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= psy1131
(353 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 = 243 bits (620), Expect = 1e-64, Method: Compositional matrix adjust.
Identities = 110/168 (65%), Positives = 141/168 (83%), Gaps = 4/168 (2%)
Query: 75 VLPWSTFRMNLRMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERH 134
V P++ +++ ELVR G ++PGAKYI+RD GERIDLR+H + D+ L+ G++VERH
Sbjct: 386 VTPYNIYQLQ----ELVRNGPDEHPGAKYIIRDTGERIDLRYHKRAGDIPLRYGWRVERH 441
Query: 135 IRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSM 194
IRDGD+VIFNRQP+LHKMSMMGHR+RV+P+STFR+NLS TSPYNADFDGDEMN+HVPQS
Sbjct: 442 IRDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMHVPQSE 501
Query: 195 ETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLDK 242
ETRAE++ I + P+QI++PQ+N+PVMGIVQDTL VRK + RD FL +
Sbjct: 502 ETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFLTR 549
Score = 189 bits (479), Expect = 3e-48, Method: Compositional matrix adjust.
Identities = 84/111 (75%), Positives = 101/111 (90%)
Query: 242 KVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLH 301
+VERHIRDGD+VIFNRQP+LHKMSMMGHR+RV+P+STFR+NLS TSPYNADFDGDEMN+H
Sbjct: 437 RVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPYSTFRLNLSVTSPYNADFDGDEMNMH 496
Query: 302 VPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFL 352
VPQS ETRAE++ I + P+QI++PQ+N+PVMGIVQDTL VRK + RD FL
Sbjct: 497 VPQSEETRAEIQEITMVPKQIVSPQSNKPVMGIVQDTLAGVRKFSLRDNFL 547
Score = 135 bits (341), Expect = 2e-32, Method: Compositional matrix adjust.
Identities = 59/85 (69%), Positives = 75/85 (88%)
Query: 3 ELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQPT 62
ELVR G ++PGAKYI+RD GERIDLR+H + D+ L+ G++VERHIRDGD+VIFNRQP+
Sbjct: 396 ELVRNGPDEHPGAKYIIRDTGERIDLRYHKRAGDIPLRYGWRVERHIRDGDVVIFNRQPS 455
Query: 63 LHKMSMMGHRVRVLPWSTFRMNLRM 87
LHKMSMMGHR+RV+P+STFR+NL +
Sbjct: 456 LHKMSMMGHRIRVMPYSTFRLNLSV 480
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 229 bits (584), Expect = 2e-60, Method: Compositional matrix adjust.
Identities = 101/156 (64%), Positives = 130/156 (83%)
Query: 86 RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR 145
R+ +LVR G +++PGAKY++RD+G+RIDLR+ + D+ LQ G+KVERHI D D V+FNR
Sbjct: 387 RLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNR 446
Query: 146 QPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHV 205
QP+LHKMSMM HRV+V+P+STFR+NLS TSPYNADFDGDEMNLHVPQS ETRAE+ +
Sbjct: 447 QPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCA 506
Query: 206 TPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 241
P QI++PQ+N+P MGIVQDTL +RK+T RD F++
Sbjct: 507 VPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIE 542
Score = 177 bits (448), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 79/112 (70%), Positives = 95/112 (84%)
Query: 242 KVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLH 301
KVERHI D D V+FNRQP+LHKMSMM HRV+V+P+STFR+NLS TSPYNADFDGDEMNLH
Sbjct: 431 KVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLH 490
Query: 302 VPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353
VPQS ETRAE+ + P QI++PQ+N+P MGIVQDTL +RK+T RD F++
Sbjct: 491 VPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIE 542
Score = 124 bits (311), Expect = 8e-29, Method: Compositional matrix adjust.
Identities = 53/87 (60%), Positives = 73/87 (83%)
Query: 1 MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQ 60
+ +LVR G +++PGAKY++RD+G+RIDLR+ + D+ LQ G+KVERHI D D V+FNRQ
Sbjct: 388 LTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQ 447
Query: 61 PTLHKMSMMGHRVRVLPWSTFRMNLRM 87
P+LHKMSMM HRV+V+P+STFR+NL +
Sbjct: 448 PSLHKMSMMAHRVKVIPYSTFRLNLSV 474
>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 = 229 bits (584), Expect = 2e-60, Method: Compositional matrix adjust.
