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= 000291
(1714 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 = 184 bits (468), Expect = 3e-46, Method: Compositional matrix adjust.
Identities = 169/638 (26%), Positives = 282/638 (44%), Gaps = 71/638 (11%)
Query: 162 DGVSTMSSDLSIAMLKKVLKQVEIIRSSRSGTPNFESQEVESNDLQLAVGQYL--EVRGT 219
DG S DL+ + + + R + G P E E LQ V Y+ E+ G
Sbjct: 259 DGTSRGEDDLTHKLSDIIKANANVRRCEQEGAPAHIVSEYEQL-LQFHVATYMDNEIAGQ 317
Query: 220 AKSSRDVDARFGVSQDPNSTTKAWLE----KMRTLFIRKGSGFSSRSVITGDAYKRVNEI 275
++ + S P + +A L+ ++R + K FS+R+VITGD ++E+
Sbjct: 318 PQALQK-------SGRPLKSIRARLKGKEGRLRGNLMGKRVDFSARTVITGDPNLSLDEL 370
Query: 276 GVPFEIAQRITFEERVNVHNINYLQELVDNK------LCLTYSDGSSSYSLREGSK-GHT 328
GVP IA+ +T+ E V +NI LQELV N D LR + G
Sbjct: 371 GVPRSIAKTLTYPETVTPYNIYQLQELVRNGPDEHPGAKYIIRDTGERIDLRYHKRAGDI 430
Query: 329 FLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDG 388
LR G V R I DGD V NR P+ HK S+ + V T ++N + P +ADFDG
Sbjct: 431 PLRYGWRVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDG 490
Query: 389 DCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSL-KVMFKKYFLDKA 447
D +++ PQS +AE+ E+ V KQ++S + + + D L + K + FL +
Sbjct: 491 DEMNMHVPQSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTRN 550
Query: 448 FTQQLAMFAL---SPLPRPALSKARCSARWTALQILQSVLPPGFDSCGDR---------- 494
+ ++ LP P + K + WT QIL ++P G + D
Sbjct: 551 AVMNIMLWVPDWDGILPPPVILKPKV--LWTGKQILSLIIPKGINLIRDDDKQSLSNPTD 608
Query: 495 --YLIKKSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGF 552
LI+ E++ G D+ T+ + +V +I+ EKGPE FF+ +Q ++ L +GF
Sbjct: 609 SGMLIENGEIIYGVVDKKTVGASQGGLVHTIWKEKGPEICKGFFNGIQRVVNYWLLHNGF 668
Query: 553 SVSLEDFSLSKAALWNIQKEI--------QALYSLLYHRMSTQNELVDLQ--------IE 596
S+ + D + + + + + + ++R+ + + + I
Sbjct: 669 SIGIGDTIADADTMKEVTRTVKEARRQVAECIQDAQHNRLKPEPGMTLRESFEAKVSRIL 728
Query: 597 NHIRHVKMLVAKFILK-SSTLGYLIXXXXXXXXXXXXXXXGFLGLQLSDRGK----FYSK 651
N R A+ LK S+ + ++ +G Q+ + + F +
Sbjct: 729 NQARDNAGRSAEHSLKDSNNVKQMVAAGSKGSFINISQMSACVGQQIVEGKRIPFGFKYR 788
Query: 652 TLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLS 711
TL HF P D + P ++ G I+ + GL P E H+++ RE ++ ++ +
Sbjct: 789 TL-----PHF----PKDDDSPESR-GFIENSYLRGLTPQEFFFHAMAGREGLIDTAVKTA 838
Query: 712 EPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYA 749
E G + + L+ + DV++ YDGTVRN + IIQF Y
Sbjct: 839 ETGYIQRRLVKAMEDVMVRYDGTVRNAMGD-IIQFAYG 875
Score = 47.4 bits (111), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 47/85 (55%), Gaps = 11/85 (12%)
Query: 17 IRFGLATQKEICTASISDC----SISHASQ------LANPFLGLPLEFGKCESCGTSEPG 66
++FG+ + +EI + S++ ++ + Q L +P LG KC++CG +
Sbjct: 19 VQFGILSPEEIRSMSVAKIEFPETMDESGQRPRVGGLLDPRLGTIDRQFKCQTCGETM-A 77
Query: 67 KCEGHFGYIELPIPIYHPSHISELK 91
C GHFG+IEL P++H +S++K
Sbjct: 78 DCPGHFGHIELAKPVFHIGFLSKIK 102
>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 = 171 bits (433), Expect = 3e-42, Method: Compositional matrix adjust.
