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= psy6965
(1764 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3H0G|A Chain A, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|M Chain M, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 1752
Score = 233 bits (594), Expect = 7e-61, Method: Compositional matrix adjust.
Identities = 111/200 (55%), Positives = 146/200 (73%), Gaps = 9/200 (4%)
Query: 1480 MEDDMFLRCIEANMLSDMTLQGIEAIGKVYM--HLPQTDSKKRIIITESGEFKAIADWLL 1537
+E+D+FL+ IE +ML ++L+G+ I +VYM H K + E G F+ +W+L
Sbjct: 1260 IEEDVFLKTIEGHMLESISLRGVPNITRVYMMEH-------KIVRQIEDGTFERADEWVL 1312
Query: 1538 ETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYR 1597
ETDG +L + ++ VD RT+SN EI Q+LGIEA R ++ KE+ V++F G YVNYR
Sbjct: 1313 ETDGINLTEAMTVEGVDATRTYSNSFVEILQILGIEATRSALLKELRNVIEFDGSYVNYR 1372
Query: 1598 HLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSE 1657
HLALLCDVMT++GHLMAITRHGINR +TGALMRCSFEETV++LMDAAA E D +G+SE
Sbjct: 1373 HLALLCDVMTSRGHLMAITRHGINRAETGALMRCSFEETVEILMDAAASGEKDDCKGISE 1432
Query: 1658 NIIMGQLPRMGTGCFDLLLD 1677
NI++GQL MGTG FD+ LD
Sbjct: 1433 NIMLGQLAPMGTGAFDIYLD 1452
Score = 45.8 bits (107), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 35/117 (29%), Positives = 67/117 (57%), Gaps = 7/117 (5%)
Query: 4 ISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRCIEA 63
++ KI F DL I+++DNA+KL++R RI+ DD K +D+++ + E+D+FL+ IE
Sbjct: 1215 VAGKIAESFERDLFTIWSEDNADKLIIRCRIIRDDDRKAEDDDNMI---EEDVFLKTIEG 1271
Query: 64 NMLSDMTLQFI----RIMNSDDSKMQDEEDAVDKMEDDMFLRCIEANMLSDMTLQFI 116
+ML ++L+ + R+ + ++ ED + D+ L N+ MT++ +
Sbjct: 1272 HMLESISLRGVPNITRVYMMEHKIVRQIEDGTFERADEWVLETDGINLTEAMTVEGV 1328
>pdb|1I3Q|A Chain A, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
pdb|1I50|A Chain A, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
pdb|1I6H|A Chain A, Rna Polymerase Ii Elongation Complex
pdb|1K83|A Chain A, Crystal Structure Of Yeast Rna Polymerase Ii Complexed With
The Inhibitor Alpha Amanitin
pdb|1NIK|A Chain A, Wild Type Rna Polymerase Ii
pdb|1NT9|A Chain A, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|A Chain A, Rna Polymerase Ii-Tfiis Complex
pdb|1R5U|A Chain A, Rna Polymerase Ii Tfiib Complex
pdb|1SFO|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex
pdb|1R9S|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Matched Nucleotide
pdb|1R9T|A Chain A, Rna Polymerase Ii Strand Separated Elongation Complex,
Mismatched Nucleotide
pdb|1TWA|A Chain A, Rna Polymerase Ii Complexed With Atp
pdb|1TWC|A Chain A, Rna Polymerase Ii Complexed With Gtp
pdb|1TWF|A Chain A, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
pdb|1TWG|A Chain A, Rna Polymerase Ii Complexed With Ctp
pdb|1TWH|A Chain A, Rna Polymerase Ii Complexed With 2'datp
pdb|1WCM|A Chain A, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|A Chain A, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|A Chain A, Complete Rna Polymerase Ii Elongation Complex With Substrate
Analogue Gmpcpp
pdb|1Y1V|A Chain A, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|A Chain A, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|A Chain A, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|A Chain A, 12-Subunit Rna Polymerase Ii
pdb|2E2H|A Chain A, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
pdb|2E2I|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dgtp
pdb|2E2J|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
Gmpcpp
pdb|2NVQ|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
2'dutp
pdb|2NVT|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
Gmpcpp
pdb|2NVX|A Chain A, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
Dutp
pdb|2NVY|A Chain A, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
pdb|2NVZ|A Chain A, Rna Polymerase Ii Elongation Complex With Utp, Updated