Identities = 101/156 (64%), Positives = 130/156 (83%)
Query: 86 RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR 145
R+ +LVR G +++PGAKY++RD+G+RIDLR+ + D+ LQ G+KVERHI D D V+FNR
Sbjct: 387 RLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNR 446
Query: 146 QPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHV 205
QP+LHKMSMM HRV+V+P+STFR+NLS TSPYNADFDGDEMNLHVPQS ETRAE+ +
Sbjct: 447 QPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCA 506
Query: 206 TPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 241
P QI++PQ+N+P MGIVQDTL +RK+T RD F++
Sbjct: 507 VPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIE 542
Score = 177 bits (448), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 79/112 (70%), Positives = 95/112 (84%)
Query: 242 KVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLH 301
KVERHI D D V+FNRQP+LHKMSMM HRV+V+P+STFR+NLS TSPYNADFDGDEMNLH
Sbjct: 431 KVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLH 490
Query: 302 VPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353
VPQS ETRAE+ + P QI++PQ+N+P MGIVQDTL +RK+T RD F++
Sbjct: 491 VPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIE 542
Score = 124 bits (311), Expect = 8e-29, Method: Compositional matrix adjust.
Identities = 53/87 (60%), Positives = 73/87 (83%)
Query: 1 MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQ 60
+ +LVR G +++PGAKY++RD+G+RIDLR+ + D+ LQ G+KVERHI D D V+FNRQ
Sbjct: 388 LTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQ 447
Query: 61 PTLHKMSMMGHRVRVLPWSTFRMNLRM 87
P+LHKMSMM HRV+V+P+STFR+NL +
Sbjct: 448 PSLHKMSMMAHRVKVIPYSTFRLNLSV 474
>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 = 229 bits (584), Expect = 2e-60, Method: Compositional matrix adjust.
Identities = 101/156 (64%), Positives = 130/156 (83%)
Query: 86 RMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR 145
R+ +LVR G +++PGAKY++RD+G+RIDLR+ + D+ LQ G+KVERHI D D V+FNR
Sbjct: 387 RLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNR 446
Query: 146 QPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHV 205
QP+LHKMSMM HRV+V+P+STFR+NLS TSPYNADFDGDEMNLHVPQS ETRAE+ +
Sbjct: 447 QPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCA 506
Query: 206 TPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 241
P QI++PQ+N+P MGIVQDTL +RK+T RD F++
Sbjct: 507 VPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIE 542
Score = 177 bits (448), Expect = 1e-44, Method: Compositional matrix adjust.
Identities = 79/112 (70%), Positives = 95/112 (84%)
Query: 242 KVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLH 301
KVERHI D D V+FNRQP+LHKMSMM HRV+V+P+STFR+NLS TSPYNADFDGDEMNLH
Sbjct: 431 KVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLH 490
Query: 302 VPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVFLD 353
VPQS ETRAE+ + P QI++PQ+N+P MGIVQDTL +RK+T RD F++
Sbjct: 491 VPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIE 542
Score = 124 bits (311), Expect = 8e-29, Method: Compositional matrix adjust.
Identities = 53/87 (60%), Positives = 73/87 (83%)
Query: 1 MFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNRQ 60
+ +LVR G +++PGAKY++RD+G+RIDLR+ + D+ LQ G+KVERHI D D V+FNRQ
Sbjct: 388 LTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQ 447
Query: 61 PTLHKMSMMGHRVRVLPWSTFRMNLRM 87
P+LHKMSMM HRV+V+P+STFR+NL +
Sbjct: 448 PSLHKMSMMAHRVKVIPYSTFRLNLSV 474
>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 = 162 bits (409), Expect = 3e-40, Method: Compositional matrix adjust.
Identities = 82/159 (51%), Positives = 107/159 (67%), Gaps = 6/159 (3%)
Query: 74 RVLPWSTFRMNLRMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLH--LQCGYKV 131
R+ PW+ + LR F V G ++PGA Y++R +G RIDLR+ +L L GY V
Sbjct: 352 RITPWNIEK--LRQF--VINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYVV 407
Query: 132 ERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVP 191
ERH+ DGD+V+FNRQP+LH++SMM HRVRVL TFR+NL PYNADFDGDEMNLHVP
Sbjct: 408 ERHLTDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVP 467
Query: 192 QSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAV 230
QS E AE + I + + IITP+ P++G QD ++
Sbjct: 468 QSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGA 506
Score = 129 bits (324), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 59/100 (59%), Positives = 74/100 (74%)
Query: 243 VERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHV 302
VERH+ DGD+V+FNRQP+LH++SMM HRVRVL TFR+NL PYNADFDGDEMNLHV
Sbjct: 407 VERHLTDGDVVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHV 466
Query: 303 PQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAV 342
PQS E AE + I + + IITP+ P++G QD ++
Sbjct: 467 PQSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGA 506
Score = 95.1 bits (235), Expect = 6e-20, Method: Compositional matrix adjust.