Identities = 161/628 (25%), Positives = 278/628 (44%), Gaps = 67/628 (10%)
Query: 170 DLSIAMLKKVLKQVEIIRSSRSGTPNFESQEVESNDLQLAVGQYLE--VRGTAKSSRDVD 227
DL+ + + + + +G P+ +E ES LQ V Y++ + G ++ +
Sbjct: 261 DLTFKLADILKANISLETLEHNGAPHHAIEEAESL-LQFHVATYMDNDIAGQPQALQK-- 317
Query: 228 ARFGVSQDPNSTTKAWLE----KMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQ 283
S P + +A L+ ++R + K FS+R+VI+GD ++++GVP IA+
Sbjct: 318 -----SGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAK 372
Query: 284 RITFEERVNVHNINYLQELVDNK------LCLTYSDGSSSYSLREGSK-GHTFLRPGQVV 336
+T+ E V +NI+ L +LV N D LR + G L+ G V
Sbjct: 373 TLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKV 432
Query: 337 HRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYP 396
R IMD D V NR P+ HK S+ A V V T ++N + P +ADFDGD ++L P
Sbjct: 433 ERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVP 492
Query: 397 QSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSL-KVMFKKYFLDKAFTQQLAMF 455
QS +AE+ +L +V Q++S + + + D L + K+ + F++ Q L M
Sbjct: 493 QSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIE--LDQVLNML 550
Query: 456 ALSP-----LPRPALSKARCSARWTALQILQSVLPPG-----FDSC-------GDRYLIK 498
P +P PA+ K + W+ QIL +P G FD + LI
Sbjct: 551 YWVPDWDGVIPTPAIIKPK--PLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLII 608
Query: 499 KSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSL-- 556
+++ G ++ T+ S ++ + EKGP+ + F ++Q ++ L +GFS +
Sbjct: 609 DGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGD 668
Query: 557 ------------EDFSLSKAALWNIQKEIQALYSLLYHRMSTQNELVD--LQIENHIRHV 602
E + +K + ++ KE QA H M+ + D ++ N R
Sbjct: 669 TIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDK 728
Query: 603 KMLVAKFILKS-STLGYLIXXXXXXXXXXXXXXXGFLGLQLSDRGKFYSKTLVEDIASHF 661
+A+ LK + + ++ +G Q S GK + V+ HF
Sbjct: 729 AGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVG-QQSVEGKRIAFGFVDRTLPHF 787
Query: 662 ERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLM 721
+ +Y G ++ + GL P E H++ RE ++ ++ +E G + + L+
Sbjct: 788 SKD-----DYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLV 842
Query: 722 AVLRDVVICYDGTVRNVCSNSIIQFDYA 749
L D+++ YD T RN N +IQF Y
Sbjct: 843 KALEDIMVHYDNTTRNSLGN-VIQFIYG 869
Score = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 15/87 (17%)
Query: 17 IRFGLATQKEICTASISDCSI----------SHASQLANPFLGLPLEFGKCESC--GTSE 64
++FGL + +E+ S++ + L +P LG KC++C G +E
Sbjct: 17 VQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNE 76
Query: 65 PGKCEGHFGYIELPIPIYHPSHISELK 91
C GHFG+I+L P++H I+++K
Sbjct: 77 ---CPGHFGHIDLAKPVFHVGFIAKIK 100
>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 = 171 bits (433), Expect = 3e-42, Method: Compositional matrix adjust.
Identities = 161/628 (25%), Positives = 278/628 (44%), Gaps = 67/628 (10%)
Query: 170 DLSIAMLKKVLKQVEIIRSSRSGTPNFESQEVESNDLQLAVGQYLE--VRGTAKSSRDVD 227
DL+ + + + + +G P+ +E ES LQ V Y++ + G ++ +
Sbjct: 261 DLTFKLADILKANISLETLEHNGAPHHAIEEAESL-LQFHVATYMDNDIAGQPQALQK-- 317
Query: 228 ARFGVSQDPNSTTKAWLE----KMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQ 283
S P + +A L+ ++R + K FS+R+VI+GD ++++GVP IA+
Sbjct: 318 -----SGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAK 372
Query: 284 RITFEERVNVHNINYLQELVDNK------LCLTYSDGSSSYSLREGSK-GHTFLRPGQVV 336
+T+ E V +NI+ L +LV N D LR + G L+ G V
Sbjct: 373 TLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKV 432
Query: 337 HRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYP 396
R IMD D V NR P+ HK S+ A V V T ++N + P +ADFDGD ++L P
Sbjct: 433 ERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVP 492
Query: 397 QSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSL-KVMFKKYFLDKAFTQQLAMF 455
QS +AE+ +L +V Q++S + + + D L + K+ + F++ Q L M
Sbjct: 493 QSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIE--LDQVLNML 550
Query: 456 ALSP-----LPRPALSKARCSARWTALQILQSVLPPG-----FDSC-------GDRYLIK 498
P +P PA+ K + W+ QIL +P G FD + LI
Sbjct: 551 YWVPDWDGVIPTPAIIKPK--PLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLII 608
Query: 499 KSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSL-- 556
+++ G ++ T+ S ++ + EKGP+ + F ++Q ++ L +GFS +
Sbjct: 609 DGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGD 668
