1079 RNQEMIYKKCSGQLDASNAYIMELPDALKDNAE--KFADKFLSNEMAKQDFLKLVK--HK 1134
R E++ +L+ M+ L AE + + + + + Q + + +
Sbjct: 1151 REVEVL----GVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYG 1206
Query: 1135 FVLSLAQP---GEPVGLLASQSVGEPSTQMTLNTFHLAG-RGEMNVTLGIPRLQEIL 1187
+ LS+A+P GE VG++A+QS+GEP TQ+T+ TFH G G ++T G+PR+ E+
Sbjct: 1207 YDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELF 1263
>pdb|1HQM|D Chain D, 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 = 1265
Score = 101 bits (252), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 79/265 (29%), Positives = 127/265 (47%), Gaps = 54/265 (20%)
Query: 344 LQQSVNVLFDG-------KNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVIS 396
LQ++V+ + D N +R + S + +L K+G FRQ L+GKRV+Y+ RSVI
Sbjct: 314 LQEAVDAVIDNGRRGSPVTNPGSERPLRS-LTDILSGKQGRFRQNLLGKRVDYSGRSVIV 372
Query: 397 PDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRL 456
P L +++ G+P AL L P L K+
Sbjct: 373 VGPQLKLHQCGLPKRMALELFKP--------------------------FLLKKMEEKAF 406
Query: 457 PPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQD---GDVVLVNRQPTLHK 513
PN K + R L+ R D +E V+ L++ G VVL+NR PTLH+
Sbjct: 407 APNVK---AARRMLERQR--------DIKDE-----VWDALEEVIHGKVVLLNRAPTLHR 450
Query: 514 PSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQY 573
I A +++G+ ++++H C +NADFDGD+M VH P ++AEA + + +
Sbjct: 451 LGIQAFQPVLVEGQ-SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNL 509
Query: 574 VRPSNGDPLRSLIQDHIVSAALLTK 598
+ P++G+PL +D I+ +T+
Sbjct: 510 LSPASGEPLAKPSRDIILGLYYITQ 534
Score = 71.2 bits (173), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 102/416 (24%), Positives = 176/416 (42%), Gaps = 85/416 (20%)
Query: 783 GSNTAGTLLSALSRL-FTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLE 841
G LL AL FT+ T G+DD +I ++K+R +LE
Sbjct: 663 GMEKTARLLDALKYYGFTLSTTSGIITIGIDDAVIPEEKQR----------------YLE 706
Query: 842 ALELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFD--MKMTSQLNKHTSSSVINELLSEG 899
E D KL+ +IE+A G +D +++ ++ + + +V N
Sbjct: 707 --------EADR-KLR-QIEQAYEMGFLTDRERYDQVIQLWTETTEKVTQAVFNNFEENY 756
Query: 900 LLKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWA 959
P + +M SGA+G N QQI G + L K PS ++
Sbjct: 757 PFNP-----LYVMAQSGARG---NPQQIRQLCGMRGLMQK-----------PSGETFEVP 797
Query: 960 PRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYD 1019
R+ F GL EY+ R+G DTA++T+ SGYL R L+ ++++
Sbjct: 798 VRSS------FREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVD------VAHE 845
Query: 1020 YSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAAXXXXXXXXXNKFCDKGSHTFVMGR 1079
VR+AD ++ V + Q +++ L + G + V+ R
Sbjct: 846 IVVREADCGTTKYI----SVPLFQMDEVTRTLRLRKRSD---------IESGLYGRVLAR 892
Query: 1080 NQEMIYKKCSGQLDASNAYIMELPDALKDNAE--KFADKFLSNEMAKQDFLKLVK--HKF 1135
E + ++ L+ +E L AE + + + + + Q + + + +
Sbjct: 893 EVEALGRR----LEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGY 948
Query: 1136 VLSLAQP---GEPVGLLASQSVGEPSTQMTLNTFHLAGRG-EMNVTLGIPRLQEIL 1187
LS+A+P GE VG++A++S+GEP TQ+T+ TFH G ++T G+PR+ E+
Sbjct: 949 DLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF 1004
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 101 bits (252), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 79/265 (29%), Positives = 127/265 (47%), Gaps = 54/265 (20%)
Query: 344 LQQSVNVLFDG-------KNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVIS 396
LQ++V+ + D N +R + S + +L K+G FRQ L+GKRV+Y+ RSVI