Identities = 46/85 (54%), Positives = 61/85 (71%), Gaps = 2/85 (2%)
Query: 3 ELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLH--LQCGYKVERHIRDGDLVIFNRQ 60
+ V G ++PGA Y++R +G RIDLR+ +L L GY VERH+ DGD+V+FNRQ
Sbjct: 363 QFVINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYVVERHLTDGDVVLFNRQ 422
Query: 61 PTLHKMSMMGHRVRVLPWSTFRMNL 85
P+LH++SMM HRVRVL TFR+NL
Sbjct: 423 PSLHRISMMAHRVRVLKGLTFRLNL 447
>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 = 161 bits (407), Expect = 6e-40, Method: Compositional matrix adjust.
Identities = 81/159 (50%), Positives = 107/159 (67%), Gaps = 6/159 (3%)
Query: 74 RVLPWSTFRMNLRMFELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLH--LQCGYKV 131
R+ PW+ + LR F V G ++PGA Y++R +G RIDLR+ +L L GY +
Sbjct: 352 RITPWNIEK--LRQF--VINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYII 407
Query: 132 ERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVP 191
ERH+ DGD+V+FNRQP+LH++SMM HRVRVL TFR+NL PYNADFDGDEMNLHVP
Sbjct: 408 ERHLIDGDIVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHVP 467
Query: 192 QSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAV 230
QS E AE + I + + IITP+ P++G QD ++
Sbjct: 468 QSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGA 506
Score = 128 bits (322), Expect = 4e-30, Method: Compositional matrix adjust.
Identities = 58/100 (58%), Positives = 74/100 (74%)
Query: 243 VERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHV 302
+ERH+ DGD+V+FNRQP+LH++SMM HRVRVL TFR+NL PYNADFDGDEMNLHV
Sbjct: 407 IERHLIDGDIVLFNRQPSLHRISMMAHRVRVLKGLTFRLNLLVCPPYNADFDGDEMNLHV 466
Query: 303 PQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAV 342
PQS E AE + I + + IITP+ P++G QD ++
Sbjct: 467 PQSEEAIAEAKEIMLVHKNIITPRYGGPIIGAAQDYISGA 506
Score = 94.0 bits (232), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 45/85 (52%), Positives = 61/85 (71%), Gaps = 2/85 (2%)
Query: 3 ELVRRGNSQYPGAKYIVRDNGERIDLRFHPKPSDLH--LQCGYKVERHIRDGDLVIFNRQ 60
+ V G ++PGA Y++R +G RIDLR+ +L L GY +ERH+ DGD+V+FNRQ
Sbjct: 363 QFVINGPDKWPGANYVIRPDGRRIDLRYVKDRKELASTLAPGYIIERHLIDGDIVLFNRQ 422
Query: 61 PTLHKMSMMGHRVRVLPWSTFRMNL 85
P+LH++SMM HRVRVL TFR+NL
Sbjct: 423 PSLHRISMMAHRVRVLKGLTFRLNL 447
>pdb|3IYD|D Chain D, Three-Dimensional Em Structure Of An Intact
Activator-Dependent Transcription Initiation Complex
Length = 1413
Score = 75.1 bits (183), Expect = 5e-14, Method: Composition-based stats.
Identities = 38/124 (30%), Positives = 70/124 (56%), Gaps = 3/124 (2%)
Query: 226 TLTAVRKMTKRD--VFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNL 283
T+ A +KM +R+ V D ++ IR+ V+ NR PTLH++ + ++ +++
Sbjct: 393 TIKAAKKMVEREEAVVWDILDEVIREHP-VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHP 451
Query: 284 SCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVR 343
+ YNADFDGD+M +HVP ++E + E + ++ I++P N P++ QD + +
Sbjct: 452 LVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLY 511
Query: 344 KMTK 347
MT+
Sbjct: 512 YMTR 515
Score = 68.6 bits (166), Expect = 6e-12, Method: Composition-based stats.
