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= 014847
(417 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 160 bits (405), Expect = 1e-39, Method: Compositional matrix adjust.
Identities = 147/506 (29%), Positives = 218/506 (43%), Gaps = 127/506 (25%)
Query: 2 SFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRP 61
S +LG++ IIP + + YQS QA+G TN N+R+DT+ L+YPQ+P
Sbjct: 746 SMILGVAASIIPFPDHNQSPRN--TYQSAM-GKQAMGVFLTNYNVRMDTMANILYYPQKP 802
Query: 62 LFWILISDCLG--------------------RPEDSLVMNQASLECGVFRSESYKAEVDN 101
L + L EDS++MNQ+S++ G+FRS +++ +D
Sbjct: 803 LGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQ 862
Query: 102 KD------IQVKSRP----------------SDDMLNFGKIQSKSGDIVIGKYAEIGADH 139
+ + +P DD L ++ D++IGK I D
Sbjct: 863 EKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDE 922
Query: 140 ---------------SIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGD 184
S L+ TE G+V +VL+++N DG F V +R + +GD
Sbjct: 923 EELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTT----KIPQIGD 978
Query: 185 KFSSMHGQKGVLGFL---EQTP-----------------------AQLLEAALGK-GACD 217
KF+S HGQKG +G E P A L+E L K A
Sbjct: 979 KFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALS 1038
Query: 218 GLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIA 277
G A+PF T +S+LL G ++ G ++ + L
Sbjct: 1039 GNEGDASPFTDIT--------VEGISKLLREHGYQSRGFEVMYNGHTGKKLM-------- 1082
Query: 278 FICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCD 337
+ IF T+YQ+ HM +DK+ R G Q LT +PV R R GG+ FGEM+ D
Sbjct: 1083 ------AQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERD 1136
Query: 338 CLIAHGASGNLHERLKCKNVA------------NVIQRVVGGPY-CRICNSADDIIKANV 384
C+IAHGA+ L ERL + A VI ++ + C+ C++ DI + ++
Sbjct: 1137 CMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHI 1196
Query: 385 PYGAKLLSQELSFSMGITLKFDTQLS 410
PY AKLL QEL +M IT + T S
Sbjct: 1197 PYAAKLLFQEL-MAMNITPRLYTDRS 1221
>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 = 154 bits (388), Expect = 1e-37, Method: Compositional matrix adjust.
Identities = 146/503 (29%), Positives = 207/503 (41%), Gaps = 126/503 (25%)
Query: 2 SFLLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRP 61
+ +LG+ IIP + + YQS QA+G TN +R+DT+ L+YPQ+P
Sbjct: 735 AMILGILASIIPFPDHNQSPRN--TYQS-AMGKQAMGVYLTNYQVRMDTMANILYYPQKP 791
Query: 62 LFWILISDCLG--------------------RPEDSLVMNQASLECGVFRSESYKAEVDN 101
L + L EDS++MNQAS++ G+FRS Y+ D
Sbjct: 792 LATTRSMEYLKFRELPAGQNAIVAILCYSGYNQEDSIIMNQASIDRGLFRSIFYRTYTDQ 851
Query: 102 KD------IQVKSRP----------------SDDMLNFGKIQSKSGDIVIGKYAEIGADH 139
+ ++ RP DD L + DI+IGK A I DH
Sbjct: 852 EKKIGMTVMEEFERPVRSTTLRMKHGTYDKLEDDGLIAPGTRVSGEDIIIGKTAPIPLDH 911
Query: 140 ---------------SIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGD 184
S L+ TE G+V +V++++N +G F V +R + +GD
Sbjct: 912 EELGQRTQLHAKRDVSTPLRSTESGIVDQVMVTTNQEGLKFVKVRMRST----RIPQIGD 967
Query: 185 KFSSMHGQKGVLGFL--------------------------EQTPAQLLEAALGK-GACD 217
KF+S HGQKG +G T A L+E L K A
Sbjct: 968 KFASRHGQKGTIGMTYRHEDMPFSAQGIVPDIIINPHAIPSRMTVAHLVECQLSKVSALS 1027
Query: 218 GLMSYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIA 277
G ATPF T VS+LL G ++ G ++ + L
Sbjct: 1028 GFEGDATPFTDVTVEA--------VSKLLRSHGFQSRGFEVMYHGHTGRKLV-------- 1071
Query: 278 FICLVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCD 337
+ +F T+YQ+ H+ +DK+ R G Q LT +PV R R GG+ FGEM+ D
Sbjct: 1072 ------AQVFLGPTYYQRLKHLVDDKIHARARGPVQILTRQPVEGRSRDGGLRFGEMERD 1125
Query: 338 CLIAHGASGNLHERL-KCKNVANVIQRVVGGPY-----------CRICNSADDIIKANVP 385
C I+HG S L ERL C + VI + G CR C + + +P
Sbjct: 1126 CQISHGCSSVLRERLFDCSDAYRVIVCDICGLIAIASYKKDSYECRSCQNRTRFSQVYLP 1185
Query: 386 YGAKLLSQELSFSMGITLKFDTQ 408
Y AKLL QEL SM I + T+
Sbjct: 1186 YAAKLLFQEL-MSMNIAPRLFTK 1207
>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 = 134 bits (338), Expect = 8e-32, Method: Compositional matrix adjust.