Query: 557 ------------EDFSLSKAALWNIQKEIQALYSLLYHRMSTQNELVD--LQIENHIRHV 602
E + +K + ++ KE QA H M+ + D ++ N R
Sbjct: 669 TIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDK 728
Query: 603 KMLVAKFILKS-STLGYLIXXXXXXXXXXXXXXXGFLGLQLSDRGKFYSKTLVEDIASHF 661
+A+ LK + + ++ +G Q S GK + V+ HF
Sbjct: 729 AGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVG-QQSVEGKRIAFGFVDRTLPHF 787
Query: 662 ERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLM 721
+ +Y G ++ + GL P E H++ RE ++ ++ +E G + + L+
Sbjct: 788 SKD-----DYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLV 842
Query: 722 AVLRDVVICYDGTVRNVCSNSIIQFDYA 749
L D+++ YD T RN N +IQF Y
Sbjct: 843 KALEDIMVHYDNTTRNSLGN-VIQFIYG 869
Score = 41.2 bits (95), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 15/87 (17%)
Query: 17 IRFGLATQKEICTASISDCSI----------SHASQLANPFLGLPLEFGKCESC--GTSE 64
++FGL + +E+ S++ + L +P LG KC++C G +E
Sbjct: 17 VQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNE 76
Query: 65 PGKCEGHFGYIELPIPIYHPSHISELK 91
C GHFG+I+L P++H I+++K
Sbjct: 77 ---CPGHFGHIDLAKPVFHVGFIAKIK 100
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 168 bits (425), Expect = 2e-41, Method: Compositional matrix adjust.
Identities = 161/628 (25%), Positives = 278/628 (44%), Gaps = 67/628 (10%)
Query: 170 DLSIAMLKKVLKQVEIIRSSRSGTPNFESQEVESNDLQLAVGQYLE--VRGTAKSSRDVD 227
DL+ + + + + +G P+ +E ES LQ V Y++ + G ++ +
Sbjct: 261 DLTFKLADILKANISLETLEHNGAPHHAIEEAESL-LQFHVATYMDNDIAGQPQALQK-- 317
Query: 228 ARFGVSQDPNSTTKAWLE----KMRTLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQ 283
S P + +A L+ ++R + K FS+R+VI+GD ++++GVP IA+
Sbjct: 318 -----SGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAK 372
Query: 284 RITFEERVNVHNINYLQELVDNK------LCLTYSDGSSSYSLREGSK-GHTFLRPGQVV 336
+T+ E V +NI+ L +LV N D LR + G L+ G V
Sbjct: 373 TLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKV 432
Query: 337 HRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYP 396
R IMD D V NR P+ HK S+ A V V T ++N + P +ADFDGD ++L P
Sbjct: 433 ERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVP 492
Query: 397 QSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALLSL-KVMFKKYFLDKAFTQQLAMF 455
QS +AE+ +L +V Q++S + + + D L + K+ + F++ Q L M
Sbjct: 493 QSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIE--LDQVLNML 550
Query: 456 ALSP-----LPRPALSKARCSARWTALQILQSVLPPG-----FDSC-------GDRYLIK 498
P +P PA+ K + W+ QIL +P G FD + LI
Sbjct: 551 YWVPDWDGVIPTPAIIKPK--PLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLII 608
Query: 499 KSEVLKGDFDRDTIPSVINEIVTSIFFEKGPEEVLEFFDSLQPLLMENLFADGFSVSL-- 556
+++ G ++ T+ S ++ + EKGP+ + F ++Q ++ L +GFS +
Sbjct: 609 DGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGD 668
Query: 557 ------------EDFSLSKAALWNIQKEIQALYSLLYHRMSTQNELVD--LQIENHIRHV 602
E + +K + ++ KE QA H M+ + D ++ N R
Sbjct: 669 TIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDK 728
Query: 603 KMLVAKFILKS-STLGYLIXXXXXXXXXXXXXXXGFLGLQLSDRGKFYSKTLVEDIASHF 661
+A+ LK + + ++ +G Q S GK + V+ HF
Sbjct: 729 AGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVG-QQSVEGKRIAFGFVDRTLPHF 787
Query: 662 ERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLM 721
+ +Y G ++ + GL P E H++ RE ++ ++ +E G + + L+
Sbjct: 788 SKD-----DYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLV 842
Query: 722 AVLRDVVICYDGTVRNVCSNSIIQFDYA 749
L D+++ YD T RN N +IQF Y
Sbjct: 843 KALEDIMVHYDNTTRNSLGN-VIQFIYG 869
Score = 41.2 bits (95), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 15/87 (17%)
Query: 17 IRFGLATQKEICTASISDCSI----------SHASQLANPFLGLPLEFGKCESC--GTSE 64
++FGL + +E+ S++ + L +P LG KC++C G +E
Sbjct: 17 VQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNE 76
Query: 65 PGKCEGHFGYIELPIPIYHPSHISELK 91
C GHFG+I+L P++H I+++K
Sbjct: 77 ---CPGHFGHIDLAKPVFHVGFIAKIK 100
>pdb|2PMZ|A Chain A, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|Q Chain Q, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|A Chain A, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
pdb|3HKZ|I Chain I, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
Length = 880
Score = 159 bits (402), Expect = 1e-38, Method: Compositional matrix adjust.
