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= 002545
(910 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 231 bits (590), Expect = 1e-60, Method: Compositional matrix adjust.
Identities = 231/889 (25%), Positives = 386/889 (43%), Gaps = 116/889 (13%)
Query: 67 ERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNY 126
E G P+MLK+ + KL+ + E+ + GGYFI+NG ERV I+ +++
Sbjct: 115 EEVYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERV----IVTQEDL 170
Query: 127 PMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGF-WLQGKEYLLP 185
+ V T A +I + VT++ L +G+ + F + GK +P
Sbjct: 171 APNRVLVDTGKTGSNITHTAKIISSTAGYRVPVTIE--RLKDGTFHVSFPAVPGK---IP 225
Query: 186 VGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRL 245
I+++AL D +I D + + E P + + I A V D
Sbjct: 226 FVILMRALGILTDRDIV--YAVSLDPEIQNEL----FPSLEQASSI--ANVDD------- 270
Query: 246 QCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHL----NDNNDKFNLLIFMLQKLF 301
L IG V G + E+ A+ +I Y HL +D K L + + K+
Sbjct: 271 -ALDFIGSR---VAIGQKRENRIEKAQQIIDKYFLPHLGTSADDRRKKAYYLAYAISKVI 326
Query: 302 SLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFF 361
L D+ D N+ + L G L + + +++ ++ + G+K
Sbjct: 327 ELYLGRREPDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKS-KVRGRKLALK 385
Query: 362 NLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFF 421
L V E+ R A TG + R G + +R N+L +S
Sbjct: 386 ALVRPDIVTERI----------------RHALATGNWVGGRTGVSQLLDRTNWLSMLSHL 429
Query: 422 RAVHRGASFA-GLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRG 480
R V +S A G R L WG +CP TP+G GL+ ++ ++A + +
Sbjct: 430 RRVI--SSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGINEK- 486
Query: 481 NIRDFSKMRTSILRVLIGVGMIPS---LPKLVKSGPP-----AVLSVLLDGRVVGVI-PS 531
+ + L +G++P + ++ + G V+L+GR+VG
Sbjct: 487 ----------IVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLVGYYRDG 536
Query: 532 SEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISL- 590
E+ K + RR I D++ VG++ +++ + RP+ +S
Sbjct: 537 EELAKKIRERRR-----KGEISDEVNVGHIVTDFINE---VHVNCDSGRVRRPLIIVSNG 588
Query: 591 -PSEESQNIELIGP----FEQVFMEIRCPDGGDGGRRNAFPA----------THEEIHPT 635
P ++IE + F+ + + + NA+ A TH EI
Sbjct: 589 NPLVTREDIEKLDSGSITFDDLVRQGKIEYLDAEEEENAYVALEPSDLTPEHTHLEIWSP 648
Query: 636 GMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRT 695
+L + A++ PY +HNQSPRN YQ MAKQ +G + R D + + L PQ P+V+T
Sbjct: 649 AILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQT 708
Query: 696 NTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHG---QIYQTETID- 751
G P G NAI+AV+++TGY+MED++I+N+SSV+RGM ++Y TE +
Sbjct: 709 RALDIIGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKY 768
Query: 752 ---------LSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYD 802
+ + G + +G++ +R +D + ++ G + + P +
Sbjct: 769 PGGQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKE 828
Query: 803 KTTNSWRTNSR---KGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHG 859
+ + ++ + E VD V + N + +R R R P IGDKF+SRHG
Sbjct: 829 LSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGN--KLVKVRVRDLRIPSIGDKFASRHG 886
Query: 860 QKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAK 908
QKGV L P +DMP++ V G+ PD+I+NPHA PSRMT+ ++E +A K
Sbjct: 887 QKGVIGMLIPQVDMPYT-VKGVVPDVILNPHALPSRMTLGQIMEGIAGK 934
>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 = 230 bits (587), Expect = 2e-60, Method: Compositional matrix adjust.