Identities = 136/497 (27%), Positives = 199/497 (40%), Gaps = 125/497 (25%)
Query: 4 LLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLF 63
+LG++ IIP + + YQS + QA+G N +R DT L YPQRPL
Sbjct: 650 ILGITASIIPYPEHNQSPRN--TYQSA-MAKQALGLYAANYQLRTDTRAHLLHYPQRPLV 706
Query: 64 WILISDCLG---RP-----------------EDSLVMNQASLECGVFRS--------ESY 95
D +G RP EDS++MN++S+E G++RS E
Sbjct: 707 QTRALDIIGYTNRPAGNNAILAVISFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEV 766
Query: 96 KAEVDNKDIQVKSRP--------------SDDMLNFGKIQSKSGDIVIGKYA-------- 133
K +D V P D+ + +++ K GD++IGK +
Sbjct: 767 KYPGGQEDKIVMPEPGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEF 826
Query: 134 ------EIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFS 187
+ D SI +H E G+V VL++ +G V +R + +GDKF+
Sbjct: 827 KELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRD----LRIPSIGDKFA 882
Query: 188 SMHGQKGVLGFL--------------------------EQTPAQLLEAALGK-GACDGLM 220
S HGQKGV+G L T Q++E GK A G +
Sbjct: 883 SRHGQKGVIGMLIPQVDMPYTVKGVVPDVILNPHALPSRMTLGQIMEGIAGKYAALSGNI 942
Query: 221 SYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFIC 280
ATPF +++ + QL N I K+ +L E D
Sbjct: 943 VDATPF-----------YKTPIEQLQNE----------ILKYGYLPDATEVTYDGRTG-Q 980
Query: 281 LVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLI 340
++S I+ + +YQ+ HM DK+ R G Q LT +P R R GG+ FGEM+ DCLI
Sbjct: 981 KIKSRIYFGVVYYQKLHHMVADKIHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLI 1040
Query: 341 AHGASGNLHERLKCKNVANVI------------QRVVGGPYCRICNSADDIIKANVPYGA 388
G + L +RL + I + C I ++ V Y
Sbjct: 1041 GFGTAMLLKDRLLDNSDRTTIYVCDQCGYIGWYDKNKNKYVCPIHGDKSNLFPVTVSYAF 1100
Query: 389 KLLSQELSFSMGITLKF 405
KLL QEL SM I+ +
Sbjct: 1101 KLLIQEL-MSMIISPRL 1116
>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 = 129 bits (323), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 134/497 (26%), Positives = 199/497 (40%), Gaps = 125/497 (25%)
Query: 4 LLGLSCGIIPSHLQTMTMQGWVLYQSQKHSPQAIGFPTTNPNIRVDTLLQQLFYPQRPLF 63
+LG++ IIP + + YQS + QA+G N +R DT L YPQRPL
Sbjct: 647 ILGITASIIPYPEHNQSPRN--TYQSA-MAKQALGLYAANYQLRTDTRAHLLHYPQRPLV 703
Query: 64 WILISDCLG---RP-----------------EDSLVMNQASLECGVFRS--------ESY 95
D +G RP EDS++MN++S+E G++RS E
Sbjct: 704 QTRALDIIGYTNRPAGNNAILAVMSFTGYNMEDSIIMNRSSVERGMYRSTFFRLYSTEEV 763
Query: 96 KAEVDNKDIQVKSRP--------------SDDMLNFGKIQSKSGDIVIGKYA-------- 133
K +D V D+ + +++ K GD++IGK +
Sbjct: 764 KYPGGQEDKIVMPEAGVRGYKGKEYYRLLEDNGVVSPEVEVKGGDVLIGKVSPPRFLQEF 823
Query: 134 ------EIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQSVNMVHSACLGDKFS 187
+ D SI +H E G+V VL++ +G V +R + +GDKF+
Sbjct: 824 KELSPEQAKRDTSIVTRHGEMGIVDLVLITETAEGNKLVKVRVRD----LRIPTIGDKFA 879
Query: 188 SMHGQKGVLGFL--------------------------EQTPAQLLEAALGK-GACDGLM 220
S HGQKGV+G L T Q++E GK A G +
Sbjct: 880 SRHGQKGVIGMLIPQVDMPYTVKGVVPDIILNPHALPSRMTLGQIMEGIAGKYAALSGNI 939
Query: 221 SYATPFATSTGGVITEQHQSFVSQLLNCIGARNSGITFIFKHYFLFCLFECPMDWIAFIC 280
ATPF +++ + QL N I ++ +L E D
Sbjct: 940 VDATPF-----------YKTPIEQLQNE----------ILRYGYLPDATEVVYDGRTG-Q 977
Query: 281 LVRSLIFTWITFYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLI 340
++S I+ + +YQ+ HM DK+ R G Q LT +P R R GG+ FGEM+ DCLI
Sbjct: 978 KIKSRIYFGVVYYQKLHHMVADKLHARARGPVQILTRQPTEGRAREGGLRFGEMERDCLI 1037
Query: 341 AHGASGNLHERLKCKNVANVI------------QRVVGGPYCRICNSADDIIKANVPYGA 388