Identities = 224/866 (25%), Positives = 353/866 (40%), Gaps = 144/866 (16%)
Query: 11 EGQIVGIRFGLATQKEICTASISDCSISHA---------SQLANPFLGLPLEFGKCESCG 61
E I GI+FG+ + EI S++ + +P LG+ KC +CG
Sbjct: 3 EKNIKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCG 62
Query: 62 TSEPGKCEGHFGYIELPIPIYH---PSHISE-LKLT-MYAFQLQIKNDGV---------- 106
+ G C GHFG+IEL P+ H HI E LK T +++I D +
Sbjct: 63 NTL-GNCPGHFGHIELVRPVIHVGLVKHIYEFLKATCRRCGRVKISEDEIEKYSRIYNAI 121
Query: 107 -------AQRLL---------SSCC--------------------EVKEMLKRI-PEETR 129
A+RL + C E KE + ++ P + R
Sbjct: 122 KKRWPSAARRLTEYVKKTAMKAQVCPHCNEKQYKIKLEKPYNFYEERKEGVAKLTPSDIR 181
Query: 130 KKLAG--------KGYFPQDG----YILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLK 177
++L GY P IL LPVPP + + + DL+ ++
Sbjct: 182 ERLEKIPDSDVEILGYDPTTSRPEWMILTVLPVPPITIRPSIMIESGIRAEDDLTHKLVD 241
Query: 178 KVLKQVEIIRSSRSGTPNFESQEVESNDLQLAVGQYL--EVRGTAKSSRDVDARFGVSQD 235
V + S +G P +++ + LQ V Y E+ G S S
Sbjct: 242 IVRINERLKESIDAGAPQLIIEDL-WDLLQYHVATYFDNEIPGLPPSKHR-------SGR 293
Query: 236 PNSTTKAWLEKMRTLFIRKGSG----FSSRSVITGDAYKRVNEIGVPFEIAQRITFEERV 291
P T L+ F SG FSSR+VI+ D ++E+GVP IA+ +T ER+
Sbjct: 294 PLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNISIDEVGVPEIIAKTLTVPERI 353
Query: 292 NVHNINYLQELVDN-------KLCLTYSDGSSS--YSLREGSKGHTFLRPGQVVHRRIMD 342
NI L++ V N + DG +++ + + L PG ++ R ++D
Sbjct: 354 TPWNIEKLRQFVINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYIIERHLID 413
Query: 343 GDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSLAAK 402
GD V NR P+ H+ S+ A V V T ++N L+C P +ADFDGD ++L PQS A
Sbjct: 414 GDIVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVPQSEEAI 473
Query: 403 AEVLELFSVEKQLLSSHNGNLNLQLATDALL-SLKVMFKKYFLDKAFTQQLAMFA--LSP 459
AE E+ V K +++ G + A D + + + K L K QQ+ A
Sbjct: 474 AEAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKTTLLTKEEAQQILGVADVKID 533
Query: 460 LPRPALSKARCSARWTALQILQSVLPPGFDSCGDRYLIKKSEVLKG-DFDRDTIPSVINE 518
L PA+ R +T Q++ + LP F+ G + + K D D+ + N
Sbjct: 534 LGEPAILAPR--EYYTGKQVISAFLPKDFNFHGQANVSSGPRLCKNEDCPHDSYVVIKNG 591
Query: 519 IVTSIFFEKG------PEEVL-----EFFDSLQPLLMENLF--------ADGFSVSLEDF 559
I+ F+K PE +L E+ D LM+NLF GF++ LED
Sbjct: 592 ILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNLFRVFIRFVELQGFTMRLEDV 651
Query: 560 SLS---KAALWN-IQKEIQALYSLLYHRMSTQNELV-----DLQIENHI-------RHVK 603
SL K ++N I + + +L+ + + E + + +EN+I R
Sbjct: 652 SLGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIPGRTLEESLENYILDTLDKLRSTA 711
Query: 604 MLVAKFILKSSTLGYLIXXXXXXXXXXXXXXXGFLGLQLSDRGKFYSKTLVEDIASHFER 663
+A L Y++ + Q S RG+ + + HF+
Sbjct: 712 GDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLGQQSVRGERIKRGYMTRTLPHFK- 770
Query: 664 IYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVIVRSSRGLSEPGTLFKNLMAV 723
P D++ P A+ G I F GL P E H+ RE +V ++ S+ G + + L+
Sbjct: 771 --PYDIS-PEAR-GFIYSSFRTGLKPTELFFHAAGGREGLVDTAVRTSQSGYMQRRLINA 826
Query: 724 LRDVVICYDGTVRNVCSNSIIQFDYA 749
L D+ YDGTVR++ ++Q Y
Sbjct: 827 LSDLRAEYDGTVRSLYG-EVVQVAYG 851
>pdb|2WAQ|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|A Chain A, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|W Chain W, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2Y0S|A Chain A, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|W Chain W, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|A Chain A, Rnap At 3.2ang
pdb|4B1O|A Chain A, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|W Chain W, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 880
Score = 149 bits (376), Expect = 1e-35, Method: Compositional matrix adjust.