Identities = 230/889 (25%), Positives = 386/889 (43%), Gaps = 116/889 (13%)
Query: 67 ERFNFGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNY 126
E G P+MLK+ + KL+ + E+ + GGYFI+NG ERV I+ +++
Sbjct: 112 EEVYIGDLPIMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERV----IVTQEDL 167
Query: 127 PMSMVRSSFRDRREGYTDKAVVIRCVRKDQSSVTLKLYYLLNGSVRLGF-WLQGKEYLLP 185
+ V T A +I + VT++ L +G+ + F + GK +P
Sbjct: 168 APNRVLVDTGKTGSNITHTAKIISSTAGYRVPVTIE--RLKDGTFHVSFPAVPGK---IP 222
Query: 186 VGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTRL 245
I+++AL D +I ++ D + + E P + + I A V D
Sbjct: 223 FVILMRALGILTDRDIVYAVSL--DPEVQNEL----FPSLEQASSI--ANVDD------- 267
Query: 246 QCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLN----DNNDKFNLLIFMLQKLF 301
L IG V G + E+ A+ +I Y HL D K L + + K+
Sbjct: 268 -ALDFIGSR---VAIGQKRENRIEKAQQIIDKYFLPHLGTSAEDRKKKAYYLAYAISKVI 323
Query: 302 SLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDFF 361
L D+ D N+ + L G L + + +++ ++ + G+K
Sbjct: 324 ELYLGRREPDDKDHYANKRLRLAGDLFASLFRVAFKAFVKDLTYQLEKS-KVRGRKLALK 382
Query: 362 NLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISFF 421
L V E+ R A TG + R G + +R N+L +S
Sbjct: 383 ALVRPDIVTERI----------------RHALATGNWVGGRTGVSQLLDRTNWLSMLSHL 426
Query: 422 RAVHRGASFA-GLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRG 480
R V +S A G R L WG +CP TP+G GL+ ++ ++A + R
Sbjct: 427 RRVI--SSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLVKNLALMAQIAVGINER- 483
Query: 481 NIRDFSKMRTSILRVLIGVGMIPS---LPKLVKSGPP-----AVLSVLLDGRVVGVIP-S 531
+ + L +G++P + ++ + G V+L+GR++G
Sbjct: 484 ----------IVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLIGYYQDG 533
Query: 532 SEIEKVVAHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPVRNISL- 590
E+ + RR I D++ VG++ +++ + RP+ +S
Sbjct: 534 GELANKIRERRR-----KGEISDEVNVGHIVTDFINE---VHVNCDSGRVRRPLIIVSNG 585
Query: 591 -PSEESQNIELIGP----FEQVFMEIRCPDGGDGGRRNAFPA----------THEEIHPT 635
P ++IE + F+ + + + NA+ A TH EI
Sbjct: 586 NPLVTIEDIEKLESGAITFDDLVRQGKIEYLDAEEEENAYVALEPNDLTPDHTHLEIWSP 645
Query: 636 GMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQTPQTPIVRT 695
+L + A++ PY +HNQSPRN YQ MAKQ +G + R D + + L PQ P+V+T
Sbjct: 646 AILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLVQT 705
Query: 696 NTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHG---QIYQTETID- 751
G P G NAI+AV+++TGY+MED++I+N+SSV+RGM ++Y TE +
Sbjct: 706 RALDIIGYTNRPAGNNAILAVMSFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEVKY 765
Query: 752 ---------LSDDGNKVDRGQKLFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYD 802
+ + G + +G++ +R +D + ++ G + + P +
Sbjct: 766 PGGQEDKIVMPEAGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEFKE 825
Query: 803 KTTNSWRTNSR---KGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHG 859
+ + ++ + E VD V + N + +R R R P IGDKF+SRHG
Sbjct: 826 LSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGN--KLVKVRVRDLRIPTIGDKFASRHG 883
Query: 860 QKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAK 908
QKGV L P +DMP++ V G+ PD+I+NPHA PSRMT+ ++E +A K
Sbjct: 884 QKGVIGMLIPQVDMPYT-VKGVVPDIILNPHALPSRMTLGQIMEGIAGK 931