112006
pdb|2JA5|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex A
pdb|2JA6|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex B
pdb|2JA7|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA7|M Chain M, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex C
pdb|2JA8|A Chain A, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex D
pdb|2YU9|A Chain A, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With Utp
pdb|2R7Z|A Chain A, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|A Chain A, Elongation Complex Of Rna Polymerase Ii With Artificial Rdrp
Scaffold
pdb|2R93|A Chain A, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|A Chain A, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3CQZ|A Chain A, Crystal Structure Of 10 Subunit Rna Polymerase Ii In Complex
With The Inhibitor Alpha-Amanitin
pdb|3FKI|A Chain A, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3GTG|A Chain A, Backtracked Rna Polymerase Ii Complex With 12mer Rna
pdb|3GTJ|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer Rna
pdb|3GTK|A Chain A, Backtracked Rna Polymerase Ii Complex With 18mer Rna
pdb|3GTL|A Chain A, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
Mismatch
pdb|3GTM|A Chain A, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
pdb|3GTO|A Chain A, Backtracked Rna Polymerase Ii Complex With 15mer Rna
pdb|3GTP|A Chain A, Backtracked Rna Polymerase Ii Complex With 24mer Rna
pdb|3GTQ|A Chain A, Backtracked Rna Polymerase Ii Complex Induced By Damage
pdb|3H3V|B Chain B, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|A Chain A, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|M Chain M, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|A Chain A, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iii With A T-U
Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|A Chain A, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|A Chain A, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|A Chain A, Complete Rna Polymerase Ii Elongation Complex Iv With A T-U
Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
D
pdb|3I4N|A Chain A, 8-oxoguanine Containing Rna Polymerase Ii Elongation Complex
E
pdb|3K1F|A Chain A, Crystal Structure Of Rna Polymerase Ii In Complex With Tfiib
pdb|3K7A|A Chain A, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
pdb|3M3Y|A Chain A, Rna Polymerase Ii Elongation Complex C
pdb|3M4O|A Chain A, Rna Polymerase Ii Elongation Complex B
pdb|3PO2|A Chain A, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|A Chain A, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|A Chain A, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3RZD|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
pdb|3RZO|A Chain A, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
pdb|3S14|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
pdb|3S15|A Chain A, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
pdb|3S16|A Chain A, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
pdb|3S17|A Chain A, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
pdb|3S1M|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 1)
pdb|3S1N|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
(Variant 2)
pdb|3S1Q|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Atp
pdb|3S1R|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
Rna Soaked With Gtp
pdb|3S2D|A Chain A, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
Containing A 5br- U
pdb|3S2H|A Chain A, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
Containing A 2[prime]-Iodo Atp
pdb|4BBR|A Chain A, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|A Chain A, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 1733
Score = 204 bits (518), Expect = 5e-52, Method: Compositional matrix adjust.