Sbjct: 283 LQEAVDAVIDNGRRGSPVTNPGSERPLRS-LTDILSGKQGRFRQNLLGKRVDYSGRSVIV 341
Query: 397 PDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRL 456
P L +++ G+P AL L P L K+
Sbjct: 342 VGPQLKLHQCGLPKRMALELFKP--------------------------FLLKKMEEKAF 375
Query: 457 PPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQD---GDVVLVNRQPTLHK 513
PN K + R L+ R D +E V+ L++ G VVL+NR PTLH+
Sbjct: 376 APNVK---AARRMLERQR--------DIKDE-----VWDALEEVIHGKVVLLNRAPTLHR 419
Query: 514 PSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQY 573
I A +++G+ ++++H C +NADFDGD+M VH P ++AEA + + +
Sbjct: 420 LGIQAFQPVLVEGQ-SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNL 478
Query: 574 VRPSNGDPLRSLIQDHIVSAALLTK 598
+ P++G+PL +D I+ +T+
Sbjct: 479 LSPASGEPLAKPSRDIILGLYYITQ 503
Score = 72.4 bits (176), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 104/417 (24%), Positives = 175/417 (41%), Gaps = 88/417 (21%)
Query: 783 GSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEA 842
G LL AL G T G+DD +I ++K+R +LE
Sbjct: 632 GMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQR----------------YLE- 674
Query: 843 LELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLK 902
E D KL+ +IE+A G +D + QL T+ V ++ + K
Sbjct: 675 -------EADR-KLR-QIEQAYEMGFLTDRERYDQVI--QLWTETTEKV-----TQAVFK 718
Query: 903 PTGKNW----ISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDW 958
+N+ + +M SGA+G N QQI G + L K PS ++
Sbjct: 719 NFEENYPFNPLYVMAQSGARG---NPQQIRQLCGMRGLMQK-----------PSGETFEV 764
Query: 959 APRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISY 1018
R+ F GL EY+ R+G DTA++T+ SGYL R L+ +++
Sbjct: 765 PVRSS------FREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVD------VAH 812
Query: 1019 DYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAAXXXXXXXXXNKFCDKGSHTFVMG 1078
+ VR+AD + V + Q +++ L + G + V+
Sbjct: 813 EIVVREADCGTTNYI----SVPLFQMDEVTRTLRLRKRSD---------IESGLYGRVLA 859
Query: 1079 RNQEMIYKKCSGQLDASNAYIMELPDALKDNAE--KFADKFLSNEMAKQDFLKLVK--HK 1134
R E + ++ L+ +E L AE + + + + + Q + + +
Sbjct: 860 REVEALGRR----LEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYG 915
Query: 1135 FVLSLAQP---GEPVGLLASQSVGEPSTQMTLNTFHLAGRG-EMNVTLGIPRLQEIL 1187
+ LS+A+P GE VG++A++S+GEP TQ+T+ TFH G ++T G+PR+ E+
Sbjct: 916 YDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF 972
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 101 bits (251), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 79/265 (29%), Positives = 127/265 (47%), Gaps = 54/265 (20%)
Query: 344 LQQSVNVLFDG-------KNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVIS 396
LQ++V+ + D N +R + S + +L K+G FRQ L+GKRV+Y+ RSVI
Sbjct: 314 LQEAVDAVIDNGRRGSPVTNPGSERPLRS-LTDILSGKQGRFRQNLLGKRVDYSGRSVIV 372
Query: 397 PDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRL 456
P L +++ G+P AL L P L K+
Sbjct: 373 VGPQLKLHQCGLPKRMALELFKP--------------------------FLLKKMEEKAF 406
Query: 457 PPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQD---GDVVLVNRQPTLHK 513
PN K + R L+ R D +E V+ L++ G VVL+NR PTLH+
Sbjct: 407 APNVK---AARRMLERQR--------DIKDE-----VWDALEEVIHGKVVLLNRAPTLHR 450
Query: 514 PSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQY 573
I A +++G+ ++++H C +NADFDGD+M VH P ++AEA + + +
Sbjct: 451 LGIQAFQPVLVEGQ-SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNL 509
Query: 574 VRPSNGDPLRSLIQDHIVSAALLTK 598
+ P++G+PL +D I+ +T+
Sbjct: 510 LSPASGEPLAKPSRDIILGLYYITQ 534
Score = 73.6 bits (179), Expect = 7e-13, Method: Compositional matrix adjust.