>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 = 180 bits (457), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 113/298 (37%), Positives = 157/298 (52%), Gaps = 20/298 (6%)
Query: 628 THEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQT 687
TH EIHP +L ++A++ P+ DHNQSPRN YQ M KQ MG + + R D L
Sbjct: 728 THCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMANILYY 787
Query: 688 PQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQT 747
PQ P+ T + E P G NAIVA+L Y+GY+ ED++I+N++S+DRG+ Y+T
Sbjct: 788 PQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRT 847
Query: 748 ETIDLSDDGNKVDRGQKLFRRNKDAKSLHSVIDS---DGLPYVGQ-------MIHPGEPY 797
T G V + R+ + H D DGL G +I P
Sbjct: 848 YTDQEKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPI 907
Query: 798 CSIYDKTTNSWRTNSR-------KGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPII 850
+++ + +++ + +ES VD V V N + L + +R R TR P I
Sbjct: 908 PLDHEELGQRTQLHAKRDVSTPLRSTESGIVDQVMV-TTNQEGL-KFVKVRMRSTRIPQI 965
Query: 851 GDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAAK 908
GDKF+SRHGQKG + DMPFS G+ PD+IINPHA PSRMT+A L+E +K
Sbjct: 966 GDKFASRHGQKGTIGMTYRHEDMPFSA-QGIVPDIIINPHAIPSRMTVAHLVECQLSK 1022
Score = 80.5 bits (197), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 119/527 (22%), Positives = 202/527 (38%), Gaps = 67/527 (12%)
Query: 71 FGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSM 130
G+ P+ML++ C L G +L L E + GGYFI+NG E+V I+ ++ ++
Sbjct: 152 IGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIINGSEKV----IIAQERSAANI 207
Query: 131 VRSSFRDRREGYTDKAVVIRCVRKDQSSV--TLKLYYLLNGSVRLGFWLQGK-EYL---L 184
V+ F+ IR + S + ++++ + + G ++ Y+ +
Sbjct: 208 VQV-FKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTENSGQTIRATLPYIRSDI 266
Query: 185 PVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAEVQDLSLTTR 244
P+ IV +AL D +I H+ CYD + + P + E I QD +
Sbjct: 267 PIVIVFRALGVVPDRDILEHI--CYDPN-DFQMLEMMKPCIEEAFVI-----QDKDI--- 315
Query: 245 LQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLND----NNDKFNLLIFMLQKL 300
L +IG+ G+ E A +++ + H+ K L +M+ ++
Sbjct: 316 --ALDYIGKRGSTT--GVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIHRM 371
Query: 301 FSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKFDF 360
D+ D + + L G L+ + R K +Q +E N +
Sbjct: 372 LLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYKYMQKCVETNRE---- 427
Query: 361 FNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFISF 420
FNL K S I + L TG Q + R G + R F +S
Sbjct: 428 FNLTLAVK------SNIITNGLRYSLATGNWGDQKR-SMVNRVGVSQVLNRYTFASTLSH 480
Query: 421 FRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRG 480
R + G + R+L WG +CP TP+G+ CGL+ +++ V+ S
Sbjct: 481 LRRTNTPIGRDG-KLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPS-- 537
Query: 481 NIRDFSKMRTSILRVLIGVGMIPSLPKLVKSGPPAVLSVLLDGRVVGV--IPSSEIEKVV 538
I+ L G+ +L S P V ++G +GV P+ E +
Sbjct: 538 ---------APIIEFLEEWGL-ETLEDYNPSASPNATKVFVNGVWLGVHRDPAHLTETLR 587
Query: 539 AHLRRLKVSAASVIPDDLEVGYVPLSLGGAYPGLYLFTSPPKFVRPV 585
+ RRL +SA I D+ L LFT + RP+
Sbjct: 588 SLRRRLDISAEVSIVRDIR-----------EKELRLFTDAGRICRPL 623
>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 = 175 bits (443), Expect = 1e-43, Method: Compositional matrix adjust.