Identities = 100/205 (48%), Positives = 143/205 (69%), Gaps = 5/205 (2%)
Query: 1475 DAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIAD 1534
DA + E+D L+ IE ML ++TL+G+E I +V M + D K + + +GE+ +
Sbjct: 1249 DAETEAEEDHMLKKIENTMLENITLRGVENIERVVMM--KYDRK---VPSPTGEYVKEPE 1303
Query: 1535 WLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYV 1594
W+LETDG +L +V++ +DP R ++N +I +VLGIEA R ++ KE+ V+ G YV
Sbjct: 1304 WVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYV 1363
Query: 1595 NYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRG 1654
NYRH+ALL DVMT +G L ++TRHG NR +TGALMRCSFEETV++L +A A AE D RG
Sbjct: 1364 NYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRG 1423
Query: 1655 VSENIIMGQLPRMGTGCFDLLLDAE 1679
VSEN+I+GQ+ +GTG FD+++D E
Sbjct: 1424 VSENVILGQMAPIGTGAFDVMIDEE 1448
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 1 MEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRC 60
M + E+I F +DL I+++DN EKL++R R++ DA + E+D L+
Sbjct: 1209 MGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSL------DAETEAEEDHMLKK 1262
Query: 61 IEANMLSDMTLQFI 74
IE ML ++TL+ +
Sbjct: 1263 IENTMLENITLRGV 1276
>pdb|4A3C|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|A Chain A, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|A Chain A, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|A Chain A, Rna Polymerase Ii Elongation Complex Containing A Cpd Lesion
Length = 1732
Score = 204 bits (518), Expect = 5e-52, Method: Compositional matrix adjust.
Identities = 100/205 (48%), Positives = 143/205 (69%), Gaps = 5/205 (2%)
Query: 1475 DAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIAD 1534
DA + E+D L+ IE ML ++TL+G+E I +V M + D K + + +GE+ +
Sbjct: 1249 DAETEAEEDHMLKKIENTMLENITLRGVENIERVVMM--KYDRK---VPSPTGEYVKEPE 1303
Query: 1535 WLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYV 1594
W+LETDG +L +V++ +DP R ++N +I +VLGIEA R ++ KE+ V+ G YV
Sbjct: 1304 WVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYV 1363
Query: 1595 NYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRG 1654
NYRH+ALL DVMT +G L ++TRHG NR +TGALMRCSFEETV++L +A A AE D RG
Sbjct: 1364 NYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRG 1423
Query: 1655 VSENIIMGQLPRMGTGCFDLLLDAE 1679
VSEN+I+GQ+ +GTG FD+++D E
Sbjct: 1424 VSENVILGQMAPIGTGAFDVMIDEE 1448
Score = 42.4 bits (98), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 1 MEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRC 60
M + E+I F +DL I+++DN EKL++R R++ DA + E+D L+
Sbjct: 1209 MGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSL------DAETEAEEDHMLKK 1262
Query: 61 IEANMLSDMTLQFI 74
IE ML ++TL+ +
Sbjct: 1263 IENTMLENITLRGV 1276
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 203 bits (517), Expect = 5e-52, Method: Compositional matrix adjust.
Identities = 100/205 (48%), Positives = 143/205 (69%), Gaps = 5/205 (2%)
Query: 1475 DAVDKMEDDMFLRCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITESGEFKAIAD 1534
DA + E+D L+ IE ML ++TL+G+E I +V M + D K + + +GE+ +
Sbjct: 1249 DAETEAEEDHMLKKIENTMLENITLRGVENIERVVMM--KYDRK---VPSPTGEYVKEPE 1303
Query: 1535 WLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYV 1594
W+LETDG +L +V++ +DP R ++N +I +VLGIEA R ++ KE+ V+ G YV
Sbjct: 1304 WVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYV 1363
Query: 1595 NYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRG 1654
NYRH+ALL DVMT +G L ++TRHG NR +TGALMRCSFEETV++L +A A AE D RG
Sbjct: 1364 NYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRG 1423
Query: 1655 VSENIIMGQLPRMGTGCFDLLLDAE 1679
VSEN+I+GQ+ +GTG FD+++D E
Sbjct: 1424 VSENVILGQMAPIGTGAFDVMIDEE 1448
Score = 42.7 bits (99), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 6/74 (8%)
Query: 1 MEAISEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDDSKMQDEEDAVDKMEDDMFLRC 60
M + E+I F +DL I+++DN EKL++R R++ DA + E+D L+
Sbjct: 1209 MGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSL------DAETEAEEDHMLKK 1262
Query: 61 IEANMLSDMTLQFI 74
IE ML ++TL+ +
Sbjct: 1263 IENTMLENITLRGV 1276
>pdb|2WAQ|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|C Chain C, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|Y Chain Y, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 395
Score = 104 bits (259), Expect = 5e-22, Method: Composition-based stats.
