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= 001532
(1058 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 = 652 bits (1681), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 374/1052 (35%), Positives = 586/1052 (55%), Gaps = 52/1052 (4%)
Query: 27 SVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVR 86
S+ ++++++ + K +GLV+QHLDS+N FV +++I+ I + I P + +R +R
Sbjct: 9 SIDERWKVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTEI-PGLKVRLGKIR 67
Query: 87 IGQPSMTVDGVSEK-LNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIP 145
IG+P + E+ ++P RL ++TYAAP+ + + V+ + E +V IG +P
Sbjct: 68 IGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPVENN----IEAEPEEVYIGDLP 123
Query: 146 IMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKG 205
IML+S + +L +GE P DPGGYFI+ G+E+V++ QE L+ NRV++DT K G
Sbjct: 124 IMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLVDTGKTG 183
Query: 206 -NINAXXXXXXXXXXXXXXIQMEK---GKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQ 261
NI + +E+ G ++ KIP +++M+A+G+ +D+++V
Sbjct: 184 SNITHTAKIISSTAGYRVPVTIERLKDGTFHVSFPAVPGKIPFVILMRALGILTDRDIVY 243
Query: 262 MVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRD 321
V DP L PS+E+ ++ I + AL+++ +V G +R +A I+
Sbjct: 244 AVSLDPEIQNELFPSLEQASS--IANVDDALDFIGSRV---AIGQKRENRIEKAQQIIDK 298
Query: 322 VFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFE 381
FL ++ ++ R K +Y+A + +++E L + DDKD+ NKRL L+G L + LF
Sbjct: 299 YFLPHLGTSADDRRKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFASLFR 358
Query: 382 DLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHR 441
FK + ++ ++ R + L + D +T + L+TGN+ R
Sbjct: 359 VAFKAFVKDLTYQLE---KSKVRGRKLALKALVRPDIVTERIRHALATGNW-----VGGR 410
Query: 442 KGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLV 501
G++Q+L R +++ L H+ RV + + R L +QWG +CP +TPEG GLV
Sbjct: 411 TGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLV 470
Query: 502 KNLALMTHVTTDEEEGPLISLCYCLGVEDLELL---SGEELHNPNSFL----VIFNGLIL 554
KNLALM + E + Y +GV +E + E + N +L VI NG ++
Sbjct: 471 KNLALMAQIAVGINEKIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLV 530
Query: 555 GKHRRPKCFADVMRKLRRAGKI------GEFVSVFVNEKQRCVYIASDGGRVCRPLVIAD 608
G +R + A +R+ RR G+I G V+ F+NE V++ D GRV RPL+I
Sbjct: 531 GYYRDGEELAKKIRERRRKGEISDEVNVGHIVTDFINE----VHVNCDSGRVRRPLIIVS 586
Query: 609 KGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIE 668
G + +++L G +FDD +R+G IEYLD EE NA +AL D TP+ TH+EI
Sbjct: 587 NGNPLVTREDIEKLDSGSITFDDLVRQGKIEYLDAEEEENAYVALEPSDLTPEHTHLEIW 646
Query: 669 PFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLL 728
ILG+ A +IPYP HNQSPRNTYQ AM KQA+G A N R D+ +LL YPQRPL+
Sbjct: 647 SPAILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLV 706
Query: 729 TTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQ 788
TR ++++GY AG NA +AV+S++GY++ED+I+MN+SS++RG R + Y+
Sbjct: 707 QTRALDIIGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEV 766
Query: 789 KYANSTSDRILRPD---RTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSI 845
KY D+I+ P+ R G E ++L+D+G+ +P +K DV I K SP
Sbjct: 767 KYPGGQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEF 826
Query: 846 MSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFS 905
+ + R S + GE +VD V + G+ +K +R R P +GDKF+
Sbjct: 827 KELSPEQAKRDTSIVTRH----GEMGIVDLVLITETAEGNKLVKVRVRDLRIPSIGDKFA 882
Query: 906 SRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRF 965
SRHGQKGV G ++ Q D P++ +G+ PD+I+NPH PSRMT+G+++E + GK G
Sbjct: 883 SRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAALSGNI 942
Query: 966 HYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLK 1025
+ F + +E + ++K+G+ + ++ Y G TG +++ I+ G +YYQKL
Sbjct: 943 VDATPF-----YKTPIEQLQNEILKYGYLPDATEVTYDGRTGQKIKSRIYFGVVYYQKLH 997
Query: 1026 HMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057
HMV DK+HAR GP +LTRQPTEGRAR GG
Sbjct: 998 HMVADKIHARARGPVQILTRQPTEGRAREGGL 1029
>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 = 649 bits (1675), Expect = 0.0, Method: Compositional matrix adjust.