Identities = 116/301 (38%), Positives = 155/301 (51%), Gaps = 26/301 (8%)
Query: 628 THEEIHPTGMLSVVANLTPYSDHNQSPRNMYQCQMAKQTMGFSVQALKFRADQKLYHLQT 687
TH EIHP+ +L V A++ P+ DHNQSPRN YQ M KQ MG + R D L
Sbjct: 739 THCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYY 798
Query: 688 PQTPIVRTNTYTKYGIDEYPTGTNAIVAVLAYTGYDMEDAMILNKSSVDRGMCHGQIYQT 747
PQ P+ T E P G NAIVA+ Y+GY+ ED+MI+N+SS+DRG+ +++
Sbjct: 799 PQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRS 858
Query: 748 ETIDLSDDGNKVDRGQKLFRRNKDAKSLHSV---IDSDGLPYVGQMIHPGEPYCSIYDKT 804
G + + +R + H +D DGL G + GE I KT
Sbjct: 859 YMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRV-SGEDV--IIGKT 915
Query: 805 T---------------NSWRTNSR--KGSESVFVDYVAVDMKNSKNLPQKANIRFRHTRN 847
T +S R S + +E+ VD V V N L + +R R T+
Sbjct: 916 TPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLV-TTNQDGL-KFVKVRVRTTKI 973
Query: 848 PIIGDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLESVAA 907
P IGDKF+SRHGQKG + DMPF+ G+ PDLIINPHA PSRMT+A L+E + +
Sbjct: 974 PQIGDKFASRHGQKGTIGITYRREDMPFTA-EGIVPDLIINPHAIPSRMTVAHLIECLLS 1032
Query: 908 K 908
K
Sbjct: 1033 K 1033
Score = 87.0 bits (214), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 98/409 (23%), Positives = 167/409 (40%), Gaps = 47/409 (11%)
Query: 71 FGQFPVMLKTRRCHLQGADSQKLVSLKEEAAEMGGYFILNGLERVFRSVILPKQNYPMSM 130
G+ P+ML+++ C+L A L LKE +MGGYFI+NG E+V L Q
Sbjct: 167 IGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKV-----LIAQERSAGN 221
Query: 131 VRSSFRDRREGYTDKAVVIRCVRKDQ----SSVTLKLYYLLNGSVR-LGFWLQGKEYLLP 185
+ F+ IR + S++ +KLY S R + L + +P
Sbjct: 222 IVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIP 281
Query: 186 VGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERVKIILAE---VQDLSLT 242
+ I+ +AL D EI H+ CYD V + E +K + + +QD
Sbjct: 282 IVIIFRALGIIPDGEILEHI--CYD---------VNDWQMLEMLKPCVEDGFVIQD---- 326
Query: 243 TRLQCLQHIGEHFQPVIDGLQSESYYAVAETVIRDYIFVHLND----NNDKFNLLIFMLQ 298
R L IG + G++ E A+ +++ H+ + K L +M+
Sbjct: 327 -RETALDFIGRRGTAL--GIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMIN 383
Query: 299 KLFSLVDHTSVSDNPDSLQNQEILLPGHLITIYLKEKLEDWLRKGKKLIQDEIENNGKKF 358
+L D+ D + + L G L+ K + + + +Q +E +
Sbjct: 384 RLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVE---EAH 440
Query: 359 DFFNLANIKKVMEKNPSKQIGTSIETMLKTGRLATQTGLDLQQRAGYTVQAERLNFLRFI 418
DF N+K + +K I + ++ L TG Q + RAG + R + +
Sbjct: 441 DF----NMKLAIN---AKTITSGLKYALATGNWGEQKKA-MSSRAGVSQVLNRYTYSSTL 492
Query: 419 SFFRAVHRGASFAGLRTTSVRKLLPESWGFLCPVHTPDGEPCGLLNHMT 467
S R + G + R+L WG +CP TP+G+ CGL+ +++
Sbjct: 493 SHLRRTNTPIGRDG-KLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLS 540
>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 = 66.2 bits (160), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 56/227 (24%), Positives = 100/227 (44%), Gaps = 38/227 (16%)
Query: 709 GTNAIVAVLAYTGYDMEDAMILNKSSVDRGM---CHGQIYQTETIDLSDDGNKVDRGQKL 765
G N +VA++ + GY+ EDA+++++ + R H + Y+ E D ++ R
Sbjct: 669 GQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPH 728
Query: 766 FRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTNSWRTNSRKGSESVFVDYVA 825
+++ +D +G+ +G + PG+ S T + S+F + A