Identities = 101/415 (24%), Positives = 173/415 (41%), Gaps = 84/415 (20%)
Query: 783 GSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEA 842
G LL AL G T G+DD +I ++K+R +LE
Sbjct: 663 GMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQR----------------YLE- 705
Query: 843 LELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFD--MKMTSQLNKHTSSSVINELLSEGL 900
E D KL+ +IE+A G +D +++ ++ + + +V N
Sbjct: 706 -------EADR-KLR-QIEQAYEMGFLTDRERYDQVIQLWTETTEKVTQAVFNNFEENYP 756
Query: 901 LKPTGKNWISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDWAP 960
P + +M SGA+G N QQI G + L K PS ++
Sbjct: 757 FNP-----LYVMAQSGARG---NPQQIRQLCGMRGLMQK-----------PSGETFEVPV 797
Query: 961 RAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISYDY 1020
R+ F GL EY+ R+G DTA++T+ SGYL R L+ ++++
Sbjct: 798 RSS------FREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVD------VAHEI 845
Query: 1021 SVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAAXXXXXXXXXNKFCDKGSHTFVMGRN 1080
VR+AD + V + Q +++ L + G + V+ R
Sbjct: 846 VVREADCGTTNYI----SVPLFQMDEVTRTLRL---------RKRSDIESGLYGRVLARE 892
Query: 1081 QEMIYKKCSGQLDASNAYIMELPDALKDNAE--KFADKFLSNEMAKQDFLKLVK--HKFV 1136
E + ++ L+ +E L AE + + + + + Q + + + +
Sbjct: 893 VEALGRR----LEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYGYD 948
Query: 1137 LSLAQP---GEPVGLLASQSVGEPSTQMTLNTFHLAGRGE-MNVTLGIPRLQEIL 1187
LS+A+P GE VG++A++S+GEP TQ+T+ TFH G ++T G+PR+ E+
Sbjct: 949 LSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF 1003
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1YNJ|D Chain D, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNJ|J Chain J, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|D Chain D, Taq Rna Polymerase-rifampicin Complex
pdb|1YNN|J Chain J, Taq Rna Polymerase-rifampicin Complex
Length = 1524
Score = 101 bits (251), Expect = 3e-21, Method: Compositional matrix adjust.
Identities = 79/265 (29%), Positives = 127/265 (47%), Gaps = 54/265 (20%)
Query: 344 LQQSVNVLFDG-------KNAAGQRDMASGICQLLEKKEGLFRQKLMGKRVNYACRSVIS 396
LQ++V+ + D N +R + S + +L K+G FRQ L+GKRV+Y+ RSVI
Sbjct: 574 LQEAVDAVIDNGRRGSPVTNPGSERPLRS-LTDILSGKQGRFRQNLLGKRVDYSGRSVIV 632
Query: 397 PDPYLAVNEIGIPPYFALRLTYPERVTPWNVVKLRDSIINGAEIHPGATHYLDKLSTMRL 456
P L +++ G+P AL L P L K+
Sbjct: 633 VGPQLKLHQCGLPKRMALELFKP--------------------------FLLKKMEEKAF 666
Query: 457 PPNKKMRISIGRKLDTSRGAIVQPGKDSDNEFEGKMVYRHLQD---GDVVLVNRQPTLHK 513
PN K + R L+ R D +E V+ L++ G VVL+NR PTLH+
Sbjct: 667 APNVK---AARRMLERQR--------DIKDE-----VWDALEEVIHGKVVLLNRAPTLHR 710
Query: 514 PSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNVHFPQDEVSRAEAYNIVNANNQY 573
I A +++G+ ++++H C +NADFDGD+M VH P ++AEA + + +
Sbjct: 711 LGIQAFQPVLVEGQ-SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNL 769
Query: 574 VRPSNGDPLRSLIQDHIVSAALLTK 598
+ P++G+PL +D I+ +T+
Sbjct: 770 LSPASGEPLAKPSRDIILGLYYITQ 794
Score = 72.4 bits (176), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 104/417 (24%), Positives = 175/417 (41%), Gaps = 88/417 (21%)