Identities = 372/1052 (35%), Positives = 586/1052 (55%), Gaps = 52/1052 (4%)
Query: 27 SVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIVSGIDPSIFLRFKDVR 86
++ ++++++ + K +GLV+QHLDS+N FV +++I+ I + I P + +R +R
Sbjct: 6 TIDERWRVIEAYFKSKGLVRQHLDSYNDFVRNKLQEIIDEQGEIPTEI-PGLKVRLGKIR 64
Query: 87 IGQPSMTVDGVSEK-LNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKNDVVIGRIP 145
IG+P + E+ ++P RL ++TYAAP+ + + V+ + E +V IG +P
Sbjct: 65 IGKPRVRESDRGEREISPMEARLRNLTYAAPLWLTMIPVENN----IEAEPEEVYIGDLP 120
Query: 146 IMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRVIIDTDKKG 205
IML+S + +L +GE P DPGGYFI+ G+E+V++ QE L+ NRV++DT K G
Sbjct: 121 IMLKSAIDPISQYTLDKLIEIGEDPKDPGGYFIVNGSERVIVTQEDLAPNRVLVDTGKTG 180
Query: 206 -NINAXXXXXXXXXXXXXXIQMEK---GKMYLLLNQFVKKIPIMVVMKAMGMESDQEVVQ 261
NI + +E+ G ++ KIP +++M+A+G+ +D+++V
Sbjct: 181 SNITHTAKIISSTAGYRVPVTIERLKDGTFHVSFPAVPGKIPFVILMRALGILTDRDIVY 240
Query: 262 MVGRDPRYSALLLPSIEECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRD 321
V DP L PS+E+ ++ I + AL+++ +V G +R +A I+
Sbjct: 241 AVSLDPEVQNELFPSLEQASS--IANVDDALDFIGSRV---AIGQKRENRIEKAQQIIDK 295
Query: 322 VFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFE 381
FL ++ + + K +Y+A + +++E L + DDKD+ NKRL L+G L + LF
Sbjct: 296 YFLPHLGTSAEDRKKKAYYLAYAISKVIELYLGRREPDDKDHYANKRLRLAGDLFASLFR 355
Query: 382 DLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHR 441
FK + ++ ++ R + L + D +T + L+TGN+ R
Sbjct: 356 VAFKAFVKDLTYQLE---KSKVRGRKLALKALVRPDIVTERIRHALATGNW-----VGGR 407
Query: 442 KGMTQVLARLSFIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLV 501
G++Q+L R +++ L H+ RV + + R L +QWG +CP +TPEG GLV
Sbjct: 408 TGVSQLLDRTNWLSMLSHLRRVISSLARGQPNFEARDLHGTQWGRMCPFETPEGPNSGLV 467
Query: 502 KNLALMTHVTTDEEEGPLISLCYCLGVEDLELL---SGEELHNPNSFL----VIFNGLIL 554
KNLALM + E + Y +GV +E + E + N +L VI NG ++
Sbjct: 468 KNLALMAQIAVGINERIVEKTLYEMGVVPVEEVIRRVTEGGEDQNEYLKWSKVILNGRLI 527
Query: 555 GKHRRPKCFADVMRKLRRAGKI------GEFVSVFVNEKQRCVYIASDGGRVCRPLVIAD 608
G ++ A+ +R+ RR G+I G V+ F+NE V++ D GRV RPL+I
Sbjct: 528 GYYQDGGELANKIRERRRKGEISDEVNVGHIVTDFINE----VHVNCDSGRVRRPLIIVS 583
Query: 609 KGISRIKEHHMKELLDGVRSFDDFLREGLIEYLDVNEENNALIALYEGDATPDTTHIEIE 668
G + +++L G +FDD +R+G IEYLD EE NA +AL D TPD TH+EI
Sbjct: 584 NGNPLVTIEDIEKLESGAITFDDLVRQGKIEYLDAEEEENAYVALEPNDLTPDHTHLEIW 643
Query: 669 PFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLYLLVYPQRPLL 728
ILG+ A +IPYP HNQSPRNTYQ AM KQA+G A N R D+ +LL YPQRPL+
Sbjct: 644 SPAILGITASIIPYPEHNQSPRNTYQSAMAKQALGLYAANYQLRTDTRAHLLHYPQRPLV 703
Query: 729 TTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQ 788
TR ++++GY AG NA +AVMS++GY++ED+I+MN+SS++RG R + Y+
Sbjct: 704 QTRALDIIGYTNRPAGNNAILAVMSFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEV 763
Query: 789 KYANSTSDRILRPD---RTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESPLETRGSI 845
KY D+I+ P+ R G E ++L+D+G+ +P +K DV I K SP
Sbjct: 764 KYPGGQEDKIVMPEAGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEF 823
Query: 846 MSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNGDLCIKFLIRHTRRPELGDKFS 905
+ + R S + GE +VD V + G+ +K +R R P +GDKF+
Sbjct: 824 KELSPEQAKRDTSIVTRH----GEMGIVDLVLITETAEGNKLVKVRVRDLRIPTIGDKFA 879
Query: 906 SRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRF 965
SRHGQKGV G ++ Q D P++ +G+ PD+I+NPH PSRMT+G+++E + GK G
Sbjct: 880 SRHGQKGVIGMLIPQVDMPYTVKGVVPDIILNPHALPSRMTLGQIMEGIAGKYAALSGNI 939
Query: 966 HYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLK 1025
+ F + +E + ++++G+ + +++Y G TG +++ I+ G +YYQKL
Sbjct: 940 VDATPF-----YKTPIEQLQNEILRYGYLPDATEVVYDGRTGQKIKSRIYFGVVYYQKLH 994
Query: 1026 HMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057
HMV DK+HAR GP +LTRQPTEGRAR GG
Sbjct: 995 HMVADKLHARARGPVQILTRQPTEGRAREGGL 1026
>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 = 629 bits (1621), Expect = e-180, Method: Compositional matrix adjust.
Identities = 395/1133 (34%), Positives = 603/1133 (53%), Gaps = 123/1133 (10%)
Query: 22 AAPVKSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIV---------- 71
+AP+ + D + ++ F + +GLV Q LDSFN FV+ ++ I+ + ++
Sbjct: 22 SAPI-TAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTE 80
Query: 72 -SGIDPSIFLRFKDVRIGQPSMT-VDGVSEKLNPHMCRLSDMTYAAPILVNIE------- 122
I + F + + +P + DGV+ L P RL ++TY++ + V+++
Sbjct: 81 SDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAI 140
Query: 123 --------YVQGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPG 174
Y + + E V IGR+PIMLRS C L E++L +L ECP D G
Sbjct: 141 DVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMG 200
Query: 175 GYFIIKGTEKVLLIQEQLSKNRVIIDTDKKGN---INAXXXXXXXXXXXXXXIQMEKGKM 231
GYFII G+EKVL+ QE+ + N I+ KK I+ I + K+
Sbjct: 201 GYFIINGSEKVLIAQERSAGN--IVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKL 258
Query: 232 Y-----------LLLNQFVKKIPIMVVMKAMGMESDQEVVQMVG---RDPRYSALLLPSI 277
Y L + IPI+++ +A+G+ D E+++ + D + +L P +
Sbjct: 259 YGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCV 318
Query: 278 EECANLDIYTQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPK 337
E+ I +E AL+++ G+ + + G R A IL+ FL ++ K
Sbjct: 319 ED--GFVIQDRETALDFI-GR-RGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRK 374
Query: 338 CFYVAVMLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEV----QK 393
F++ M+ R++ L++ DD+D+ G KRL+L+G L++ LF+ LFK + ++ Q+
Sbjct: 375 AFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQR 434
Query: 394 TVDIILSKPSRSSRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMH-RKGMTQVLARLS 452
TV+ + F++ I +IT GL+ L+TGN+ ++ M R G++QVL R +
Sbjct: 435 TVE-------EAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYT 487
Query: 453 FIGTLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTT 512
+ TL H+ R + + K++ PR L + WG++CP +TPEG+ACGLVKNL+LM+ ++
Sbjct: 488 YSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISV 547
Query: 513 DEEEGPLISLCYCLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRR 572
+ P+I+ G+E LE + +P++ V NG+ G HR P + +R LRR
Sbjct: 548 GTDPMPIITFLSEWGMEPLEDYVPHQ--SPDATRVFVNGVWHGVHRNPARLMETLRTLRR 605
Query: 573 AGKIGEFVSVFVNEKQRCVYIASDGGRVCRPLVIADKGIS------RIKEHHMKELL--- 623
G I VS+ + +++ + I +D GRV RPL I + S ++++ H+ +L+
Sbjct: 606 KGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATE 665
Query: 624 --DGVRSFDD--------FLREGLIEYLDVNEENNALIALYEGDATPDT----------- 662
D F+D L EGL+EY+D EE + LIA+ D P
Sbjct: 666 YQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDP 725
Query: 663 -------------THIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQ 709
TH EI P ILGV A +IP+P HNQSPRNTYQ AMGKQAMG N
Sbjct: 726 AKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNY 785
Query: 710 LCRMDSLLYLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSS 769
RMD++ +L YPQ+PL TTR +E + + +L AGQNA VA+ YSGY+ ED+++MN+SS
Sbjct: 786 NVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSS 845
Query: 770 LDRGFGRCIVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQ-----ILDDDGLAAPGE 824
+DRG R + + Y +KY S ++ +P RT RM+ LDDDGL APG
Sbjct: 846 IDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRT--NTLRMKHGTYDKLDDDGLIAPGV 903
Query: 825 IIKPNDVYINKESPLETRGSIMSPTGQTDSRYRSARQTYKGPDGETCVVDRVALCSDKNG 884
+ DV I K +P+ + GQ + + + E +VD+V + ++++G
Sbjct: 904 RVSGEDVIIGKTTPISPDEEEL---GQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDG 960
Query: 885 DLCIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSR 944
+K +R T+ P++GDKF+SRHGQKG G ++ED PF+ GI PDLI+NPH PSR
Sbjct: 961 LKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSR 1020
Query: 945 MTVGKMIELLGGKAGVSCGRFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSG 1004
MTV +IE L K G S F + TVE IS+ L +HG+ G +++Y+G
Sbjct: 1021 MTVAHLIECLLSKVAALSGNEGDASPFTDI-----TVEGISKLLREHGYQSRGFEVMYNG 1075
Query: 1005 ITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057
TG L A IF GP YYQ+L+HMV DK+HAR GP +LTRQP EGR+R+GG
Sbjct: 1076 HTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGL 1128
>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 = 625 bits (1613), Expect = e-179, Method: Compositional matrix adjust.
Identities = 396/1127 (35%), Positives = 602/1127 (53%), Gaps = 124/1127 (11%)
Query: 30 DKFQLLPEFLKVRGLVKQHLDSFNYFVNTGIRKIVRANDRIV-------SGIDPSIFLR- 81
D + ++ F + L +Q L SF+ FV +++IV + + +G + R
Sbjct: 16 DCWTVISSFFEETSLARQQLFSFDEFVQNTMQEIVDDDSTLTLDQYAQHTGAQGDVTRRY 75
Query: 82 ---FKDVRIGQPSMT-VDGVSEKLNPHMCRLSDMTYAAPILVNIEY-------------V 124
F + + +P+MT DG + + P RL ++TY++P+ V++
Sbjct: 76 EINFGQIYLSRPTMTEADGSTTTMFPQEARLRNLTYSSPLYVDMRKKVMVAADSNVPIGE 135
Query: 125 QGSHTEKTTMEKNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEK 184
+ E+ E + V IG+IPIMLRS C+L G ++EL L ECP D GGYFII G+EK
Sbjct: 136 EEWLVEEEDEEPSKVFIGKIPIMLRSTFCILNGVSDSELYDLNECPYDQGGYFIINGSEK 195
Query: 185 VLLIQEQLSKNRVIIDTDKKGNINAXXXXXXXXXXXXXXIQMEKGKMYLLLNQFVKK--- 241
V++ QE+ + N I+ KK + ++ L+ + +
Sbjct: 196 VIIAQERSAAN--IVQVFKKAAPSPIAYVAEIRSALERGSRLISSMQIKLMARNTENSGQ 253
Query: 242 ------------IPIMVVMKAMGMESDQEVVQMVGRDP---RYSALLLPSIEECANLDIY 286
IPI++V +A+G+ D+++++ + DP + ++ P IEE I
Sbjct: 254 TIRATLPYIRSDIPIVIVFRALGVVPDRDILEHICYDPNDFQMLEMMKPCIEEA--FVIQ 311
Query: 287 TQEKALEYLEGKVKRSTFGSPPNDREGRAFSILRDVFLANVPVHNNNFRPKCFYVAVMLR 346
++ AL+Y+ GK + ST G R A IL+ L ++ K F++ M+
Sbjct: 312 DKDIALDYI-GK-RGSTTGVTREKRLRYAHDILQKELLPHITTMEGFETRKAFFLGYMIH 369
Query: 347 RMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSS 406
RM+ L + DD+D+ G KRL+L+G L++ LF LF+ M +V K + K ++
Sbjct: 370 RMLLCALERREPDDRDHFGKKRLDLAGPLLASLFRMLFRKMTRDVYK----YMQKCVETN 425
Query: 407 R-FDLSQFIVRDSITVGLERTLSTGNF-DVKRFKMHRKGMTQVLARLSFIGTLGHMTRVS 464
R F+L+ + + IT GL +L+TGN+ D KR ++R G++QVL R +F TL H+ R +
Sbjct: 426 REFNLTLAVKSNIITNGLRYSLATGNWGDQKRSMVNRVGVSQVLNRYTFASTLSHLRRTN 485
Query: 465 PQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVTTDEEEGPLISLCY 524
+ K++ PR L + WGM+CP +TPEG+ACGLVKNL+LM++V+ P+I
Sbjct: 486 TPIGRDGKLAKPRQLHNTHWGMVCPAETPEGQACGLVKNLSLMSYVSVGSPSAPIIEFLE 545
Query: 525 CLGVEDLELLSGEELHNPNSFLVIFNGLILGKHRRPKCFADVMRKLRRAGKIGEFVSVFV 584
G+E LE + +PN+ V NG+ LG HR P + +R LRR I VS+
Sbjct: 546 EWGLETLEDYNPSA--SPNATKVFVNGVWLGVHRDPAHLTETLRSLRRRLDISAEVSIVR 603
Query: 585 NEKQRCVYIASDGGRVCRPLVIAD-------KGISRIKEHHMKELLDGVRSFD------- 630
+ +++ + + +D GR+CRPL I D +G I++ H+++L++ +D
Sbjct: 604 DIREKELRLFTDAGRICRPLFIVDNNPNSERRGELCIRKEHIQQLIEDKDRYDIDPEQRF 663
Query: 631 ---DFLREGLIEYLDVNEENNALIAL--------------YEGDATPD------------ 661
+ GLIEYLD EE +IA+ YE D
Sbjct: 664 GWTALVSSGLIEYLDAEEEETVMIAMSPEDLEASRQMQAGYEVKEELDPAQRVKPAPNPH 723
Query: 662 ---TTHIEIEPFTILGVIAGLIPYPHHNQSPRNTYQCAMGKQAMGNIAFNQLCRMDSLLY 718
TH EI P ILG++A +IP+P HNQSPRNTYQ AMGKQAMG N RMD++
Sbjct: 724 VHAWTHCEIHPAMILGILASIIPFPDHNQSPRNTYQSAMGKQAMGVYLTNYQVRMDTMAN 783
Query: 719 LLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCI 778