Sbjct: 729 L-----SEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEK-A 782
Query: 826 VDMKNS--KNLPQKANIRFRHTR----NP----------------------IIGDKFSSR 857
D+K++ + P + I R R +P +GDK ++R
Sbjct: 783 RDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANR 842
Query: 858 HGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLES 904
HG KGV +++ P DMP G D+I+NP PSRM + +LE+
Sbjct: 843 HGNKGVVAKILPVEDMPHL-PDGTPVDVILNPLGVPSRMNLGQILET 888
Score = 33.1 bits (74), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 30/62 (48%), Gaps = 10/62 (16%)
Query: 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIRDFSKMRTSILRVLI 497
VR + +G +CPV TP+G GL+ + + RV D G I RT RV+
Sbjct: 427 VRDVHRTHYGRICPVETPEGANIGLITSLAAYARV----DELGFI------RTPYRRVVG 476
Query: 498 GV 499
GV
Sbjct: 477 GV 478
>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 = 63.9 bits (154), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 54/227 (23%), Positives = 98/227 (43%), Gaps = 38/227 (16%)
Query: 709 GTNAIVAVLAYTGYDMEDAMILNKSSVDRGM---CHGQIYQTETIDLSDDGNKVDRGQKL 765
G N +VA++ + GY+ EDA+++++ + R H + Y+ E D ++ R
Sbjct: 669 GQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPH 728
Query: 766 FRRNKDAKSLHSVIDSDGLPYVGQMIHPG-------------EP------YCSIYDKTTN 806
+++ +D +G+ +G + PG EP SI+ +
Sbjct: 729 L-----SEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKAR 783
Query: 807 SWRTNSRK---GSESVFVDYVAVDMKNSKNLPQKANIR------FRHTRNPIIGDKFSSR 857
+ S + G + V + + + + K +R R +GDK ++R
Sbjct: 784 DVKDTSLRVPPGEGGIVVGRLRL-RRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANR 842
Query: 858 HGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLES 904
HG KGV +++ P DMP G D+I+NP PSRM + +LE+
Sbjct: 843 HGNKGVVAKILPVEDMPHL-PDGTPVDVILNPLGVPSRMNLGQILET 888
Score = 33.9 bits (76), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIR 483
VR + +G +CPV TP+G GL+ + + RV D+ G IR
Sbjct: 427 VRDVHRTHYGRICPVETPEGANIGLITSLAAYARV----DALGFIR 468
>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 = 63.9 bits (154), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 54/227 (23%), Positives = 98/227 (43%), Gaps = 38/227 (16%)
Query: 709 GTNAIVAVLAYTGYDMEDAMILNKSSVDRGM---CHGQIYQTETIDLSDDGNKVDRGQKL 765
G N +VA++ + GY+ EDA+++++ + R H + Y+ E D ++ R
Sbjct: 669 GQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPH 728
Query: 766 FRRNKDAKSLHSVIDSDGLPYVGQMIHPG-------------EP------YCSIYDKTTN 806
+++ +D +G+ +G + PG EP SI+ +
Sbjct: 729 L-----SEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKAR 783
Query: 807 SWRTNSRK---GSESVFVDYVAVDMKNSKNLPQKANIR------FRHTRNPIIGDKFSSR 857
+ S + G + V + + + + K +R R +GDK ++R
Sbjct: 784 DVKDTSLRVPPGEGGIVVGRLRL-RRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANR 842
Query: 858 HGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLES 904
HG KGV +++ P DMP G D+I+NP PSRM + +LE+
Sbjct: 843 HGNKGVVAKILPVEDMPHL-PDGTPVDVILNPLGVPSRMNLGQILET 888
Score = 33.9 bits (76), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIR 483
VR + +G +CPV TP+G GL+ + + RV D+ G IR
Sbjct: 427 VRDVHRTHYGRICPVETPEGANIGLITSLAAYARV----DALGFIR 468