Identities = 190/706 (26%), Positives = 302/706 (42%), Gaps = 80/706 (11%)
Query: 102 KNDGVAQRLLSSCCEVKEMLKRIPEETRKKLAGKGYFPQDG----YILEYLPVPPNCLSV 157
+ +GVA+ + +++E L+++PE + L GY P IL LPVPP +
Sbjct: 168 RKEGVAK---LTPSDIRERLEKVPESDVEIL---GYDPTTSRPEWMILTVLPVPPITIRP 221
Query: 158 PDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSRSGTPNFESQEVESNDLQLAVGQYL--E 215
+ + DL+ ++ V + S +G P +++ + LQ V Y E
Sbjct: 222 SIMIESGIRAEDDLTHKLVDIVRINERLKESIDAGAPQLIIEDL-WDLLQYHVATYFDNE 280
Query: 216 VRGTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSG----FSSRSVITGDAYKR 271
+ G S S P T L+ F SG FSSR+VI+ D
Sbjct: 281 IPGLPPSKHR-------SGRPLRTLAQRLKGKEGRFRGNLSGKRVDFSSRTVISPDPNIS 333
Query: 272 VNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKL-------CLTYSDGSSS--YSLRE 322
++E+GVP IA+ +T ER+ NI L++ V N + DG +++
Sbjct: 334 IDEVGVPEIIARTLTVPERITPWNIEKLRQFVINGPDKWPGANYVIRPDGRRIDLRYVKD 393
Query: 323 GSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPL 382
+ + L PG VV R + DGD V NR P+ H+ S+ A V V T ++N L+C P
Sbjct: 394 RKELASTLAPGYVVERHLTDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPY 453
Query: 383 SADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLATDALL-SLKVMFKK 441
+ADFDGD ++L PQS A AE E+ V K +++ G + A D + + + K
Sbjct: 454 NADFDGDEMNLHVPQSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGAYLLTVKT 513
Query: 442 YFLDKAFTQQLAMFA--LSPLPRPALSKARCSARWTALQILQSVLPPGFDSCGDRYLIKK 499
L K QQ+ A L PA+ R +T Q++ + LP F+ G +
Sbjct: 514 TLLTKEEAQQILGVADVKIDLGEPAILAPR--EYYTGKQVVSAFLPKDFNFHGQANVSSG 571
Query: 500 SEVLKG-DFDRDTIPSVINEIVTSIFFEKG------PEEVL-----EFFDSLQPLLMENL 547
+ K D D+ + N I+ F+K PE +L E+ D LM+NL
Sbjct: 572 PRLCKNEDCPHDSYVVIKNGILLEGVFDKKAIGNQQPESILHWLIKEYSDEYGKWLMDNL 631
Query: 548 F--------ADGFSVSLEDFSLS---KAALWN-IQKEIQALYSLLYHRMSTQNELV---- 591
F GF++ LED SL K ++N I + + +L+ + + E +
Sbjct: 632 FRVFIRFVELQGFTMRLEDVSLGDDVKKEIYNEIDRAKVEVDNLIQKYKNGELEPIPGRT 691
Query: 592 -DLQIENHI-------RHVKMLVAKFILKSSTLGYLIXXXXXXXXXXXXXXXGFLGLQLS 643
+ +EN+I R +A L Y++ + Q S
Sbjct: 692 LEESLENYILDTLDKLRSTAGDIASKYLDPFNFAYVMARTGARGSVLNITQMAAMLGQQS 751
Query: 644 DRGKFYSKTLVEDIASHFERIYPMDLNYPTAKYGLIKGCFFHGLDPYEEMTHSISTREVI 703
RG+ + + HF+ P D++ P A+ G I F GL P E H+ RE +
Sbjct: 752 VRGERIKRGYMTRTLPHFK---PYDIS-PEAR-GFIYSSFRTGLKPTELFFHAAGGREGL 806
Query: 704 VRSSRGLSEPGTLFKNLMAVLRDVVICYDGTVRNVCSNSIIQFDYA 749
V ++ S+ G + + L+ L D+ YDGTVR++ +IQ Y
Sbjct: 807 VDTAVRTSQSGYMQRRLINALSDLRAEYDGTVRSLYG-EVIQVAYG 851
Score = 46.2 bits (108), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 39/82 (47%), Gaps = 10/82 (12%)
Query: 11 EGQIVGIRFGLATQKEICTASISDCSISHA---------SQLANPFLGLPLEFGKCESCG 61
E I GI+FG+ + EI S++ + +P LG+ KC +CG
Sbjct: 3 EKNIKGIKFGILSPDEIRKMSVTAIITPDVYDEDGTPIEGSVMDPRLGVIEPGQKCPTCG 62
Query: 62 TSEPGKCEGHFGYIELPIPIYH 83
+ G C GHFG+IEL P+ H
Sbjct: 63 NTL-GNCPGHFGHIELVRPVIH 83
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 71.2 bits (173), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 91/371 (24%), Positives = 152/371 (40%), Gaps = 55/371 (14%)
Query: 91 KLTMYAFQLQIKNDGVAQRLLSSCCEVKEMLKRIPEET-RKKLAGK----GYFPQDG--- 142
K+ A Q +K+ + Q C +++E L ET RKKL + F Q G
Sbjct: 179 KMGAEAIQALLKSMDLEQ----ECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKP 234
Query: 143 --YILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSRSGTPNFESQE 200
IL LPV P L DG +SDL+ + + + + R P+ +
Sbjct: 235 EWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRN 294
Query: 201 VESNDLQLAVGQYLEVRGTAKSSRDVDARFGVSQDPNSTTKAWLE----KMRTLFIRKGS 256
E LQ AV L+ + R A G ++ P + ++ + R + K