G + L +RL + +I + C I ++ V Y
Sbjct: 1038 GFGTAMLLKDRLLDNSDRTMIYVCDQCGYIGWYDKNKNKYVCPIHGDKSNLFPVTVSYAF 1097
Query: 389 KLLSQELSFSMGITLKF 405
KLL QEL SM I+ +
Sbjct: 1098 KLLIQEL-MSMIISPRL 1113
>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 = 57.0 bits (136), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 75/324 (23%), Positives = 129/324 (39%), Gaps = 64/324 (19%)
Query: 128 VIGKYAEIGADHSIKLKHTERGLVLK-VLLSSNDDG---KNFAVVSIRQSVNMVHSACLG 183
+ G+ A D S+++ E G+V++ V L D G K +R V +G
Sbjct: 777 IFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVG 836
Query: 184 DKFSSMHGQKGVLGFLEQTPAQLLEAALGKGACDGLMSYATPFATSTGGVITEQH----- 238
DK ++ HG KGV+ + P + + D +++ + G I E H
Sbjct: 837 DKLANRHGNKGVVAKI--LPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAG 894
Query: 239 ----QSFVSQLLNCIGARNSGITFI----FKHYF-------------------------L 265
Q ++S + + GA+ I + F+ YF L
Sbjct: 895 YFLGQRYISPIFD--GAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGL 952
Query: 266 FCLFECPMDWIAFICL--------------VRSLIFTWITFYQQFIHMSEDKVKFRNTGS 311
+ P + + + L + I F + HM EDK+ R+TG
Sbjct: 953 VTPGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGP 1012
Query: 312 FQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKNVANVIQRVVGGPYCR 371
+ +T +P+ + +FGG FGEM+ L A+GA+ L E L K+ ++ R Y
Sbjct: 1013 YSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKS-DDIEGR--NAAYEA 1069
Query: 372 ICNSADDIIKANVPYGAKLLSQEL 395
I +D+ + +VP ++L +EL
Sbjct: 1070 IIK-GEDVPEPSVPESFRVLVKEL 1092
>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 = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 35/104 (33%), Positives = 57/104 (54%), Gaps = 4/104 (3%)
Query: 292 FYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHER 351
F + HM EDK+ R+TG + +T +P+ + +FGG FGEM+ L A+GA+ L E
Sbjct: 993 FIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEM 1052
Query: 352 LKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQEL 395
L K+ ++ R Y I +D+ + +VP ++L +EL
Sbjct: 1053 LTIKS-DDIEGR--NAAYQAIIK-GEDVPEPSVPESFRVLVKEL 1092
>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 = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 35/104 (33%), Positives = 57/104 (54%), Gaps = 4/104 (3%)
Query: 292 FYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHER 351
F + HM EDK+ R+TG + +T +P+ + +FGG FGEM+ L A+GA+ L E
Sbjct: 993 FIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEM 1052
Query: 352 LKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQEL 395
L K+ ++ R Y I +D+ + +VP ++L +EL
Sbjct: 1053 LTIKS-DDIEGR--NAAYQAIIK-GEDVPEPSVPESFRVLVKEL 1092
>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 = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 35/104 (33%), Positives = 57/104 (54%), Gaps = 4/104 (3%)
Query: 292 FYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHER 351
F + HM EDK+ R+TG + +T +P+ + +FGG FGEM+ L A+GA+ L E
Sbjct: 992 FIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEM 1051
Query: 352 LKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQEL 395
L K+ ++ R Y I +D+ + +VP ++L +EL
Sbjct: 1052 LTIKS-DDIEGR--NAAYQAIIK-GEDVPEPSVPESFRVLVKEL 1091
>pdb|1I6V|C Chain C, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1118
Score = 55.5 bits (132), Expect = 5e-08, Method: Compositional matrix adjust.