>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 = 63.9 bits (154), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 54/227 (23%), Positives = 98/227 (43%), Gaps = 38/227 (16%)
Query: 709 GTNAIVAVLAYTGYDMEDAMILNKSSVDRGM---CHGQIYQTETIDLSDDGNKVDRGQKL 765
G N +VA++ + GY+ EDA+++++ + R H + Y+ E D ++ R
Sbjct: 668 GQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPH 727
Query: 766 FRRNKDAKSLHSVIDSDGLPYVGQMIHPG-------------EP------YCSIYDKTTN 806
+++ +D +G+ +G + PG EP SI+ +
Sbjct: 728 L-----SEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKAR 782
Query: 807 SWRTNSRK---GSESVFVDYVAVDMKNSKNLPQKANIR------FRHTRNPIIGDKFSSR 857
+ S + G + V + + + + K +R R +GDK ++R
Sbjct: 783 DVKDTSLRVPPGEGGIVVGRLRL-RRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANR 841
Query: 858 HGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLES 904
HG KGV +++ P DMP G D+I+NP PSRM + +LE+
Sbjct: 842 HGNKGVVAKILPVEDMPHL-PDGTPVDVILNPLGVPSRMNLGQILET 887
Score = 33.5 bits (75), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIR 483
VR + +G +CPV TP+G GL+ + + RV D+ G IR
Sbjct: 427 VRDVHRTHYGRICPVETPEGANIGLITSLAAYARV----DALGFIR 468
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 63.5 bits (153), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 54/227 (23%), Positives = 98/227 (43%), Gaps = 38/227 (16%)
Query: 709 GTNAIVAVLAYTGYDMEDAMILNKSSVDRGM---CHGQIYQTETIDLSDDGNKVDRGQKL 765
G N +VA++ + GY+ EDA+++++ + R H + Y+ E D ++ R
Sbjct: 668 GQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPH 727
Query: 766 FRRNKDAKSLHSVIDSDGLPYVGQMIHPG-------------EP------YCSIYDKTTN 806
+++ +D +G+ +G + PG EP SI+ +
Sbjct: 728 L-----SEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGEKAR 782
Query: 807 SWRTNSRK---GSESVFVDYVAVDMKNSKNLPQKANIR------FRHTRNPIIGDKFSSR 857
+ S + G + V + + + + K +R R +GDK ++R
Sbjct: 783 DVKDTSLRVPPGEGGIVVGRLRL-RRGDPGVELKPGVREVVRVFVAQKRKLQVGDKLANR 841
Query: 858 HGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLES 904
HG KGV +++ P DMP G D+I+NP PSRM + +LE+
Sbjct: 842 HGNKGVVAKILPVEDMPHL-PDGTPVDVILNPLGVPSRMNLGQILET 887
Score = 33.5 bits (75), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 4/46 (8%)
Query: 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASYYDSRGNIR 483
VR + +G +CPV TP+G GL+ + + RV D+ G IR
Sbjct: 427 VRDVHRTHYGRICPVETPEGANIGLITSLAAYARV----DALGFIR 468
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
Length = 1342
Score = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/61 (45%), Positives = 38/61 (62%), Gaps = 4/61 (6%)
Query: 851 GDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLES---VAA 907
GDK + RHG KGV S++ P DMP+ G D+++NP PSRM I +LE+ +AA
Sbjct: 1063 GDKMAGRHGNKGVISKINPIEDMPYDE-NGTPVDIVLNPLGVPSRMNIGQILETHLGMAA 1121
Query: 908 K 908
K
Sbjct: 1122 K 1122
Score = 36.2 bits (82), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASY 475
VR + P +G +CP+ TP+G GL+N ++ + Y
Sbjct: 547 VRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEY 584
>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 = 54.7 bits (130), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/61 (45%), Positives = 38/61 (62%), Gaps = 4/61 (6%)
Query: 851 GDKFSSRHGQKGVCSQLWPDIDMPFSGVTGMRPDLIINPHAFPSRMTIAMLLES---VAA 907