Identities = 29/95 (30%), Positives = 54/95 (56%)
Query: 141 VIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEV 200
V+ NR PTLH++ + ++ +++ + YNADFDGD+M +HVP ++E + E
Sbjct: 421 VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA 480
Query: 201 ENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTK 235
+ ++ I++P N P++ QD + + MT+
Sbjct: 481 RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR 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 = 75.1 bits (183), Expect = 5e-14, Method: Composition-based stats.
Identities = 38/124 (30%), Positives = 70/124 (56%), Gaps = 3/124 (2%)
Query: 226 TLTAVRKMTKRD--VFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNL 283
T+ A +KM +R+ V D ++ IR+ V+ NR PTLH++ + ++ +++
Sbjct: 393 TIKAAKKMVEREEAVVWDILDEVIREHP-VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHP 451
Query: 284 SCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVR 343
+ YNADFDGD+M +HVP ++E + E + ++ I++P N P++ QD + +
Sbjct: 452 LVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLY 511
Query: 344 KMTK 347
MT+
Sbjct: 512 YMTR 515
Score = 68.6 bits (166), Expect = 6e-12, Method: Composition-based stats.
Identities = 29/95 (30%), Positives = 54/95 (56%)
Query: 141 VIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEV 200
V+ NR PTLH++ + ++ +++ + YNADFDGD+M +HVP ++E + E
Sbjct: 421 VLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEA 480
Query: 201 ENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTK 235
+ ++ I++P N P++ QD + + MT+
Sbjct: 481 RALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTR 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 = 60.8 bits (146), Expect = 1e-09, Method: Composition-based stats.
Identities = 38/136 (27%), Positives = 68/136 (50%), Gaps = 12/136 (8%)
Query: 223 VQDTLTAVRKMTKR-----DVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWS 277
+ + A R+M +R D D +E I G +V+ NR PTLH++ + + ++
Sbjct: 666 IAPNVKAARRMLERQRDIKDEVWDALEEVIH-GKVVLLNRAPTLHRLGIQAFQPVLVEGQ 724
Query: 278 TFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQD 337
+ +++ +NADFDGD+M +HVP S +AE ++ +++P + P+ +D
Sbjct: 725 SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRD 784
Query: 338 T------LTAVRKMTK 347
+T VRK K
Sbjct: 785 IILGLYYITQVRKEKK 800
Score = 57.8 bits (138), Expect = 1e-08, Method: Composition-based stats.
Identities = 30/104 (28%), Positives = 55/104 (52%), Gaps = 6/104 (5%)
Query: 138 GDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETR 197
G +V+ NR PTLH++ + + ++ + +++ +NADFDGD+M +HVP S +
Sbjct: 697 GKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQ 756
Query: 198 AEVENIHVTPRQIITPQNNRPVMGIVQDT------LTAVRKMTK 235
AE ++ +++P + P+ +D +T VRK K
Sbjct: 757 AEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKK 800
>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 = 60.8 bits (146), Expect = 1e-09, Method: Composition-based stats.
Identities = 38/136 (27%), Positives = 68/136 (50%), Gaps = 12/136 (8%)
Query: 223 VQDTLTAVRKMTKR-----DVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWS 277
+ + A R+M +R D D +E I G +V+ NR PTLH++ + + ++
Sbjct: 666 IAPNVKAARRMLERQRDIKDEVWDALEEVIH-GKVVLLNRAPTLHRLGIQAFQPVLVEGQ 724
Query: 278 TFRMNLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQD 337
+ +++ +NADFDGD+M +HVP S +AE ++ +++P + P+ +D
Sbjct: 725 SIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRD 784
Query: 338 T------LTAVRKMTK 347
+T VRK K
Sbjct: 785 IILGLYYITQVRKEKK 800
Score = 57.8 bits (138), Expect = 1e-08, Method: Composition-based stats.