Identities = 35/104 (33%), Positives = 57/104 (54%), Gaps = 4/104 (3%)
Query: 292 FYQQFIHMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHER 351
F + HM EDK+ R+TG + +T +P+ + +FGG FGEM+ L A+GA+ L E
Sbjct: 992 FIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEM 1051
Query: 352 LKCKNVANVIQRVVGGPYCRICNSADDIIKANVPYGAKLLSQEL 395
L K+ ++ R Y I +D+ + +VP ++L +EL
Sbjct: 1052 LTIKS-DDIEGR--NAAYQAIIK-GEDVPEPSVPESFRVLVKEL 1091
>pdb|3LU0|C Chain C, Molecular Model Of Escherichia Coli Core Rna Polymerase
Length = 1342
Score = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 38/59 (64%)
Query: 298 HMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKN 356
H+ +DK+ R+TGS+ +T +P+ + +FGG FGEM+ L A+GA+ L E L K+
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295
>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 = 50.4 bits (119), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/59 (40%), Positives = 38/59 (64%)
Query: 298 HMSEDKVKFRNTGSFQPLTGRPVADRKRFGGIEFGEMKCDCLIAHGASGNLHERLKCKN 356
H+ +DK+ R+TGS+ +T +P+ + +FGG FGEM+ L A+GA+ L E L K+
Sbjct: 1237 HLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKS 1295
>pdb|2OGS|A Chain A, Crystal Structure Of The Geobacillus Stearothermophilus
Carboxylesterase Est55 At Ph 6.2
Length = 498
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 161 DGKNFA------VVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPA 204
DG FA VV+I +N+ LGD F + Q G LG L+Q A
Sbjct: 121 DGTAFAKHGDVVVVTINYRMNVFGFLHLGDSFGEAYAQAGNLGILDQVAA 170
>pdb|2OGT|A Chain A, Crystal Structure Of The Geobacillus Stearothermophilus
Carboxylesterase Est55 At Ph 6.8
Length = 498
Score = 30.4 bits (67), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 24/50 (48%), Gaps = 6/50 (12%)
Query: 161 DGKNFA------VVSIRQSVNMVHSACLGDKFSSMHGQKGVLGFLEQTPA 204
DG FA VV+I +N+ LGD F + Q G LG L+Q A
Sbjct: 121 DGTAFAKHGDVVVVTINYRMNVFGFLHLGDSFGEAYAQAGNLGILDQVAA 170
>pdb|3PMP|A Chain A, Crystal Structure Of Cyclophilin A From Moniliophthora
Perniciosa In Complex With Cyclosporin A
pdb|3PMP|B Chain B, Crystal Structure Of Cyclophilin A From Moniliophthora
Perniciosa In Complex With Cyclosporin A
Length = 164
Score = 28.5 bits (62), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 132 YAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQS 173
Y E AD + ++KHT+ GL+ +N +G F + ++ S
Sbjct: 78 YGEKFADENFQVKHTKPGLLSMANAGANTNGSQFFITTVPTS 119
>pdb|3O7T|A Chain A, Crystal Structure Of Cyclophilin A From Moniliophthora
Perniciosa
Length = 164
Score = 28.5 bits (62), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 13/42 (30%), Positives = 23/42 (54%)
Query: 132 YAEIGADHSIKLKHTERGLVLKVLLSSNDDGKNFAVVSIRQS 173
Y E AD + ++KHT+ GL+ +N +G F + ++ S
Sbjct: 79 YGEKFADENFQVKHTKPGLLSMANAGANTNGSQFFITTVPTS 120
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
0.323 0.138 0.420
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,082,362
Number of Sequences: 62578
Number of extensions: 489491
Number of successful extensions: 1024
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 982
Number of HSP's gapped (non-prelim): 27
length of query: 417
length of database: 14,973,337
effective HSP length: 101
effective length of query: 316
effective length of database: 8,652,959
effective search space: 2734335044
effective search space used: 2734335044
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)