Identities = 63/158 (39%), Positives = 98/158 (62%), Gaps = 5/158 (3%)
Query: 1519 KRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKS 1578
KR I+ + G+ ++++ TDG++L VLS + VD + +N+I EI +V GIEA R+
Sbjct: 238 KRAIVQKKGD-----EYIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREI 292
Query: 1579 VEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVD 1638
+ +E++ VL GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV
Sbjct: 293 IIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVK 352
Query: 1639 VLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLL 1676
L+DAAA + + +GV ENII+G ++GTG +L +
Sbjct: 353 HLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 390
>pdb|2Y0S|C Chain C, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|Y Chain Y, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|C Chain C, Rnap At 3.2ang
pdb|4B1O|C Chain C, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|Y Chain Y, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 395
Score = 104 bits (259), Expect = 5e-22, Method: Composition-based stats.
Identities = 63/158 (39%), Positives = 98/158 (62%), Gaps = 5/158 (3%)
Query: 1519 KRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKS 1578
KR I+ + G+ ++++ TDG++L VLS + VD + +N+I EI +V GIEA R+
Sbjct: 238 KRAIVQKKGD-----EYIILTDGSNLSGVLSVKGVDIAKVETNNIREIEEVFGIEAAREI 292
Query: 1579 VEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVD 1638
+ +E++ VL GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV
Sbjct: 293 IIREISKVLAEQGLDVDMRHILLVADVMTRTGVVRQIGRHGVTGEKNSVLARAAFEVTVK 352
Query: 1639 VLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLL 1676
L+DAAA + + +GV ENII+G ++GTG +L +
Sbjct: 353 HLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 390
>pdb|2PMZ|C Chain C, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|G Chain G, Archaeal Rna Polymerase From Sulfolobus Solfataricus
Length = 392
Score = 103 bits (257), Expect = 8e-22, Method: Composition-based stats.
Identities = 63/158 (39%), Positives = 98/158 (62%), Gaps = 5/158 (3%)
Query: 1519 KRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKS 1578
KR I+ + G+ ++++ TDG++L VLS + VD + +N+I EI +V GIEA R+
Sbjct: 235 KRAIVQKKGD-----EYIILTDGSNLSGVLSVKGVDVAKVETNNIREIEEVFGIEAAREI 289
Query: 1579 VEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVD 1638
+ +E++ VL GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV
Sbjct: 290 IIREISKVLAEQGLDVDIRHILLIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVK 349
Query: 1639 VLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLL 1676
L+DAAA + + +GV ENII+G ++GTG +L +
Sbjct: 350 HLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 387
>pdb|3HKZ|C Chain C, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|M Chain M, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 395
Score = 103 bits (257), Expect = 9e-22, Method: Composition-based stats.