+L YPQ+PL TTR++E + + +L AGQNA VA++ YSGY+ ED+I+MN++S+DRG R I
Sbjct: 784 ILYYPQKPLATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSI 843
Query: 779 VVKKYTAINQKYANSTSDRILRPDRTGPGAERMQ-----ILDDDGLAAPGEIIKPNDVYI 833
+ YT +K + + RP R+ RM+ L+DDGL APG + D+ I
Sbjct: 844 FYRTYTDQEKKIGMTVMEEFERPVRS--TTLRMKHGTYDKLEDDGLIAPGTRVSGEDIII 901
Query: 834 NKESPLETRGSIMSPTGQTDSRYRSARQTYKGP--DGETCVVDRVALCSDKNGDLCIKFL 891
K +P+ + Q A++ P E+ +VD+V + +++ G +K
Sbjct: 902 GKTAPIPLDHEELGQRTQL-----HAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVR 956
Query: 892 IRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMI 951
+R TR P++GDKF+SRHGQKG G + ED PFS +GI PD+I+NPH PSRMTV ++
Sbjct: 957 MRSTRIPQIGDKFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLV 1016
Query: 952 ELLGGKAGVSCGRFHYGSAFGEPSGHAD-TVESISETLVKHGFSYNGKDMIYSGITGCPL 1010
E K G F G+ + D TVE++S+ L HGF G +++Y G TG L
Sbjct: 1017 ECQLSKVSALSG-FE-----GDATPFTDVTVEAVSKLLRSHGFQSRGFEVMYHGHTGRKL 1070
Query: 1011 QAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGGF 1057
A +F+GP YYQ+LKH+V DK+HAR GP +LTRQP EGR+R+GG
Sbjct: 1071 VAQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGL 1117
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 140 bits (352), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 112/372 (30%), Positives = 173/372 (46%), Gaps = 64/372 (17%)
Query: 741 LGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR 800
L GQN VA+M + GY+ EDAIV+++ L R F I +++Y I + +RI R
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYE-IEARDTKLGPERITR 723
Query: 801 PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKES------PLETRGSIMSPTGQTDS 854
D ++ LD++G+ G +KP D+ + + S P + S G+
Sbjct: 724 -DIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGE--- 779
Query: 855 RYRSARQT-YKGPDGETCVVDRVALCSDKNGD----------LCIKFLIRHTRRPELGDK 903
+ R + T + P GE +V V + GD ++ + R+ ++GDK
Sbjct: 780 KARDVKDTSLRVPPGEGGIV--VGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDK 837
Query: 904 FSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCG 963
++RHG KGV I+ ED P G D+I+NP G PSRM +G+++E G AG G
Sbjct: 838 LANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLG 897
Query: 964 R------------------------FHYGSAFGEPSG----------HADTVESIS---- 985
+ ++G GE G A+ + +S
Sbjct: 898 QRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKS 957
Query: 986 -ETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLT 1044
E +K F GK ++Y G TG P + I +G ++ KL HMV DKMHAR +GP ++T
Sbjct: 958 PEEQLKELFDL-GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLIT 1016
Query: 1045 RQPTEGRARNGG 1056
+QP G+A+ GG
Sbjct: 1017 QQPLGGKAQFGG 1028
Score = 66.2 bits (160), Expect = 8e-11, Method: Compositional matrix adjust.
Identities = 98/465 (21%), Positives = 187/465 (40%), Gaps = 99/465 (21%)
Query: 78 IFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKN 137
+ L F + RIG P + D CR D+TY AP+ ++ + H + ++++
Sbjct: 64 LVLDFLEYRIGDPPFSQD---------ECREKDLTYQAPLYARLQLI---HKDTGLIKED 111
Query: 138 DVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRV 197
+V +G +P+M ++ G D ++++ P G YF I
Sbjct: 112 EVFLGHLPLMTEDGSFIINGADRVIVSQIHRSP---GVYFTPDPARPGRYIAS------- 161
Query: 198 IIDTDKKGNINAXXXXXXXXXXXXXXIQME---KGKMYLLLNQFVKKIPIMVVMKAMGME 254
II K+G I +E G + + +N+ +K P++++++ +G +
Sbjct: 162 IIPLPKRG----------------PWIDLEVEASGVVTMKVNK--RKFPLVLLLRVLGYD 203
Query: 255 SDQEVVQMVGRDPRYSALLLPSI----EECANLDIYT---------QEKALEYLEGKV-- 299
+ V ++ LL ++ E A + ++T ++KAL YL G +
Sbjct: 204 QETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLAD 263
Query: 300 -KRSTFGSPPNDREGRAFSI-LRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDA 357
KR G + + L L V + F+ + F + + A +
Sbjct: 264 PKRYDLGEAGRYKAEEKLGVGLSGRTL--VRFEDGEFKDEVFLPTLRYLFALTAGVPGHE 321
Query: 358 MDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVD--IILSKP----------SRS 405
+DD D++GN+R+ G+L++ D F+ ++ + + V +++ P SR
Sbjct: 322 VDDIDHLGNRRIRTVGELMA----DQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRP 377
Query: 406 SRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP 465
L +F R ++ + T + KR R+S +G G +TR
Sbjct: 378 LEAALREFFSRSQLSQFKDETNPLSSLRHKR-------------RISALGP-GGLTRERA 423
Query: 466 QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHV 510
F+ R + + +G +CP +TPEG GL+ +LA V
Sbjct: 424 GFDV-------RDVHRTHYGRICPVETPEGANIGLITSLAAYARV 461
>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 = 140 bits (352), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 112/372 (30%), Positives = 173/372 (46%), Gaps = 64/372 (17%)
Query: 741 LGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR 800
L GQN VA+M + GY+ EDAIV+++ L R F I +++Y I + +RI R
Sbjct: 665 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYE-IEARDTKLGPERITR 723
Query: 801 PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKES------PLETRGSIMSPTGQTDS 854
D ++ LD++G+ G +KP D+ + + S P + S G+
Sbjct: 724 -DIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGE--- 779
Query: 855 RYRSARQT-YKGPDGETCVVDRVALCSDKNGD----------LCIKFLIRHTRRPELGDK 903
+ R + T + P GE +V V + GD ++ + R+ ++GDK
Sbjct: 780 KARDVKDTSLRVPPGEGGIV--VGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDK 837
Query: 904 FSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCG 963
++RHG KGV I+ ED P G D+I+NP G PSRM +G+++E G AG G
Sbjct: 838 LANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLG 897
Query: 964 R------------------------FHYGSAFGEPSG----------HADTVESIS---- 985