Identities = 30/104 (28%), Positives = 55/104 (52%), Gaps = 6/104 (5%)
Query: 138 GDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETR 197
G +V+ NR PTLH++ + + ++ + +++ +NADFDGD+M +HVP S +
Sbjct: 697 GKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQ 756
Query: 198 AEVENIHVTPRQIITPQNNRPVMGIVQDT------LTAVRKMTK 235
AE ++ +++P + P+ +D +T VRK K
Sbjct: 757 AEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKK 800
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For
Structural Studies
Length = 1233
Score = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 38/132 (28%), Positives = 67/132 (50%), Gaps = 12/132 (9%)
Query: 227 LTAVRKMTKR-----DVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRM 281
+ A R+M +R D D +E I G +V+ NR PTLH++ + + ++ + ++
Sbjct: 379 VKAARRMLERQRDIKDEVWDALEEVIH-GKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQL 437
Query: 282 NLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDT--- 338
+ +NADFDGD+M +HVP S +AE ++ +++P + P+ +D
Sbjct: 438 HPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILG 497
Query: 339 ---LTAVRKMTK 347
+T VRK K
Sbjct: 498 LYYITQVRKEKK 509
Score = 57.4 bits (137), Expect = 1e-08, Method: Composition-based stats.
Identities = 30/104 (28%), Positives = 55/104 (52%), Gaps = 6/104 (5%)
Query: 138 GDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETR 197
G +V+ NR PTLH++ + + ++ + +++ +NADFDGD+M +HVP S +
Sbjct: 406 GKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQ 465
Query: 198 AEVENIHVTPRQIITPQNNRPVMGIVQDT------LTAVRKMTK 235
AE ++ +++P + P+ +D +T VRK K
Sbjct: 466 AEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKK 509
>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 = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 38/132 (28%), Positives = 67/132 (50%), Gaps = 12/132 (9%)
Query: 227 LTAVRKMTKR-----DVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRM 281
+ A R+M +R D D +E I G +V+ NR PTLH++ + + ++ + ++
Sbjct: 670 VKAARRMLERQRDIKDEVWDALEEVIH-GKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQL 728
Query: 282 NLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDT--- 338
+ +NADFDGD+M +HVP S +AE ++ +++P + P+ +D
Sbjct: 729 HPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILG 788
Query: 339 ---LTAVRKMTK 347
+T VRK K
Sbjct: 789 LYYITQVRKEKK 800
Score = 57.4 bits (137), Expect = 1e-08, Method: Composition-based stats.
Identities = 30/104 (28%), Positives = 55/104 (52%), Gaps = 6/104 (5%)
Query: 138 GDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETR 197
G +V+ NR PTLH++ + + ++ + +++ +NADFDGD+M +HVP S +
Sbjct: 697 GKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQ 756
Query: 198 AEVENIHVTPRQIITPQNNRPVMGIVQDT------LTAVRKMTK 235
AE ++ +++P + P+ +D +T VRK K
Sbjct: 757 AEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKK 800
>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 = 60.5 bits (145), Expect = 1e-09, Method: Composition-based stats.
Identities = 38/132 (28%), Positives = 67/132 (50%), Gaps = 12/132 (9%)
Query: 227 LTAVRKMTKR-----DVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRM 281
+ A R+M +R D D +E I G +V+ NR PTLH++ + + ++ + ++
Sbjct: 410 VKAARRMLERQRDIKDEVWDALEEVIH-GKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQL 468
Query: 282 NLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDT--- 338
+ +NADFDGD+M +HVP S +AE ++ +++P + P+ +D
Sbjct: 469 HPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILG 528
Query: 339 ---LTAVRKMTK 347
+T VRK K
Sbjct: 529 LYYITQVRKEKK 540
Score = 57.4 bits (137), Expect = 1e-08, Method: Composition-based stats.
Identities = 30/104 (28%), Positives = 55/104 (52%), Gaps = 6/104 (5%)
Query: 138 GDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETR 197
G +V+ NR PTLH++ + + ++ + +++ +NADFDGD+M +HVP S +
Sbjct: 437 GKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQ 496
Query: 198 AEVENIHVTPRQIITPQNNRPVMGIVQDT------LTAVRKMTK 235
AE ++ +++P + P+ +D +T VRK K
Sbjct: 497 AEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKK 540
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 60.5 bits (145), Expect = 2e-09, Method: Composition-based stats.
Identities = 38/132 (28%), Positives = 67/132 (50%), Gaps = 12/132 (9%)
Query: 227 LTAVRKMTKR-----DVFLDKVERHIRDGDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRM 281
+ A R+M +R D D +E I G +V+ NR PTLH++ + + ++ + ++
Sbjct: 410 VKAARRMLERQRDIKDEVWDALEEVIH-GKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQL 468
Query: 282 NLSCTSPYNADFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDT--- 338
+ +NADFDGD+M +HVP S +AE ++ +++P + P+ +D
Sbjct: 469 HPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILG 528
Query: 339 ---LTAVRKMTK 347
+T VRK K
Sbjct: 529 LYYITQVRKEKK 540
Score = 57.4 bits (137), Expect = 1e-08, Method: Composition-based stats.