Sbjct: 295 -EKRMLQEAVDALLD------NGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRV 347
Query: 257 GFSSRSVITGDAYKRVNEIGVPFEIAQRI-------TFEERVNVHNINYLQELVDNKLCL 309
+S RSVIT Y R+++ G+P ++A + E R I +++V+ + +
Sbjct: 348 DYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAV 407
Query: 310 TYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDD 369
+ L E + H V +NR PT H+ +QA + +
Sbjct: 408 VWD------ILDEVIREHP-----------------VLLNRAPTLHRLGIQAFEPVLIEG 444
Query: 370 HTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLAT 429
++++PL+C +ADFDGD + + P +L A+ E L +LS NG + +
Sbjct: 445 KAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQ 504
Query: 430 DALLSLKVMFK 440
D +L L M +
Sbjct: 505 DVVLGLYYMTR 515
>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 = 71.2 bits (173), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 91/371 (24%), Positives = 152/371 (40%), Gaps = 55/371 (14%)
Query: 91 KLTMYAFQLQIKNDGVAQRLLSSCCEVKEMLKRIPEET-RKKLAGK----GYFPQDG--- 142
K+ A Q +K+ + Q C +++E L ET RKKL + F Q G
Sbjct: 179 KMGAEAIQALLKSMDLEQ----ECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKP 234
Query: 143 --YILEYLPVPPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSRSGTPNFESQE 200
IL LPV P L DG +SDL+ + + + + R P+ +
Sbjct: 235 EWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRN 294
Query: 201 VESNDLQLAVGQYLEVRGTAKSSRDVDARFGVSQDPNSTTKAWLE----KMRTLFIRKGS 256
E LQ AV L+ + R A G ++ P + ++ + R + K
Sbjct: 295 -EKRMLQEAVDALLD------NGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRV 347
Query: 257 GFSSRSVITGDAYKRVNEIGVPFEIAQRI-------TFEERVNVHNINYLQELVDNKLCL 309
+S RSVIT Y R+++ G+P ++A + E R I +++V+ + +
Sbjct: 348 DYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAV 407
Query: 310 TYSDGSSSYSLREGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDD 369
+ L E + H V +NR PT H+ +QA + +
Sbjct: 408 VWD------ILDEVIREHP-----------------VLLNRAPTLHRLGIQAFEPVLIEG 444
Query: 370 HTVKINPLICGPLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHNGNLNLQLAT 429
++++PL+C +ADFDGD + + P +L A+ E L +LS NG + +
Sbjct: 445 KAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQ 504
Query: 430 DALLSLKVMFK 440
D +L L M +
Sbjct: 505 DVVLGLYYMTR 515
>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 = 62.4 bits (150), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 67/280 (23%), Positives = 120/280 (42%), Gaps = 27/280 (9%)
Query: 144 ILEYLPV-PPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSRSGTPNFESQEVE 202
ILE +PV PP+ + + DG +SDL+ + + + + + G P + E
Sbjct: 513 ILEAVPVLPPDLRPMVQV-DGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRN-E 570
Query: 203 SNDLQLAVGQYLE--VRGTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSS 260
LQ AV L+ RG ++ D D S + + R + K +S
Sbjct: 571 KRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQG---RFRQNLLGKRVDYSG 627
Query: 261 RSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSDGSSSYSL 320
RSVI ++++ G+P +A + + L+++ + +
Sbjct: 628 RSVIVVGPQLKLHQCGLPKRMA--------LELFKPFLLKKMEEKGIAPNVKAARRMLER 679
Query: 321 REGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICG 380
+ K + +V+H G V +NR PT H+ +QA + + +++++PL+C
Sbjct: 680 QRDIKDEVWDALEEVIH-----GKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCE 734
Query: 381 PLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHN 420
+ADFDGD + + P S A+AE Q+LS+HN
Sbjct: 735 AFNADFDGDQMAVHVPLSSFAQAE------ARIQMLSAHN 768
>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 = 62.4 bits (150), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 67/280 (23%), Positives = 120/280 (42%), Gaps = 27/280 (9%)