+ ++G GE G A+ + +S
Sbjct: 898 QRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKS 957
Query: 986 -ETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLT 1044
E +K F GK ++Y G TG P + I +G ++ KL HMV DKMHAR +GP ++T
Sbjct: 958 PEEQLKELFDL-GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLIT 1016
Query: 1045 RQPTEGRARNGG 1056
+QP G+A+ GG
Sbjct: 1017 QQPLGGKAQFGG 1028
Score = 66.2 bits (160), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 98/465 (21%), Positives = 187/465 (40%), Gaps = 99/465 (21%)
Query: 78 IFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKN 137
+ L F + RIG P + D CR D+TY AP+ ++ + H + ++++
Sbjct: 64 LVLDFLEYRIGDPPFSQD---------ECREKDLTYQAPLYARLQLI---HKDTGLIKED 111
Query: 138 DVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRV 197
+V +G +P+M ++ G D ++++ P G YF I
Sbjct: 112 EVFLGHLPLMTEDGSFIINGADRVIVSQIHRSP---GVYFTPDPARPGRYIAS------- 161
Query: 198 IIDTDKKGNINAXXXXXXXXXXXXXXIQME---KGKMYLLLNQFVKKIPIMVVMKAMGME 254
II K+G I +E G + + +N+ +K P++++++ +G +
Sbjct: 162 IIPLPKRG----------------PWIDLEVEASGVVTMKVNK--RKFPLVLLLRVLGYD 203
Query: 255 SDQEVVQMVGRDPRYSALLLPSI----EECANLDIYT---------QEKALEYLEGKV-- 299
+ V ++ LL ++ E A + ++T ++KAL YL G +
Sbjct: 204 QETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLAD 263
Query: 300 -KRSTFGSPPNDREGRAFSI-LRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDA 357
KR G + + L L V + F+ + F + + A +
Sbjct: 264 PKRYDLGEAGRYKAEEKLGVGLSGRTL--VRFEDGEFKDEVFLPTLRYLFALTAGVPGHE 321
Query: 358 MDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVD--IILSKP----------SRS 405
+DD D++GN+R+ G+L++ D F+ ++ + + V +++ P SR
Sbjct: 322 VDDIDHLGNRRIRTVGELMA----DQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRP 377
Query: 406 SRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP 465
L +F R ++ + T + KR R+S +G G +TR
Sbjct: 378 LEAALREFFSRSQLSQFKDETNPLSSLRHKR-------------RISALGP-GGLTRERA 423
Query: 466 QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHV 510
F+ R + + +G +CP +TPEG GL+ +LA V
Sbjct: 424 GFDV-------RDVHRTHYGRICPVETPEGANIGLITSLAAYARV 461
>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 = 140 bits (352), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 112/372 (30%), Positives = 173/372 (46%), Gaps = 64/372 (17%)
Query: 741 LGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR 800
L GQN VA+M + GY+ EDAIV+++ L R F I +++Y I + +RI R
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYE-IEARDTKLGPERITR 724
Query: 801 PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKES------PLETRGSIMSPTGQTDS 854
D ++ LD++G+ G +KP D+ + + S P + S G+
Sbjct: 725 -DIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGE--- 780
Query: 855 RYRSARQT-YKGPDGETCVVDRVALCSDKNGD----------LCIKFLIRHTRRPELGDK 903
+ R + T + P GE +V V + GD ++ + R+ ++GDK
Sbjct: 781 KARDVKDTSLRVPPGEGGIV--VGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDK 838
Query: 904 FSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCG 963
++RHG KGV I+ ED P G D+I+NP G PSRM +G+++E G AG G
Sbjct: 839 LANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLG 898
Query: 964 R------------------------FHYGSAFGEPSG----------HADTVESIS---- 985
+ ++G GE G A+ + +S
Sbjct: 899 QRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKS 958
Query: 986 -ETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLT 1044
E +K F GK ++Y G TG P + I +G ++ KL HMV DKMHAR +GP ++T
Sbjct: 959 PEEQLKELFDL-GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLIT 1017
Query: 1045 RQPTEGRARNGG 1056
+QP G+A+ GG
Sbjct: 1018 QQPLGGKAQFGG 1029
Score = 66.2 bits (160), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 98/465 (21%), Positives = 187/465 (40%), Gaps = 99/465 (21%)
Query: 78 IFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKN 137
+ L F + RIG P + D CR D+TY AP+ ++ + H + ++++
Sbjct: 64 LVLDFLEYRIGDPPFSQD---------ECREKDLTYQAPLYARLQLI---HKDTGLIKED 111
Query: 138 DVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRV 197
+V +G +P+M ++ G D ++++ P G YF I
Sbjct: 112 EVFLGHLPLMTEDGSFIINGADRVIVSQIHRSP---GVYFTPDPARPGRYIAS------- 161
Query: 198 IIDTDKKGNINAXXXXXXXXXXXXXXIQME---KGKMYLLLNQFVKKIPIMVVMKAMGME 254
II K+G I +E G + + +N+ +K P++++++ +G +
Sbjct: 162 IIPLPKRG----------------PWIDLEVEASGVVTMKVNK--RKFPLVLLLRVLGYD 203
Query: 255 SDQEVVQMVGRDPRYSALLLPSI----EECANLDIYT---------QEKALEYLEGKV-- 299
+ V ++ LL ++ E A + ++T ++KAL YL G +
Sbjct: 204 QETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLAD 263
Query: 300 -KRSTFGSPPNDREGRAFSI-LRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDA 357
KR G + + L L V + F+ + F + + A +
Sbjct: 264 PKRYDLGEAGRYKAEEKLGVGLSGRTL--VRFEDGEFKDEVFLPTLRYLFALTAGVPGHE 321
Query: 358 MDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVD--IILSKP----------SRS 405
+DD D++GN+R+ G+L++ D F+ ++ + + V +++ P SR
Sbjct: 322 VDDIDHLGNRRIRTVGELMA----DQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRP 377
Query: 406 SRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP 465
L +F R ++ + T + KR R+S +G G +TR
Sbjct: 378 LEAALREFFSRSQLSQFKDETNPLSSLRHKR-------------RISALGP-GGLTRERA 423
Query: 466 QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHV 510
F+ R + + +G +CP +TPEG GL+ +LA V
Sbjct: 424 GFDV-------RDVHRTHYGRICPVETPEGANIGLITSLAAYARV 461
>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 = 140 bits (352), Expect = 4e-33, Method: Compositional matrix adjust.