Identities = 30/104 (28%), Positives = 55/104 (52%), Gaps = 6/104 (5%)
Query: 138 GDLVIFNRQPTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFDGDEMNLHVPQSMETR 197
G +V+ NR PTLH++ + + ++ + +++ +NADFDGD+M +HVP S +
Sbjct: 437 GKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQ 496
Query: 198 AEVENIHVTPRQIITPQNNRPVMGIVQDT------LTAVRKMTK 235
AE ++ +++P + P+ +D +T VRK K
Sbjct: 497 AEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKK 540
>pdb|4IFD|C Chain C, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 393
Score = 30.4 bits (67), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 30/64 (46%)
Query: 180 DFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVF 239
D D D++N + ++T AE +IH T + P N + ++ +M KR +
Sbjct: 319 DIDMDKLNTVLIADLDTEAEETSIHSTISILAAPSGNYKQLTLMGGGAKITPEMIKRSLL 378
Query: 240 LDKV 243
L +V
Sbjct: 379 LSRV 382
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 28/61 (45%)
Query: 292 DFDGDEMNLHVPQSMETRAEVENIHVTPRQIITPQNNRPVMGIVQDTLTAVRKMTKRDVF 351
D D D++N + ++T AE +IH T + P N + ++ +M KR +
Sbjct: 319 DIDMDKLNTVLIADLDTEAEETSIHSTISILAAPSGNYKQLTLMGGGAKITPEMIKRSLL 378
Query: 352 L 352
L
Sbjct: 379 L 379
>pdb|1VYF|A Chain A, Schistosoma Mansoni Fatty Acid Binding Protein In Complex
With Oleic Acid
pdb|1VYG|A Chain A, Schistosoma Mansoni Fatty Acid Binding Protein In Complex
With Arachidonic Acid
Length = 135
Score = 28.5 bits (62), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 147 PTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFD 182
PT+ +M G ++ +L STF+ NLSCT + +FD
Sbjct: 40 PTVT-FTMDGDKMTMLTESTFK-NLSCTFKFGEEFD 73
Score = 28.5 bits (62), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 23/36 (63%), Gaps = 2/36 (5%)
Query: 259 PTLHKMSMMGHRVRVLPWSTFRMNLSCTSPYNADFD 294
PT+ +M G ++ +L STF+ NLSCT + +FD
Sbjct: 40 PTVT-FTMDGDKMTMLTESTFK-NLSCTFKFGEEFD 73
>pdb|2AN1|A Chain A, Structural Genomics, The Crystal Structure Of A Putative
Kinase From Salmonella Typhimurim Lt2
pdb|2AN1|B Chain B, Structural Genomics, The Crystal Structure Of A Putative
Kinase From Salmonella Typhimurim Lt2
pdb|2AN1|C Chain C, Structural Genomics, The Crystal Structure Of A Putative
Kinase From Salmonella Typhimurim Lt2
pdb|2AN1|D Chain D, Structural Genomics, The Crystal Structure Of A Putative
Kinase From Salmonella Typhimurim Lt2
Length = 292
Score = 28.1 bits (61), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 15 AKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR 59
A+ +V ++ I LRF + SDL + C ++ I++G+ V+ R
Sbjct: 218 ARPLVINSSSTIRLRFSHRRSDLEISCDSQIALPIQEGEDVLIRR 262
Score = 28.1 bits (61), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 26/45 (57%)
Query: 101 AKYIVRDNGERIDLRFHPKPSDLHLQCGYKVERHIRDGDLVIFNR 145
A+ +V ++ I LRF + SDL + C ++ I++G+ V+ R
Sbjct: 218 ARPLVINSSSTIRLRFSHRRSDLEISCDSQIALPIQEGEDVLIRR 262
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
0.324 0.138 0.426
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,947,398
Number of Sequences: 62578
Number of extensions: 459934
Number of successful extensions: 1116
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1063
Number of HSP's gapped (non-prelim): 50
length of query: 353
length of database: 14,973,337
effective HSP length: 100
effective length of query: 253
effective length of database: 8,715,537
effective search space: 2205030861
effective search space used: 2205030861
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)