Identities = 63/158 (39%), Positives = 98/158 (62%), Gaps = 5/158 (3%)
Query: 1519 KRIIITESGEFKAIADWLLETDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKS 1578
KR I+ + G+ ++++ TDG++L VLS + VD + +N+I EI +V GIEA R+
Sbjct: 238 KRAIVQKKGD-----EYIILTDGSNLSGVLSVKGVDVAKVETNNIREIEEVFGIEAAREI 292
Query: 1579 VEKEMNTVLQFYGLYVNYRHLALLCDVMTAKGHLMAITRHGINRQDTGALMRCSFEETVD 1638
+ +E++ VL GL V+ RH+ L+ DVMT G + I RHG+ + L R +FE TV
Sbjct: 293 IIREISKVLAEQGLDVDIRHILLIADVMTRTGIVRQIGRHGVTGEKNSVLARAAFEVTVK 352
Query: 1639 VLMDAAAHAEADPMRGVSENIIMGQLPRMGTGCFDLLL 1676
L+DAAA + + +GV ENII+G ++GTG +L +
Sbjct: 353 HLLDAAARGDVEEFKGVVENIIIGHPIKLGTGMVELTM 390
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 43.9 bits (102), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 56/230 (24%), Positives = 98/230 (42%), Gaps = 62/230 (26%)
Query: 1487 RCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITE---SGEFKA-IADW----LLE 1538
R E +L++++ GI + GK +T K+R++IT S ++ I W + E
Sbjct: 1149 RPKEPAILAEIS--GIVSFGK------ETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE 1200
Query: 1539 TDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRH 1598
+ V+S+ P +I ++ G+ AV + + E+ V + G+ +N +H
Sbjct: 1201 GERVERGDVISDGPEAP--------HDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKH 1252
Query: 1599 LALLCDVMTAK-------------GHLMAITRHGI-NRQ-----DTGA------------ 1627
+ ++ M K G + +R I NR+ GA
Sbjct: 1253 IEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKA 1312
Query: 1628 -------LMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
+ SF+ET VL +AA + D +RG+ EN+I+G+L GTG
Sbjct: 1313 SLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
>pdb|3LU0|D Chain D, Molecular Model Of Escherichia Coli Core Rna Polymerase
pdb|4IGC|D Chain D, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
pdb|4IGC|I Chain I, X-ray Crystal Structure Of Escherichia Coli Sigma70
Holoenzyme
Length = 1407
Score = 43.9 bits (102), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 56/230 (24%), Positives = 98/230 (42%), Gaps = 62/230 (26%)
Query: 1487 RCIEANMLSDMTLQGIEAIGKVYMHLPQTDSKKRIIITE---SGEFKA-IADW----LLE 1538
R E +L++++ GI + GK +T K+R++IT S ++ I W + E
Sbjct: 1149 RPKEPAILAEIS--GIVSFGK------ETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFE 1200
Query: 1539 TDGTSLMKVLSERDVDPVRTFSNDICEIFQVLGIEAVRKSVEKEMNTVLQFYGLYVNYRH 1598
+ V+S+ P +I ++ G+ AV + + E+ V + G+ +N +H
Sbjct: 1201 GERVERGDVISDGPEAP--------HDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKH 1252
Query: 1599 LALLCDVMTAK-------------GHLMAITRHGI-NRQ-----DTGA------------ 1627
+ ++ M K G + +R I NR+ GA
Sbjct: 1253 IEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKA 1312
Query: 1628 -------LMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
+ SF+ET VL +AA + D +RG+ EN+I+G+L GTG
Sbjct: 1313 SLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTG 1362
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 40.4 bits (93), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 1612 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1161 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1217
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For Structural
Studies
Length = 1233
Score = 40.4 bits (93), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 1612 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1130 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1186
>pdb|1HQM|D Chain D, Crystal Structure Of Thermus Aquaticus Core Rna Polymerase-
Includes Complete Structure With Side-Chains (Except For
Disordered Regions)-Further Refined From Original
Deposition-Contains Additional Sequence Information
Length = 1265
Score = 40.4 bits (93), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 1612 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1162 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1218
>pdb|4GZY|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
pdb|4GZZ|D Chain D, Crystal Structures Of Bacterial Rna Polymerase Paused
Elongation Complexes
Length = 1534
Score = 40.4 bits (93), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 1612 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1421 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
>pdb|1IW7|D Chain D, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1IW7|N Chain N, Crystal Structure Of The Rna Polymerase Holoenzyme From
Thermus Thermophilus At 2.6a Resolution
pdb|1SMY|D Chain D, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1SMY|N Chain N, Structural Basis For Transcription Regulation By Alarmone
Ppgpp
pdb|1ZYR|D Chain D, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|1ZYR|N Chain N, Structure Of Thermus Thermophilus Rna Polymerase Holoenzyme