Identities = 112/372 (30%), Positives = 173/372 (46%), Gaps = 64/372 (17%)
Query: 741 LGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR 800
L GQN VA+M + GY+ EDAIV+++ L R F I +++Y I + +RI R
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYE-IEARDTKLGPERITR 724
Query: 801 PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKES------PLETRGSIMSPTGQTDS 854
D ++ LD++G+ G +KP D+ + + S P + S G+
Sbjct: 725 -DIPHLSEAALRDLDEEGIVRIGAEVKPGDILVGRTSFKGEQEPSPEERLLRSIFGE--- 780
Query: 855 RYRSARQT-YKGPDGETCVVDRVALCSDKNGD----------LCIKFLIRHTRRPELGDK 903
+ R + T + P GE +V V + GD ++ + R+ ++GDK
Sbjct: 781 KARDVKDTSLRVPPGEGGIV--VGRLRLRRGDPGVELKPGVREVVRVFVAQKRKLQVGDK 838
Query: 904 FSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCG 963
++RHG KGV I+ ED P G D+I+NP G PSRM +G+++E G AG G
Sbjct: 839 LANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLG 898
Query: 964 R------------------------FHYGSAFGEPSG----------HADTVESIS---- 985
+ ++G GE G A+ + +S
Sbjct: 899 QRYISPVFDGATEPEIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGLVSPGKS 958
Query: 986 -ETLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLT 1044
E +K F GK ++Y G TG P + I +G ++ KL HMV DKMHAR +GP ++T
Sbjct: 959 PEEQLKELFDL-GKVVLYDGRTGEPFEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLIT 1017
Query: 1045 RQPTEGRARNGG 1056
+QP G+A+ GG
Sbjct: 1018 QQPLGGKAQFGG 1029
Score = 66.2 bits (160), Expect = 9e-11, Method: Compositional matrix adjust.
Identities = 98/465 (21%), Positives = 187/465 (40%), Gaps = 99/465 (21%)
Query: 78 IFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKN 137
+ L F + RIG P + D CR D+TY AP+ ++ + H + ++++
Sbjct: 64 LVLDFLEYRIGDPPFSQD---------ECREKDLTYQAPLYARLQLI---HKDTGLIKED 111
Query: 138 DVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKNRV 197
+V +G +P+M ++ G D ++++ P G YF I
Sbjct: 112 EVFLGHLPLMTEDGSFIINGADRVIVSQIHRSP---GVYFTPDPARPGRYIAS------- 161
Query: 198 IIDTDKKGNINAXXXXXXXXXXXXXXIQME---KGKMYLLLNQFVKKIPIMVVMKAMGME 254
II K+G I +E G + + +N+ +K P++++++ +G +
Sbjct: 162 IIPLPKRG----------------PWIDLEVEASGVVTMKVNK--RKFPLVLLLRVLGYD 203
Query: 255 SDQEVVQMVGRDPRYSALLLPSI----EECANLDIYT---------QEKALEYLEGKV-- 299
+ V ++ LL ++ E A + ++T ++KAL YL G +
Sbjct: 204 QETLVRELSAYGDLVQGLLDEAVLAMRPEEAMVRLFTLLRPGDPPKKDKALAYLFGLLAD 263
Query: 300 -KRSTFGSPPNDREGRAFSI-LRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDA 357
KR G + + L L V + F+ + F + + A +
Sbjct: 264 PKRYDLGEAGRYKAEEKLGVGLSGRTL--VRFEDGEFKDEVFLPTLRYLFALTAGVPGHE 321
Query: 358 MDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVD--IILSKP----------SRS 405
+DD D++GN+R+ G+L++ D F+ ++ + + V +++ P SR
Sbjct: 322 VDDIDHLGNRRIRTVGELMA----DQFRVGLARLARGVRERMVMGSPDTLTPAKLVNSRP 377
Query: 406 SRFDLSQFIVRDSITVGLERTLSTGNFDVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP 465
L +F R ++ + T + KR R+S +G G +TR
Sbjct: 378 LEAALREFFSRSQLSQFKDETNPLSSLRHKR-------------RISALGP-GGLTRERA 423
Query: 466 QFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHV 510
F+ R + + +G +CP +TPEG GL+ +LA V
Sbjct: 424 GFDV-------RDVHRTHYGRICPVETPEGANIGLITSLAAYARV 461
>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 = 139 bits (351), Expect = 6e-33, Method: Compositional matrix adjust.