Query: 144 ILEYLPV-PPNCLSVPDISDGVSTMSSDLSIAMLKKVLKQVEIIRSSRSGTPNFESQEVE 202
ILE +PV PP+ + + DG +SDL+ + + + + + G P + E
Sbjct: 513 ILEAVPVLPPDLRPMVQV-DGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRN-E 570
Query: 203 SNDLQLAVGQYLE--VRGTAKSSRDVDARFGVSQDPNSTTKAWLEKMRTLFIRKGSGFSS 260
LQ AV L+ RG ++ D D S + + R + K +S
Sbjct: 571 KRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQG---RFRQNLLGKRVDYSG 627
Query: 261 RSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLCLTYSDGSSSYSL 320
RSVI ++++ G+P +A + + L+++ + +
Sbjct: 628 RSVIVVGPQLKLHQCGLPKRMA--------LELFKPFLLKKMEEKGIAPNVKAARRMLER 679
Query: 321 REGSKGHTFLRPGQVVHRRIMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICG 380
+ K + +V+H G V +NR PT H+ +QA + + +++++PL+C
Sbjct: 680 QRDIKDEVWDALEEVIH-----GKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCE 734
Query: 381 PLSADFDGDCIHLFYPQSLAAKAEVLELFSVEKQLLSSHN 420
+ADFDGD + + P S A+AE Q+LS+HN
Sbjct: 735 AFNADFDGDQMAVHVPLSSFAQAE------ARIQMLSAHN 768
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 62.0 bits (149), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 47/81 (58%), Gaps = 6/81 (7%)
Query: 340 IMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSL 399
++ G V +NR PT H+ +QA + + +++++PL+C +ADFDGD + + P S
Sbjct: 403 VIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSS 462
Query: 400 AAKAEVLELFSVEKQLLSSHN 420
A+AE Q+LS+HN
Sbjct: 463 FAQAE------ARIQMLSAHN 477
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 62.0 bits (149), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 47/81 (58%), Gaps = 6/81 (7%)
Query: 340 IMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSL 399
++ G V +NR PT H+ +QA + + +++++PL+C +ADFDGD + + P S
Sbjct: 434 VIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSS 493
Query: 400 AAKAEVLELFSVEKQLLSSHN 420
A+AE Q+LS+HN
Sbjct: 494 FAQAE------ARIQMLSAHN 508
>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 = 62.0 bits (149), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 47/81 (58%), Gaps = 6/81 (7%)
Query: 340 IMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSL 399
++ G V +NR PT H+ +QA + + +++++PL+C +ADFDGD + + P S
Sbjct: 434 VIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSS 493
Query: 400 AAKAEVLELFSVEKQLLSSHN 420
A+AE Q+LS+HN
Sbjct: 494 FAQAE------ARIQMLSAHN 508
>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 = 62.0 bits (149), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 47/81 (58%), Gaps = 6/81 (7%)
Query: 340 IMDGDTVFINRPPTTHKHSLQALSVYVHDDHTVKINPLICGPLSADFDGDCIHLFYPQSL 399
++ G V +NR PT H+ +QA + + +++++PL+C +ADFDGD + + P S
Sbjct: 694 VIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSS 753
Query: 400 AAKAEVLELFSVEKQLLSSHN 420
A+AE Q+LS+HN
Sbjct: 754 FAQAE------ARIQMLSAHN 768
>pdb|2K0M|A Chain A, Solution Nmr Structure Of The Uncharacterized Protein From
Rhodospirillum Rubrum Gene Locus Rru_a0810. Northeast
Structural Genomics Target Rrr43
Length = 104
Score = 50.4 bits (119), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 42/69 (60%), Gaps = 3/69 (4%)
Query: 1601 YNDGDRLSADDKSFIFDNVFNYHPDKAMKMGAGIDHFKVDKHGSFQDSRCLFVVSTDGSQ 1660
Y GD +S D +F+ + HPD K+G G+ +F+V + ++C +++ TDGS+
Sbjct: 31 YRPGDIVSTVDGAFLVE-ALKRHPDATSKIGPGVRNFEV--RSADYGTQCFWILRTDGSE 87
Query: 1661 QDFSYRKCL 1669
+ FSY+KC+
Sbjct: 88 ERFSYKKCV 96
>pdb|3QQC|A Chain A, Crystal Structure Of Archaeal Spt45 BOUND TO THE RNAP
CLAMP DOMAIN
Length = 436
Score = 42.7 bits (99), Expect = 0.002, Method: Composition-based stats.