GDK + RHG KGV S++ P DMP+ G D+++NP PSRM I +LE+ +AA
Sbjct: 1063 GDKMAGRHGNKGVISKINPIEDMPYDE-NGTPVDIVLNPLGVPSRMNIGQILETHLGMAA 1121
Query: 908 K 908
K
Sbjct: 1122 K 1122
Score = 36.6 bits (83), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 438 VRKLLPESWGFLCPVHTPDGEPCGLLNHMTSTCRVASY 475
VR + P +G +CP+ TP+G GL+N ++ + Y
Sbjct: 547 VRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEY 584
>pdb|3VQK|A Chain A, Small Heat Shock Protein Hsp14.0 Of Wild Type
pdb|3VQK|B Chain B, Small Heat Shock Protein Hsp14.0 Of Wild Type
pdb|3VQK|C Chain C, Small Heat Shock Protein Hsp14.0 Of Wild Type
pdb|3VQK|D Chain D, Small Heat Shock Protein Hsp14.0 Of Wild Type
pdb|3VQK|E Chain E, Small Heat Shock Protein Hsp14.0 Of Wild Type
pdb|3VQK|F Chain F, Small Heat Shock Protein Hsp14.0 Of Wild Type
Length = 123
Score = 34.3 bits (77), Expect = 0.33, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 570 PGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGG 617
PG+ T PK+VR V I LP +++ E+ G +E + IR P G
Sbjct: 71 PGVKYLTQRPKYVRKV--IRLPYNVAKDAEISGKYENGVLTIRIPIAG 116
>pdb|3AAB|A Chain A, Small Heat Shock Protein Hsp14.0 With The Mutations Of
I120f And I122f In The Form I Crystal
pdb|3AAB|B Chain B, Small Heat Shock Protein Hsp14.0 With The Mutations Of
I120f And I122f In The Form I Crystal
pdb|3AAC|A Chain A, Small Heat Shock Protein Hsp14.0 With The Mutations Of
I120f And I122f In The Form Ii Crystal
pdb|3AAC|B Chain B, Small Heat Shock Protein Hsp14.0 With The Mutations Of
I120f And I122f In The Form Ii Crystal
Length = 123
Score = 34.3 bits (77), Expect = 0.34, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 570 PGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCPDGG 617
PG+ T PK+VR V I LP +++ E+ G +E + IR P G
Sbjct: 71 PGVKYLTQRPKYVRKV--IRLPYNVAKDAEISGKYENGVLTIRIPIAG 116
>pdb|3VQL|A Chain A, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant
pdb|3VQL|B Chain B, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant
pdb|3VQM|A Chain A, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
pdb|3VQM|B Chain B, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
pdb|3VQM|C Chain C, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
pdb|3VQM|D Chain D, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
pdb|3VQM|E Chain E, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
pdb|3VQM|F Chain F, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
pdb|3VQM|G Chain G, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
pdb|3VQM|H Chain H, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
pdb|3VQM|I Chain I, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
pdb|3VQM|J Chain J, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
pdb|3VQM|K Chain K, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
pdb|3VQM|L Chain L, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
pdb|3VQM|M Chain M, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
pdb|3VQM|N Chain N, Small Heat Shock Protein Hsp14.0 Of C-Terminal Deletion
Variant With C-Terminal Peptide
Length = 115
Score = 33.1 bits (74), Expect = 0.73, Method: Composition-based stats.