Identities = 110/370 (29%), Positives = 171/370 (46%), Gaps = 60/370 (16%)
Query: 741 LGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAINQKYANSTSDRILR 800
L GQN VA+M + GY+ EDAIV+++ L R F I +++Y I + +RI R
Sbjct: 666 LALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYE-IEARDTKLGPERITR 724
Query: 801 PDRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKES------PLETRGSIMSPTGQTDS 854
D ++ LD++G+ G +KP D+ + + S P + S G+
Sbjct: 725 -DIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGE--- 780
Query: 855 RYRSARQT-YKGPDGETCVVDRVALC--SDKNGDL------CIKFLIRHTRRPELGDKFS 905
+ R + T + P GE +V R D +L ++ + R+ ++GDK +
Sbjct: 781 KARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLA 840
Query: 906 SRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMTVGKMIELLGGKAGVSCGRF 965
+RHG KGV I+ ED P G D+I+NP G PSRM +G+++E G AG G+
Sbjct: 841 NRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQR 900
Query: 966 H--------------------YGSAFGEPSGHADTVE-------------------SISE 986
+ + FG+ G V+ E
Sbjct: 901 YISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPE 960
Query: 987 TLVKHGFSYNGKDMIYSGITGCPLQAYIFMGPIYYQKLKHMVLDKMHARGSGPRVMLTRQ 1046
+K F GK ++Y G TG P++ I +G ++ KL HMV DKMHAR +GP ++T+Q
Sbjct: 961 EQLKELF-LQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQ 1019
Query: 1047 PTEGRARNGG 1056
P G+A+ GG
Sbjct: 1020 PLGGKAQFGG 1029
Score = 62.4 bits (150), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 90/464 (19%), Positives = 183/464 (39%), Gaps = 97/464 (20%)
Query: 78 IFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKN 137
+ L F + R+G+P D CR D+TY AP+ ++ + H + ++++
Sbjct: 64 LVLDFLEYRLGEPPFPQD---------ECREKDLTYQAPLYARLQLI---HKDTGLIKED 111
Query: 138 DVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQE--QLSKN 195
+V +G IP+M ++ G D ++++ P G YF I L K
Sbjct: 112 EVFLGHIPLMTEDGSFIINGADRVIVSQIHRSP---GVYFTPDPARPGRYIASIIPLPKR 168
Query: 196 RVIIDTDKKGNINAXXXXXXXXXXXXXXIQMEKGKMYLLLNQFVKKIPIMVVMKAMGMES 255
ID + + N G + + +N+ +K P++++++ +G +
Sbjct: 169 GPWIDLEVEPN----------------------GVVSMKVNK--RKFPLVLLLRVLGYDQ 204
Query: 256 DQEVVQMVGRDPRYSALLLPSI----EECANLDIYT---------QEKALEYLEGKV--- 299
+ ++ L+ S+ E A + ++T ++KA+ Y+ G +
Sbjct: 205 ETLARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADP 264
Query: 300 KRSTFGSPPNDREGRAFSI-LRDVFLANVPVHNNNFRPKCFYVAVMLRRMVEAMLNKDAM 358
+R G + I L LA + F+ + F + + A + +
Sbjct: 265 RRYDLGEAGRYKAEEKLGIRLSGRTLARF--EDGEFKDEVFLPTLRYLFALTAGVPGHEV 322
Query: 359 DDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPSRSSRFDLSQFIVRDS 418
DD D++GN+R+ G+L++ D F+ ++ + + V R+
Sbjct: 323 DDIDHLGNRRIRTVGELMT----DQFRVGLARLARGV--------------------RER 358
Query: 419 ITVGLERTLSTGNF--------DVKRFKMHRKGMTQVLARLSFIGTLGHMTRVSP----Q 466
+ +G E +L+ ++ F R ++Q + + +L H R+S
Sbjct: 359 MLMGSEDSLTPAKLVNSRPLEAAIREF-FSRSQLSQFKDETNPLSSLRHKRRISALGPGG 417
Query: 467 FEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHV 510
+ R R + + +G +CP +TPEG GL+ +LA V
Sbjct: 418 LTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARV 461
>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 = 89.0 bits (219), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 61/219 (27%), Positives = 87/219 (39%), Gaps = 49/219 (22%)
Query: 887 CIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMT 946
+K + RR + GDK + RHG KGV I ED P+ E G D+++NP G PSRM
Sbjct: 1049 IVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMN 1108
Query: 947 VGKMIELLGGKAGVSCG------------------------------------------- 963
+G+++E G A G
Sbjct: 1109 IGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEE 1168
Query: 964 ------RFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMG 1017
G P I E L +G+ +Y G TG + + +G
Sbjct: 1169 VMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVG 1228
Query: 1018 PIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGG 1056
+Y KL H+V DKMHAR +G ++T+QP G+A+ GG
Sbjct: 1229 YMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGG 1267
Score = 50.4 bits (119), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 41/176 (23%), Positives = 83/176 (47%), Gaps = 29/176 (16%)
Query: 344 MLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPS 403
+++++++ K +DD D++GN+R+ G++ E+ F+ + V++ V
Sbjct: 428 VMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMA----ENQFRVGLVRVERAV------KE 477
Query: 404 RSSRFDLSQFIVRDSITVGLERTLST------GNFDVKRFKMHRKGMTQVLA--RLSFIG 455
R S DL + +D I + +S G+ + +F ++++ R+S +G
Sbjct: 478 RLSLGDLDTLMPQDMINA---KPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALG 534
Query: 456 TLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVT 511
G +TR FE R + P+ +G +CP +TPEG GL+ +L++
Sbjct: 535 P-GGLTRERAGFE-------VRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTN 582
Score = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 29/105 (27%), Positives = 51/105 (48%), Gaps = 14/105 (13%)
Query: 740 KLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAIN-QKYANSTSDRI 798
+L GQN VA M ++GY+ ED+I++++ R + ++T I+ Q+ A + D
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSE--------RVVQEDRFTTIHIQELACVSRDTK 844
Query: 799 LRP-----DRTGPGAERMQILDDDGLAAPGEIIKPNDVYINKESP 838
L P D G + LD+ G+ G + D+ + K +P
Sbjct: 845 LGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
Score = 38.9 bits (89), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 46/188 (24%), Positives = 75/188 (39%), Gaps = 45/188 (23%)
Query: 26 KSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNT------GIRKIVRANDRIVSGIDPSIF 79
K + F P+ L V L+ LDSF F+ G+ R+ I S S
Sbjct: 9 KRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNS-E 67
Query: 80 LRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYV----QGSHTEKTTME 135
L++ R+G+P V C++ +TY+AP+ V + V + ++