In Complex With The Antibiotic Streptolydigin
pdb|2A68|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A68|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifabutin
pdb|2A69|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A69|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Rifapentin
pdb|2A6E|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6E|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme
pdb|2A6H|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2A6H|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Sterptolydigin
pdb|2CW0|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2CW0|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme At 3.3 Angstroms Resolution
pdb|2BE5|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2BE5|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Inhibitor Tagetitoxin
pdb|2O5I|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5I|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Elongation Complex
pdb|2O5J|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2O5J|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog
pdb|2PPB|D Chain D, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|2PPB|N Chain N, Crystal Structure Of The T. Thermophilus Rnap Polymerase
Elongation Complex With The Ntp Substrate Analog And
Antibiotic Streptolydigin
pdb|3DXJ|D Chain D, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3DXJ|N Chain N, Crystal Structure Of Thermus Thermophilus Rna Polymerase
Holoenzyme In Complex With The Antibiotic Myxopyronin
pdb|3EQL|D Chain D, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3EQL|N Chain N, Crystal Structure Of The T. Thermophilus Rna Polymerase
Holoenzyme In Complex With Antibiotic Myxopyronin
pdb|3AOH|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOH|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 1)
pdb|3AOI|D Chain D, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|I Chain I, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|3AOI|N Chain N, Rna Polymerase-Gfh1 Complex (Crystal Type 2)
pdb|4G7H|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7H|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex
pdb|4G7O|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7O|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 2 Nt Of Rna
pdb|4G7Z|D Chain D, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
pdb|4G7Z|N Chain N, Crystal Structure Of Thermus Thermophilus Transcription
Initiation Complex Containing 5-Bru At Template-Strand
Position +1
Length = 1524
Score = 40.4 bits (93), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 1612 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1421 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
>pdb|1L9U|D Chain D, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9U|M Chain M, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
Resolution
pdb|1L9Z|D Chain D, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
Promoter Dna Complex At 6.5 A Resolution
pdb|1YNJ|D Chain D, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNJ|J Chain J, Taq Rna Polymerase-Sorangicin Complex
pdb|1YNN|D Chain D, Taq Rna Polymerase-rifampicin Complex
pdb|1YNN|J Chain J, Taq Rna Polymerase-rifampicin Complex
Length = 1524
Score = 40.0 bits (92), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 34/59 (57%), Gaps = 2/59 (3%)
Query: 1612 LMAITRHGINRQDTGALMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQLPRMGTG 1670
LM +T+ ++ + L SF+ T VL +AA + D + G+ EN+I+G+L GTG
Sbjct: 1421 LMGVTKSALSTKSW--LSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTG 1477
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP CLAMP
DOMAIN
Length = 436
Score = 36.6 bits (83), Expect = 0.13, Method: Composition-based stats.
Identities = 17/36 (47%), Positives = 23/36 (63%)
Query: 1628 LMRCSFEETVDVLMDAAAHAEADPMRGVSENIIMGQ 1663
L R +FE TV L +AA E D + GV EN+++GQ
Sbjct: 394 LARAAFEITVQHLFEAAEKGEVDNLNGVIENVLIGQ 429
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 0.133 0.364
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 43,522,733
Number of Sequences: 62578
Number of extensions: 1624638
Number of successful extensions: 4284
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 17
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 4218
Number of HSP's gapped (non-prelim): 48
length of query: 1764
length of database: 14,973,337
effective HSP length: 113
effective length of query: 1651
effective length of database: 7,902,023
effective search space: 13046239973
effective search space used: 13046239973
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: 59 (27.3 bits)