Identities = 17/45 (37%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 570 PGLYLFTSPPKFVRPVRNISLPSEESQNIELIGPFEQVFMEIRCP 614
PG+ T PK+VR V I LP +++ E+ G +E + IR P
Sbjct: 71 PGVKYLTQRPKYVRKV--IRLPYNVAKDAEISGKYENGVLTIRIP 113
>pdb|3NYD|A Chain A, Crystal Structure Of Kemp Eliminase Hg-2 Complexed With
Transition State Analog 5-Nitro Benzotriazole
pdb|3NYD|B Chain B, Crystal Structure Of Kemp Eliminase Hg-2 Complexed With
Transition State Analog 5-Nitro Benzotriazole
Length = 316
Score = 31.6 bits (70), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 32/76 (42%), Gaps = 6/76 (7%)
Query: 498 GVGMIPSLPKLVKSGPPAVLSVLLDGRVVGVIPSSEIEKVVAHLRRLKVSAASVI----P 553
G G++ +LP L +G P V ++LD V G P+ + V A L SV P
Sbjct: 215 GAGVLQALPLLASAGTPEVSILMLD--VAGASPTDYVNVVNACLNVQSCVGISVFGVADP 272
Query: 554 DDLEVGYVPLSLGGAY 569
D PL G +
Sbjct: 273 DSWRASTTPLLFDGNF 288
>pdb|1W36|B Chain B, Recbcd:dna Complex
pdb|1W36|E Chain E, Recbcd:dna Complex
pdb|3K70|B Chain B, Crystal Structure Of The Complete Initiation Complex Of
Recbcd
pdb|3K70|E Chain E, Crystal Structure Of The Complete Initiation Complex Of
Recbcd
Length = 1180
Score = 31.2 bits (69), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 33/149 (22%), Positives = 59/149 (39%), Gaps = 18/149 (12%)
Query: 765 LFRRNKDAKSLHSVIDSDGLPYVGQMIHPGEPYCSIYDKTTN--------SWRTNSRKGS 816
L RR D K V S +G+++ GEP + +T +W+T +
Sbjct: 820 LVRRRGDKKGDTDVHQS----ALGRLLQKGEPQDAAGLRTCIEALCDDDIAWQTAQTGDN 875
Query: 817 ESVFVDYVAVDMKNSKNLPQKANIRFRHTRNPIIGDKFSSRHGQKGVCSQLWPDIDMPFS 876
+ V+ V+ N+K L + +R T + + G+ L P +D+ +
Sbjct: 876 QPWQVNDVSTAELNAKTLQRLPGDNWRVTSYSGLQQR------GHGIAQDLMPRLDVDAA 929
Query: 877 GVTGMRPDLIINPHAFPSRMTIAMLLESV 905
GV + + + PH FP + L S+
Sbjct: 930 GVASVVEEPTLTPHQFPRGASPGTFLHSL 958
>pdb|3H7U|A Chain A, Crystal Structure Of The Plant Stress-Response Enzyme
Akr4c9
Length = 335
Score = 30.4 bits (67), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 37/81 (45%), Gaps = 11/81 (13%)
Query: 170 SVRLGFWLQGKEYLLPVGIVLKALVDTNDLEIFNHLTCCYDEKYKKEKGAVGSPLVSERV 229
SV LG W Q L VG + A V + H+ C +KE GAV L +RV
Sbjct: 38 SVGLGTW-QASPGL--VGDAVAAAVKIG----YRHIDCAQIYGNEKEIGAVLKKLFEDRV 90
Query: 230 KIILAEVQDLSLTTRLQCLQH 250
+ +DL +T++L C H
Sbjct: 91 ----VKREDLFITSKLWCTDH 107
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
0.320 0.137 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,232,357
Number of Sequences: 62578
Number of extensions: 1174187
Number of successful extensions: 2639
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 2574
Number of HSP's gapped (non-prelim): 54
length of query: 910
length of database: 14,973,337
effective HSP length: 108
effective length of query: 802
effective length of database: 8,214,913
effective search space: 6588360226
effective search space used: 6588360226
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)