Query: 783 GSNTAGTLLSALSRLFTVFLQMHGFTCGVDDLLILKDKERERKNHLHGSEEIGKRVHLEA 842
G LL AL G T G+DD +I ++K+R +LE
Sbjct: 923 GMEKTARLLDALKYYGFTLSTTSGITIGIDDAVIPEEKQR----------------YLE- 965
Query: 843 LELEDGAEIDPIKLKSEIEKAMRGGGDAAVAYFDMKMTSQLNKHTSSSVINELLSEGLLK 902
E D KL+ +IE+A G +D + QL T+ V ++ + K
Sbjct: 966 -------EADR-KLR-QIEQAYEMGFLTDRERYDQVI--QLWTETTEKV-----TQAVFK 1009
Query: 903 PTGKNW----ISLMTTSGAKGSKVNFQQISSHLGQQELEGKRVPRMVSGKTLPSFHPWDW 958
+N+ + +M SGA+G N QQI G + L K PS ++
Sbjct: 1010 NFEENYPFNPLYVMAQSGARG---NPQQIRQLCGMRGLMQK-----------PSGETFEV 1055
Query: 959 APRAGGFIIDRFLTGLRPQEYYFHCMAGREGLVDTAVKTSRSGYLQRCLIKNLECLKISY 1018
R+ F GL EY+ R+G DTA++T+ SGYL R L+ +++
Sbjct: 1056 PVRSS------FREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVD------VAH 1103
Query: 1019 DYSVRDADGSIVQFCYGEDGVDVHQTSFISKFDALAAXXXXXXXXXNKFCDKGSHTFVMG 1078
+ VR+AD + V + Q +++ L + G + V+
Sbjct: 1104 EIVVREADCGTTNYI----SVPLFQMDEVTRTLRL---------RKRSDIESGLYGRVLA 1150
Query: 1079 RNQEMIYKKCSGQLDASNAYIMELPDALKDNAE--KFADKFLSNEMAKQDFLKLVK--HK 1134
R E + ++ L+ +E L AE + + + + + Q + + +
Sbjct: 1151 REVEALGRR----LEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVCQKCYG 1206
Query: 1135 FVLSLAQP---GEPVGLLASQSVGEPSTQMTLNTFHLAGRG-EMNVTLGIPRLQEIL 1187
+ LS+A+P GE VG++A++S+GEP TQ+T+ TFH G ++T G+PR+ E+
Sbjct: 1207 YDLSMARPVSIGEAVGVVAAESIGEPGTQLTMRTFHTGGVAVGTDITQGLPRVIELF 1263
>pdb|3HKZ|C Chain C, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|M Chain M, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 395
Score = 77.4 bits (189), Expect = 4e-14, Method: Composition-based stats.
Identities = 49/110 (44%), Positives = 66/110 (60%), Gaps = 9/110 (8%)
Query: 1094 ASNAYIMELPDALKD---NAEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLA 1150
ASN ++ D LK+ N E + +E+ K L ++ L PGE +G++A
Sbjct: 20 ASNILPQKIVDDLKNLILNKEIIVTR---DEIDK--IFDLAIKEYSEGLIAPGEAIGIVA 74
Query: 1151 SQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVIT 1200
+QSVGEP TQMTL TFH AG E+NVTLG+PRL EI+ A K TP++T
Sbjct: 75 AQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVD-AKKVPSTPMMT 123
>pdb|2PMZ|C Chain C, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|G Chain G, Archaeal Rna Polymerase From Sulfolobus Solfataricus
Length = 392
Score = 77.4 bits (189), Expect = 4e-14, Method: Composition-based stats.
Identities = 49/110 (44%), Positives = 66/110 (60%), Gaps = 9/110 (8%)
Query: 1094 ASNAYIMELPDALKD---NAEKFADKFLSNEMAKQDFLKLVKHKFVLSLAQPGEPVGLLA 1150
ASN ++ D LK+ N E + +E+ K L ++ L PGE +G++A
Sbjct: 17 ASNILPQKIVDDLKNLILNKEIIVTR---DEIDK--IFDLAIKEYSEGLIAPGEAIGIVA 71
Query: 1151 SQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPVIT 1200
+QSVGEP TQMTL TFH AG E+NVTLG+PRL EI+ A K TP++T
Sbjct: 72 AQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVD-AKKVPSTPMMT 120
>pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|Y Chain Y, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 395
Score = 77.4 bits (189), Expect = 5e-14, Method: Composition-based stats.