Identities = 27/86 (31%), Positives = 42/86 (48%), Gaps = 19/86 (22%)
Query: 12 GQIVG-IRFGLATQKEICTASISDCSISHASQLANPFLGLPLEFG-------------KC 57
G+++G I FG+ + +EI S + ++ G P+E G +C
Sbjct: 66 GKVIGSIEFGILSPQEIRKMSAVEVTVPDTYDDD----GYPIEGGVMDKRMGVIDPGLRC 121
Query: 58 ESCGTSEPGKCEGHFGYIELPIPIYH 83
E+CG G+C GHFG+IEL P+ H
Sbjct: 122 ETCG-GRAGECPGHFGHIELARPVIH 146
>pdb|3KT7|A Chain A, Crystal Structure Of Tpa1 From Saccharomyces Cerevisiae, A
Component Of The Messenger Ribonucleoprotein Complex
Length = 633
Score = 30.4 bits (67), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 52/122 (42%), Gaps = 12/122 (9%)
Query: 249 TLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLC 308
T+F + + +S ++ R G+ F +A + F E + N + + +++ LC
Sbjct: 462 TIFKKYLALLTSLCPVSEQILIRRFRPGMDFTLATKCRFNELLK-SNPDIIDAVLEGTLC 520
Query: 309 LTYSDGSSS--------YSLREGSKGHTFLRPG---QVVHRRIMDGDTVFINRPPTTHKH 357
LT S G S Y + + +L+ V+R GD+V IN PP +
Sbjct: 521 LTPSAGWESGELGGYELYMMDDDEDNKQYLKEDVEDASVYRADDSGDSVLINDPPAWNTF 580
Query: 358 SL 359
+L
Sbjct: 581 NL 582
>pdb|2EX5|A Chain A, Group I Intron-encoded Homing Endonuclease I-ceui
Complexed With Dna
pdb|2EX5|B Chain B, Group I Intron-encoded Homing Endonuclease I-ceui
Complexed With Dna
Length = 207
Score = 30.4 bits (67), Expect = 9.2, Method: Composition-based stats.
Identities = 28/93 (30%), Positives = 42/93 (45%), Gaps = 5/93 (5%)
Query: 218 GTAKSSRDVDARFGVSQDPNSTTKAWL--EKMRTLFIRKGSGFSSRSVITGDAYKRVNEI 275
T+K VD F V++ N +L E +T IR SG ++ V+T D + + E
Sbjct: 73 ATSKFGLVVDPEFNVTRHVNGVKVLYLALEVFKTGRIRHKSGSNATLVLTIDNRQSLEEK 132
Query: 276 GVPFEIAQRITF---EERVNVHNINYLQELVDN 305
+PF + F E+ V N L EL +N
Sbjct: 133 VIPFYEQYVVAFSSPEKVKRVANFKALLELFNN 165
>pdb|3KT1|A Chain A, Crystal Structure Of Tpa1 From Saccharomyces Cerevisiae, A
Component Of The Messenger Ribonucleoprotein Complex
Length = 633
Score = 30.4 bits (67), Expect = 9.4, Method: Compositional matrix adjust.
Identities = 29/122 (23%), Positives = 52/122 (42%), Gaps = 12/122 (9%)
Query: 249 TLFIRKGSGFSSRSVITGDAYKRVNEIGVPFEIAQRITFEERVNVHNINYLQELVDNKLC 308
T+F + + +S ++ R G+ F +A + F E + N + + +++ LC
Sbjct: 462 TIFKKYLALLTSLCPVSEQILIRRFRPGMDFTLATKCRFNELLK-SNPDIIDAVLEGTLC 520
Query: 309 LTYSDGSSS--------YSLREGSKGHTFLRPG---QVVHRRIMDGDTVFINRPPTTHKH 357
LT S G S Y + + +L+ V+R GD+V IN PP +
Sbjct: 521 LTPSAGWESGELGGYELYMMDDDEDNKQYLKEDVEDASVYRADDSGDSVLINDPPAWNTF 580
Query: 358 SL 359
+L
Sbjct: 581 NL 582
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
0.315 0.131 0.396
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 52,437,303
Number of Sequences: 62578
Number of extensions: 2266878
Number of successful extensions: 4131
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 4078
Number of HSP's gapped (non-prelim): 47
length of query: 1714
length of database: 14,973,337
effective HSP length: 112
effective length of query: 1602
effective length of database: 7,964,601
effective search space: 12759290802
effective search space used: 12759290802
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 58 (26.9 bits)