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= psy9982
(222 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 36.2 bits (82), Expect = 0.014, Method: Composition-based stats.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 83 YTQVSPAYIPVSPAYTPVSPAYT 105
Y+ SP+Y P SP Y+P SPAY+
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYS 1718
Score = 36.2 bits (82), Expect = 0.014, Method: Composition-based stats.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 90 YIPVSPAYTPVSPAYTQVSPAYT 112
Y P SP+Y+P SP Y+ SPAY+
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYS 1718
Score = 35.8 bits (81), Expect = 0.021, Method: Composition-based stats.
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 76 YTQVSPAYTQVSPAYIPVSPAYTP 99
Y+ SP+Y+ SP Y P SPAY+P
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYSP 1719
Score = 34.3 bits (77), Expect = 0.057, Method: Composition-based stats.
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 97 YTPVSPAYTQVSPAYTQVSPAYT 119
Y+P SP+Y+ SP Y+ SPAY+
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYS 1718
Score = 30.8 bits (68), Expect = 0.66, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 104 YTQVSPAYTQVSPAYTQVSPAYT 126
Y+ SP+Y+ SP Y+ SPAY+
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYS 1718
Score = 30.8 bits (68), Expect = 0.66, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 139 YTQVSPAYTQVSPAYTQVSPAYT 161
Y+ SP+Y+ SP Y+ SPAY+
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYS 1718
Score = 27.7 bits (60), Expect = 5.5, Method: Composition-based stats.
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 59 SPAYTQVSPAYTQVSPAYTQVSPA 82
SP + SP ++ SP Y+ SPA
Sbjct: 1532 SPGFGVSSPGFSPTSPTYSPTSPA 1555
Score = 27.3 bits (59), Expect = 6.4, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 22/48 (45%)
Query: 45 YLSTDEDEATVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIP 92
Y D EAT + SP + SP ++ SP Y+ SPAY P
Sbjct: 1511 YGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSP 1558
Score = 27.3 bits (59), Expect = 6.7, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 146 YTQVSPAYTQVSPAYTQVSSAYT 168
Y+ SP+Y+ SP Y+ S AY+
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYS 1718
>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 = 36.2 bits (82), Expect = 0.014, Method: Composition-based stats.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 83 YTQVSPAYIPVSPAYTPVSPAYT 105
Y+ SP+Y P SP Y+P SPAY+
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYS 1718
Score = 36.2 bits (82), Expect = 0.014, Method: Composition-based stats.
Identities = 13/23 (56%), Positives = 17/23 (73%)
Query: 90 YIPVSPAYTPVSPAYTQVSPAYT 112
Y P SP+Y+P SP Y+ SPAY+
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYS 1718
Score = 35.8 bits (81), Expect = 0.021, Method: Composition-based stats.
Identities = 13/24 (54%), Positives = 17/24 (70%)
Query: 76 YTQVSPAYTQVSPAYIPVSPAYTP 99
Y+ SP+Y+ SP Y P SPAY+P
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYSP 1719
Score = 34.3 bits (77), Expect = 0.057, Method: Composition-based stats.
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 97 YTPVSPAYTQVSPAYTQVSPAYT 119
Y+P SP+Y+ SP Y+ SPAY+
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYS 1718
Score = 30.8 bits (68), Expect = 0.66, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 104 YTQVSPAYTQVSPAYTQVSPAYT 126
Y+ SP+Y+ SP Y+ SPAY+
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYS 1718
Score = 30.8 bits (68), Expect = 0.66, Method: Composition-based stats.
Identities = 11/23 (47%), Positives = 16/23 (69%)
Query: 139 YTQVSPAYTQVSPAYTQVSPAYT 161
Y+ SP+Y+ SP Y+ SPAY+
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYS 1718
Score = 27.7 bits (60), Expect = 5.5, Method: Composition-based stats.
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 59 SPAYTQVSPAYTQVSPAYTQVSPA 82
SP + SP ++ SP Y+ SPA
Sbjct: 1532 SPGFGVSSPGFSPTSPTYSPTSPA 1555
Score = 27.3 bits (59), Expect = 6.4, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 22/48 (45%)
Query: 45 YLSTDEDEATVYTVSPAYTQVSPAYTQVSPAYTQVSPAYTQVSPAYIP 92
Y D EAT + SP + SP ++ SP Y+ SPAY P
Sbjct: 1511 YGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSP 1558
Score = 27.3 bits (59), Expect = 6.7, Method: Composition-based stats.
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 146 YTQVSPAYTQVSPAYTQVSSAYT 168
Y+ SP+Y+ SP Y+ S AY+
Sbjct: 1696 YSPTSPSYSPTSPGYSPGSPAYS 1718
>pdb|2PX6|A Chain A, Crystal Structure Of The Thioesterase Domain Of Human
Fatty Acid Synthase Inhibited By Orlistat
pdb|2PX6|B Chain B, Crystal Structure Of The Thioesterase Domain Of Human
Fatty Acid Synthase Inhibited By Orlistat
Length = 316
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 3/82 (3%)
Query: 129 SLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPGRESNSRSSAY 188
+A+ S Q SPA T S SP Y AYTQ K+ PG E+ + + A
Sbjct: 117 CVAFEMCSQLQAQQSPAPTHNSLFLFDGSPTYVL---AYTQSYRAKLTPGCEAEAETEAI 173
Query: 189 EAFFHEWVWMSWYPDINPTLPI 210
F ++ M + LP+
Sbjct: 174 CFFVQQFTDMEHNRVLEALLPL 195
>pdb|1XKT|A Chain A, Human Fatty Acid Synthase: Structure And Substrate
Selectivity Of The Thioesterase Domain
pdb|1XKT|B Chain B, Human Fatty Acid Synthase: Structure And Substrate
Selectivity Of The Thioesterase Domain
Length = 289
Score = 28.1 bits (61), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 34/82 (41%), Gaps = 3/82 (3%)
Query: 129 SLAYTQVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKIRPGRESNSRSSAY 188
+A+ S Q SPA T S SP Y AYTQ K+ PG E+ + + A
Sbjct: 99 CVAFEMCSQLQAQQSPAPTHNSLFLFDGSPTYVL---AYTQSYRAKLTPGCEAEAETEAI 155
Query: 189 EAFFHEWVWMSWYPDINPTLPI 210
F ++ M + LP+
Sbjct: 156 CFFVQQFTDMEHNRVLEALLPL 177
>pdb|1YOC|A Chain A, Crystal Structure Of Genomics Apc5556
pdb|1YOC|B Chain B, Crystal Structure Of Genomics Apc5556
Length = 147
Score = 27.3 bits (59), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 11/42 (26%), Positives = 22/42 (52%)
Query: 134 QVSLAYTQVSPAYTQVSPAYTQVSPAYTQVSSAYTQVILNKI 175
Q S Q +P + ++P + ++ P Y +V+ + +LN I
Sbjct: 17 QFSAMIGQFAPYFASIAPQFVELRPGYAEVTFPKRREVLNHI 58
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
0.313 0.125 0.374
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,244,573
Number of Sequences: 62578
Number of extensions: 238031
Number of successful extensions: 511
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 283
Number of HSP's gapped (non-prelim): 78
length of query: 222
length of database: 14,973,337
effective HSP length: 95
effective length of query: 127
effective length of database: 9,028,427
effective search space: 1146610229
effective search space used: 1146610229
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)