Identities = 38/62 (61%), Positives = 47/62 (75%), Gaps = 1/62 (1%)
Query: 1139 LAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPV 1198
L PGE +G++A+QSVGEP TQMTL TFH AG E+NVTLG+PRL EI+ A K TP+
Sbjct: 63 LIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVD-AKKVPSTPM 121
Query: 1199 IT 1200
+T
Sbjct: 122 MT 123
>pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|Y Chain Y, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|C Chain C, Rnap At 3.2ang
pdb|4B1O|C Chain C, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|Y Chain Y, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 395
Score = 77.4 bits (189), Expect = 5e-14, Method: Composition-based stats.
Identities = 38/62 (61%), Positives = 47/62 (75%), Gaps = 1/62 (1%)
Query: 1139 LAQPGEPVGLLASQSVGEPSTQMTLNTFHLAGRGEMNVTLGIPRLQEILTIASKDIKTPV 1198
L PGE +G++A+QSVGEP TQMTL TFH AG E+NVTLG+PRL EI+ A K TP+
Sbjct: 63 LIAPGEAIGIVAAQSVGEPGTQMTLRTFHFAGIRELNVTLGLPRLIEIVD-AKKVPSTPM 121
Query: 1199 IT 1200
+T
Sbjct: 122 MT 123
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 436
Score = 52.4 bits (124), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 34/63 (53%)
Query: 1 CKTCGQRQFLCPGHFGHIDLVVPVYNPXXXXXXXXXXKRICFFCHHFKASRREVEKCVRK 60
C+TCG R CPGHFGHI+L PV + + C C K + E+E+ ++K
Sbjct: 121 CETCGGRAGECPGHFGHIELARPVIHVGFAKTIYRILESTCRECGRIKLTDEEIEEYMKK 180
Query: 61 LEL 63
+EL
Sbjct: 181 IEL 183
>pdb|3H8U|A Chain A, Crystal Structure Of Uncharacterized Conserved Protein
With Double- Stranded Beta-Helix Domain (Yp_001338853.1)
From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578
At 1.80 A Resolution
pdb|3H8U|B Chain B, Crystal Structure Of Uncharacterized Conserved Protein
With Double- Stranded Beta-Helix Domain (Yp_001338853.1)
From Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578
At 1.80 A Resolution
Length = 125
Score = 34.7 bits (78), Expect = 0.35, Method: Composition-based stats.
Identities = 13/27 (48%), Positives = 22/27 (81%)
Query: 560 RAEAYNIVNANNQYVRPSNGDPLRSLI 586
RAE + + + ++YVRPSNG+P+RS++
Sbjct: 7 RAETESRIFSVDEYVRPSNGEPIRSVV 33
>pdb|3K2Z|A Chain A, Crystal Structure Of A Lexa Protein From Thermotoga
Maritima
pdb|3K2Z|B Chain B, Crystal Structure Of A Lexa Protein From Thermotoga
Maritima
Length = 196
Score = 32.3 bits (72), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 492 MVYRHLQDGDVVLVNRQPTLHKPSIMAHVVRVLKGEKTLRMHYANCSTYNADFDGDEMNV 551
M+ H+ DGD+VLV RQ I+A +V GE TL Y T EM+
Sbjct: 119 MIEEHICDGDLVLVRRQDWAQNGDIVAAMV---DGEVTLAKFYQRGDTVELRPANREMSS 175
Query: 552 HFPQDE 557
F + E
Sbjct: 176 MFFRAE 181
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
0.319 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: 34,913,947
Number of Sequences: 62578
Number of extensions: 1439363
Number of successful extensions: 3082
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 20
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 2968
Number of HSP's gapped (non-prelim): 89
length of query: 1208
length of database: 14,973,337
effective HSP length: 110
effective length of query: 1098
effective length of database: 8,089,757
effective search space: 8882553186
effective search space used: 8882553186
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 57 (26.6 bits)