Sbjct: 68 LQYVSYRLGEPVFDV---------QECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIK 118
Query: 136 KNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKN 195
+ +V +G IP+M + G F+I GTE+V++ Q S
Sbjct: 119 EQEVYMGEIPLMTDN------------------------GTFVINGTERVIVSQLHRSPG 154
Query: 196 RVIIDTDK 203
V D+DK
Sbjct: 155 -VFFDSDK 161
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
Length = 1342
Score = 89.0 bits (219), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 61/219 (27%), Positives = 87/219 (39%), Gaps = 49/219 (22%)
Query: 887 CIKFLIRHTRRPELGDKFSSRHGQKGVCGTIVQQEDFPFSERGICPDLIMNPHGFPSRMT 946
+K + RR + GDK + RHG KGV I ED P+ E G D+++NP G PSRM
Sbjct: 1049 IVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMN 1108
Query: 947 VGKMIELLGGKAGVSCG------------------------------------------- 963
+G+++E G A G
Sbjct: 1109 IGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEE 1168
Query: 964 ------RFHYGSAFGEPSGHADTVESISETLVKHGFSYNGKDMIYSGITGCPLQAYIFMG 1017
G P I E L +G+ +Y G TG + + +G
Sbjct: 1169 VMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVG 1228
Query: 1018 PIYYQKLKHMVLDKMHARGSGPRVMLTRQPTEGRARNGG 1056
+Y KL H+V DKMHAR +G ++T+QP G+A+ GG
Sbjct: 1229 YMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGG 1267
Score = 52.0 bits (123), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 41/176 (23%), Positives = 84/176 (47%), Gaps = 29/176 (16%)
Query: 344 MLRRMVEAMLNKDAMDDKDYVGNKRLELSGQLVSLLFEDLFKTMISEVQKTVDIILSKPS 403
+++++++ K +DD D++GN+R+ G++ E+ F+ + V++ V
Sbjct: 428 VMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMA----ENQFRVGLVRVERAV------KE 477
Query: 404 RSSRFDLSQFIVRDSITVGLERTLST------GNFDVKRFKMHRKGMTQVLA--RLSFIG 455
R S DL + +D I + +S G+ + +F + ++++ R+S +G
Sbjct: 478 RLSLGDLDTLMPQDMINA---KPISAAVKEFFGSSQLSQFMVQNNPLSEITHKRRISALG 534
Query: 456 TLGHMTRVSPQFEKSRKVSGPRALQPSQWGMLCPCDTPEGEACGLVKNLALMTHVT 511
G +TR FE R + P+ +G +CP +TPEG GL+ +L++
Sbjct: 535 P-GGLTRERAGFE-------VRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTN 582
Score = 39.7 bits (91), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 28/105 (26%), Positives = 51/105 (48%), Gaps = 14/105 (13%)
Query: 740 KLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRCIVVKKYTAIN-QKYANSTSDRI 798
+L GQN VA M ++GY+ ED+I++++ R + ++T I+ Q+ A + D
Sbjct: 793 ELALGQNMRVAFMPWNGYNFEDSILVSE--------RVVQEDRFTTIHIQELACVSRDTK 844
Query: 799 LRPDRTGP-----GAERMQILDDDGLAAPGEIIKPNDVYINKESP 838
L P+ G + LD+ G+ G + D+ + K +P
Sbjct: 845 LGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTP 889
Score = 38.9 bits (89), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 46/188 (24%), Positives = 75/188 (39%), Gaps = 45/188 (23%)
Query: 26 KSVVDKFQLLPEFLKVRGLVKQHLDSFNYFVNT------GIRKIVRANDRIVSGIDPSIF 79
K + F P+ L V L+ LDSF F+ G+ R+ I S S
Sbjct: 9 KRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNS-E 67
Query: 80 LRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYV----QGSHTEKTTME 135
L++ R+G+P V C++ +TY+AP+ V + V + ++
Sbjct: 68 LQYVSYRLGEPVFDV---------QECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIK 118
Query: 136 KNDVVIGRIPIMLRSCRCVLYGKDEAELARLGECPLDPGGYFIIKGTEKVLLIQEQLSKN 195
+ +V +G IP+M + G F+I GTE+V++ Q S
Sbjct: 119 EQEVYMGEIPLMTDN------------------------GTFVINGTERVIVSQLHRSPG 154
Query: 196 RVIIDTDK 203
V D+DK
Sbjct: 155 -VFFDSDK 161
>pdb|3MLQ|A Chain A, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
pdb|3MLQ|B Chain B, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
pdb|3MLQ|C Chain C, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
pdb|3MLQ|D Chain D, Crystal Structure Of The Thermus Thermophilus
Transcription-Repair Coupling Factor Rna Polymerase
Interacting Domain With The Thermus Aquaticus Rna
Polymerase Beta1 Domain
Length = 188
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 40/82 (48%), Gaps = 12/82 (14%)
Query: 78 IFLRFKDVRIGQPSMTVDGVSEKLNPHMCRLSDMTYAAPILVNIEYVQGSHTEKTTMEKN 137
+ L F + RIG P + D CR D+TY AP+ ++ + H + ++++
Sbjct: 49 LVLDFLEYRIGDPPFSQD---------ECREKDLTYQAPLYARLQLI---HKDTGLIKED 96
Query: 138 DVVIGRIPIMLRSCRCVLYGKD 159
+V +G +P+M ++ G D
Sbjct: 97 EVFLGHLPLMTEDGSFIINGAD 118
>pdb|3I52|A Chain A, Ternary Complex Structure Of Leucoanthocyanidin Reductase
From Vitis Vinifera
pdb|3I5M|A Chain A, Structure Of The Apo Form Of Leucoanthocyanidin Reductase
From Vitis Vinifera
pdb|3I6I|A Chain A, Structure Of The Binary Complex Leucoanthocyanidin
Reductase - Nadph From Vitis Vinifera
pdb|3I6Q|A Chain A, Structure Of The Binary Complex Leucoanthocyanidin
Reductase-Nadph From Vitis Vinifera
Length = 346
Score = 30.0 bits (66), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 28/114 (24%), Positives = 49/114 (42%), Gaps = 13/114 (11%)
Query: 718 YLLVYPQRPLLTTRTIELVGYDKLGAGQNATVAVMSYSGYDIEDAIVMNKSSLDRGFGRC 777
Y ++P L T ++ G + A A + ++ ++D +NKS R C
Sbjct: 168 YNNIHPSEVLPPTDFFQIYGDGNVKAYFVAGTDIGKFTMKTVDDVRTLNKSVHFRPSCNC 227
Query: 778 IVVKKYTAINQKYANSTSDRILRPDRTGPGAERMQILDDDGLAAPGEIIKPNDV 831
+ + + ++ +K + RT P R+ + +DD LAA GE I P V
Sbjct: 228 LNINELASVWEK----------KIGRTLP---RVTVTEDDLLAAAGENIIPQSV 268
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.139 0.409
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 31,432,691
Number of Sequences: 62578
Number of extensions: 1349924
Number of successful extensions: 2643
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2532
Number of HSP's gapped (non-prelim): 40
length of query: 1058
length of database: 14,973,337
effective HSP length: 109
effective length of query: 949
effective length of database: 8,152,335
effective search space: 7736565915
effective search space used: 7736565915
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 57 (26.6 bits)