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= psy16768
(154 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 63.2 bits (152), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 34/101 (33%), Positives = 60/101 (59%), Gaps = 3/101 (2%)
Query: 6 KHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGI 65
++++ TDG N++ + + + D+ K+ N+I + +GIEAA +IIRE+ V A G+
Sbjct: 248 EYIILTDGSNLSGVLSVKGV-DIAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGL 306
Query: 66 EVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVKSTTARS 106
+VD RH+ LVAD MT + ++ + + + E S AR+
Sbjct: 307 DVDMRHILLVADVMTRT--GVVRQIGRHGVTGEKNSVLARA 345
>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 = 63.2 bits (152), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 34/101 (33%), Positives = 60/101 (59%), Gaps = 3/101 (2%)
Query: 6 KHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGI 65
++++ TDG N++ + + + D+ K+ N+I + +GIEAA +IIRE+ V A G+
Sbjct: 248 EYIILTDGSNLSGVLSVKGV-DIAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGL 306
Query: 66 EVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVKSTTARS 106
+VD RH+ LVAD MT + ++ + + + E S AR+
Sbjct: 307 DVDMRHILLVADVMTRT--GVVRQIGRHGVTGEKNSVLARA 345
>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 = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 33/101 (32%), Positives = 60/101 (59%), Gaps = 3/101 (2%)
Query: 6 KHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGI 65
++++ TDG N++ + + + D+ K+ N+I + +GIEAA +IIRE+ V A G+
Sbjct: 248 EYIILTDGSNLSGVLSVKGV-DVAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGL 306
Query: 66 EVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVKSTTARS 106
+VD RH+ L+AD MT + ++ + + + E S AR+
Sbjct: 307 DVDIRHILLIADVMTRT--GIVRQIGRHGVTGEKNSVLARA 345
>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 = 62.4 bits (150), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 33/101 (32%), Positives = 60/101 (59%), Gaps = 3/101 (2%)
Query: 6 KHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGI 65
++++ TDG N++ + + + D+ K+ N+I + +GIEAA +IIRE+ V A G+
Sbjct: 245 EYIILTDGSNLSGVLSVKGV-DVAKVETNNIREIEEVFGIEAAREIIIREISKVLAEQGL 303
Query: 66 EVDPRHLSLVADYMTHSEFDLIIMVSKSWMLDEVKSTTARS 106
+VD RH+ L+AD MT + ++ + + + E S AR+
Sbjct: 304 DVDIRHILLIADVMTRT--GIVRQIGRHGVTGEKNSVLARA 342
>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 = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 8 LLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEV 67
+L+TDG+N++ + + D ++Y N + GIEA + +EV NV A G V
Sbjct: 1305 VLETDGVNLSEVMTVPGI-DPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYV 1363
Query: 68 DPRHLSLVADYMT 80
+ RH++L+ D MT
Sbjct: 1364 NYRHMALLVDVMT 1376
>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 = 45.1 bits (105), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 8 LLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEV 67
+L+TDG+N++ + + D ++Y N + GIEA + +EV NV A G V
Sbjct: 1305 VLETDGVNLSEVMTVPGI-DPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYV 1363
Query: 68 DPRHLSLVADYMT 80
+ RH++L+ D MT
Sbjct: 1364 NYRHMALLVDVMT 1376
>pdb|3J0K|A Chain A, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
Length = 1455
Score = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 8 LLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEV 67
+L+TDG+N++ + + D ++Y N + GIEA + +EV NV A G V
Sbjct: 1305 VLETDGVNLSEVMTVPGI-DPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYV 1363
Query: 68 DPRHLSLVADYMT 80
+ RH++L+ D MT
Sbjct: 1364 NYRHMALLVDVMT 1376
>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 = 44.7 bits (104), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 41/80 (51%), Gaps = 1/80 (1%)
Query: 1 METNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVF 60
E + +L+TDGIN+ + D + Y N + GIEA +++E++NV
Sbjct: 1304 FERADEWVLETDGINLTEAMTVEGV-DATRTYSNSFVEILQILGIEATRSALLKELRNVI 1362
Query: 61 AVYGIEVDPRHLSLVADYMT 80
G V+ RHL+L+ D MT
Sbjct: 1363 EFDGSYVNYRHLALLCDVMT 1382
>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 = 32.0 bits (71), Expect = 0.16, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 35 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 79
D H + G EA R ++ E++ V+ G+++ +H+ +V M
Sbjct: 1331 DPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQM 1375
>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 = 32.0 bits (71), Expect = 0.16, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 35 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 79
D H + G EA R ++ E++ V+ G+++ +H+ +V M
Sbjct: 1331 DPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQM 1375
>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 = 31.2 bits (69), Expect = 0.24, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 35 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 79
D H + G EA R ++ E++ V+ G+++ +H+ +V M
Sbjct: 1331 DPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQM 1375
>pdb|1I6V|D Chain D, Thermus Aquaticus Core Rna Polymerase-Rifampicin Complex
Length = 1264
Score = 31.2 bits (69), Expect = 0.24, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 35 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 79
D H + G EA R ++ E++ V+ G+++ +H+ +V M
Sbjct: 1071 DPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQM 1115
>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 = 31.2 bits (69), Expect = 0.24, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 35 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 79
D H + G EA R ++ E++ V+ G+++ +H+ +V M
Sbjct: 1072 DPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQM 1116
>pdb|2GHO|D Chain D, Recombinant Thermus Aquaticus Rna Polymerase For Structural
Studies
Length = 1233
Score = 31.2 bits (69), Expect = 0.24, Method: Composition-based stats.
Identities = 12/45 (26%), Positives = 24/45 (53%)
Query: 35 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 79
D H + G EA R ++ E++ V+ G+++ +H+ +V M
Sbjct: 1040 DPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHDKHIEIVVRQM 1084
>pdb|1AKW|A Chain A, G61l Oxidized Flavodoxin Mutant
Length = 147
Score = 31.2 bits (69), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 4/65 (6%)
Query: 36 IHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSWM 95
I Y ++T E I RE+ + G EVD R + V FDL+++ +W+
Sbjct: 5 IVYGSTTGNTEYTAETIARELADA----GYEVDSRDAASVEAGGLFEGFDLVLLGCSTWL 60
Query: 96 LDEVK 100
D ++
Sbjct: 61 DDSIE 65
>pdb|1AZL|A Chain A, G61v Flavodoxin Mutant From Desulfovibrio Vulgaris
Length = 147
Score = 30.4 bits (67), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 4/65 (6%)
Query: 36 IHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSWM 95
I Y ++T E I RE+ + G EVD R + V FDL+++ +W+
Sbjct: 5 IVYGSTTGNTEYTAETIARELADA----GYEVDSRDAASVEAGGLFEGFDLVLLGCSTWV 60
Query: 96 LDEVK 100
D ++
Sbjct: 61 DDSIE 65
>pdb|1FX1|A Chain A, A Crystallographic Structural Study Of The Oxidation
States Of Desulfovibrio Vulgaris Flavodoxin
Length = 148
Score = 30.0 bits (66), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 35/89 (39%), Gaps = 17/89 (19%)
Query: 36 IHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSW- 94
I Y ++T E I R++ N G EVD R + V FDL+++ +W
Sbjct: 6 IVYGSTTGNTEYTAETIARQLANA----GYEVDSRDAASVEAGGLFEGFDLVLLGCSTWG 61
Query: 95 ------------MLDEVKSTTARSVTPAC 111
+ D ++ T A+ AC
Sbjct: 62 DDSIELQDDFIPLFDSLEETGAQGRKVAC 90
>pdb|1AKR|A Chain A, G61a Oxidized Flavodoxin Mutant
Length = 147
Score = 30.0 bits (66), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 4/65 (6%)
Query: 36 IHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIMVSKSWM 95
I Y ++T E I RE+ + G EVD R + V FDL+++ +W
Sbjct: 5 IVYGSTTGNTEYTAETIARELADA----GYEVDSRDAASVEAGGLFEGFDLVLLGCSTWA 60
Query: 96 LDEVK 100
D ++
Sbjct: 61 DDSIE 65
>pdb|3T66|A Chain A, Crystal Structure Of Nickel Abc Transporter From Bacillus
Halodurans
Length = 496
Score = 28.1 bits (61), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 41/77 (53%), Gaps = 3/77 (3%)
Query: 14 INVNYISQYRHLLDLNKLYVND--IHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRH 71
I + Y+ + + L+ ++ + +H+ TYG A +I + ++ GIEV+ R
Sbjct: 306 IAIQYLEEAGYTLENGQMQKDGEPLHFTVLTYGSRAELPLIAQVFQSNAKQIGIEVEIRQ 365
Query: 72 LSLVADYM-THSEFDLI 87
+ + +YM ++ ++DLI
Sbjct: 366 IEVPEEYMASNRDWDLI 382
>pdb|3D3A|A Chain A, Crystal Structure Of A Beta-Galactosidase From Bacteroides
Thetaiotaomicron
Length = 612
Score = 26.9 bits (58), Expect = 4.8, Method: Composition-based stats.
Identities = 14/65 (21%), Positives = 31/65 (47%), Gaps = 2/65 (3%)
Query: 30 KLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHSEFDLIIM 89
KL++N++ + I +I +V+N + +GI D ++S + D + + F + +
Sbjct: 133 KLFLNEVGKQLADLQISKGGNIIXVQVENEYGAFGI--DKPYISEIRDXVKQAGFTGVPL 190
Query: 90 VSKSW 94
W
Sbjct: 191 FQCDW 195
>pdb|1QG8|A Chain A, Native (Magnesium-Containing) Spsa From Bacillus Subtilis
pdb|1QGQ|A Chain A, Udp-manganese Complex Of Spsa From Bacillus Subtilis
pdb|1QGS|A Chain A, Udp-Magnesium Complex Of Spsa From Bacillus Subtilis
pdb|1H7L|A Chain A, Dtdp-Magnesium Complex Of Spsa From Bacillus Subtilis
pdb|1H7Q|A Chain A, Dtdp-Manganese Complex Of Spsa From Bacillus Subtilis
Length = 255
Score = 26.2 bits (56), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 70 RHLSLVADYMTHSEFDLIIMVSKSWMLDEVKSTTARSVTPACE 112
R L +V + TH E +I SK++ L+E + +V PA +
Sbjct: 105 RLLKMVRELDTHPEKAVIYSASKTYHLNENRDIVKETVRPAAQ 147
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
0.318 0.134 0.388
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,627,711
Number of Sequences: 62578
Number of extensions: 159397
Number of successful extensions: 401
Number of sequences better than 100.0: 21
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 385
Number of HSP's gapped (non-prelim): 21
length of query: 154
length of database: 14,973,337
effective HSP length: 90
effective length of query: 64
effective length of database: 9,341,317
effective search space: 597844288
effective search space used: 597844288
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 bits)