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= 029343
(194 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3KD7|A Chain A, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|B Chain B, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|C Chain C, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|D Chain D, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|E Chain E, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
Length = 125
Score = 35.8 bits (81), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 124 AVVAIRRGMLLFRQGDVVGSVAEFDKAIELDPR 156
A RRG ++QGD ++ ++ KA+ELDP
Sbjct: 77 AKAWYRRGNAYYKQGDYQKAIEDYQKALELDPN 109
Score = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 131 GMLLFRQGDVVGSVAEFDKAIELDPR 156
G ++QGD ++ + KA+ELDP
Sbjct: 50 GNAYYKQGDYQKAIEYYQKALELDPN 75
>pdb|2FO7|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
(Trigonal Crystal Form)
pdb|2HYZ|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
(Orthorombic Crystal Form)
Length = 136
Score = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 120 NSREAVVAIRRGMLLFRQGDVVGSVAEFDKAIELDPR 156
+ R A G ++QGD ++ + KA+ELDPR
Sbjct: 31 DPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR 67
Score = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 120 NSREAVVAIRRGMLLFRQGDVVGSVAEFDKAIELDPR 156
+ R A G ++QGD ++ + KA+ELDPR
Sbjct: 65 DPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR 101
Score = 31.6 bits (70), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 120 NSREAVVAIRRGMLLFRQGDVVGSVAEFDKAIELDPR 156
+ R A G ++QGD ++ + KA+ELDPR
Sbjct: 99 DPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR 135
Score = 30.4 bits (67), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 131 GMLLFRQGDVVGSVAEFDKAIELDPR 156
G ++QGD ++ + KA+ELDPR
Sbjct: 8 GNAYYKQGDYDEAIEYYQKALELDPR 33
>pdb|2AVP|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
Length = 70
Score = 31.2 bits (69), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 120 NSREAVVAIRRGMLLFRQGDVVGSVAEFDKAIELDPR 156
+ R A G ++QGD ++ + KA+ELDPR
Sbjct: 33 DPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPR 69
Score = 30.0 bits (66), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 11/26 (42%), Positives = 17/26 (65%)
Query: 131 GMLLFRQGDVVGSVAEFDKAIELDPR 156
G ++QGD ++ + KA+ELDPR
Sbjct: 10 GNAYYKQGDYDEAIEYYQKALELDPR 35
>pdb|3QDL|A Chain A, Crystal Structure Of Rdxa From Helicobacter Pyroli
pdb|3QDL|B Chain B, Crystal Structure Of Rdxa From Helicobacter Pyroli
pdb|3QDL|C Chain C, Crystal Structure Of Rdxa From Helicobacter Pyroli
pdb|3QDL|D Chain D, Crystal Structure Of Rdxa From Helicobacter Pyroli
Length = 210
Score = 28.1 bits (61), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 27/61 (44%), Gaps = 1/61 (1%)
Query: 46 LTQHVLKPTINPPLYSFHRSLLTSKAPLSVQTHINSLFSTPRGHYLQNRAPTFTRRLFIP 105
+T LK I Y F+ ++ S + L V + P GHY+QN P + IP
Sbjct: 57 VTDKDLKKQIAAHSY-FNEEMIKSASALMVVCSLRPSELLPHGHYMQNLYPESYKVRVIP 115
Query: 106 S 106
S
Sbjct: 116 S 116
>pdb|2KCK|A Chain A, Nmr Solution Structure Of The Northeast Structural
Genomics Consortium (Nesg) Target Mrr121a
Length = 112
Score = 28.1 bits (61), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 130 RGMLLFRQGDVVGSVAEFDKAIELDPRQK----ISGKGAYRFT 168
G+L + G+ S+ F+KAI+LDP + + GK Y
Sbjct: 12 EGVLQYDAGNYTESIDLFEKAIQLDPEESKYWLMKGKALYNLE 54
>pdb|1WCM|D Chain D, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
Length = 177
Score = 27.7 bits (60), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 28/62 (45%)
Query: 94 RAPTFTRRLFIPSVSGIWDALTGGNNNSREAVVAIRRGMLLFRQGDVVGSVAEFDKAIEL 153
R+ TR + S+ + + TGGNN + + FR + VG+V + K+ L
Sbjct: 69 RSQKKTREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGL 128
Query: 154 DP 155
P
Sbjct: 129 HP 130
>pdb|1MPP|A Chain A, X-Ray Analyses Of Aspartic Proteinases. V. Structure And
Refinement At 2.0 Angstroms Resolution Of The Aspartic
Proteinase From Mucor Pusillus
Length = 361
Score = 26.9 bits (58), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 8/47 (17%)
Query: 130 RGMLLFRQGDVVGSVAEFDKAIELDPRQKISGKGAYRFTISIGTKFF 176
RG F V G +++D +S GA FTI GT FF
Sbjct: 205 RGGYFFWDAPVTG--------VKIDGSDAVSFDGAQAFTIDTGTNFF 243
>pdb|1PQV|D Chain D, Rna Polymerase Ii-Tfiis Complex
Length = 221
Score = 26.6 bits (57), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 26/57 (45%)
Query: 99 TRRLFIPSVSGIWDALTGGNNNSREAVVAIRRGMLLFRQGDVVGSVAEFDKAIELDP 155
TR + S+ + + TGGNN + + FR + VG+V + K+ L P
Sbjct: 118 TREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHP 174
>pdb|1NT9|D Chain D, Complete 12-Subunit Rna Polymerase Ii
pdb|1Y1W|D Chain D, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|D Chain D, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|D Chain D, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|D Chain D, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|2B63|D Chain D, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2B8K|D Chain D, 12-Subunit Rna Polymerase Ii
pdb|2JA5|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|P Chain P, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|D Chain D, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2R7Z|D Chain D, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|D Chain D, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|D Chain D, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|D Chain D, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3FKI|D Chain D, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3H3V|E Chain E, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|D Chain D, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|P Chain P, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|D Chain D, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|D Chain D, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|D Chain D, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|D Chain D, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|D Chain D, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|D Chain D, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|D Chain D, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|D Chain D, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3PO2|D Chain D, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|D Chain D, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3J0K|D Chain D, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|D Chain D, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|D Chain D, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|D Chain D, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|D Chain D, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|D Chain D, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 221
Score = 26.6 bits (57), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 26/57 (45%)
Query: 99 TRRLFIPSVSGIWDALTGGNNNSREAVVAIRRGMLLFRQGDVVGSVAEFDKAIELDP 155
TR + S+ + + TGGNN + + FR + VG+V + K+ L P
Sbjct: 118 TREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHP 174
>pdb|3QT1|D Chain D, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
Length = 219
Score = 26.6 bits (57), Expect = 9.3, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 26/57 (45%)
Query: 99 TRRLFIPSVSGIWDALTGGNNNSREAVVAIRRGMLLFRQGDVVGSVAEFDKAIELDP 155
TR + S+ + + TGGNN + + FR + VG+V + K+ L P
Sbjct: 116 TREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHP 172
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 0.137 0.406
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,495,041
Number of Sequences: 62578
Number of extensions: 211832
Number of successful extensions: 500
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 484
Number of HSP's gapped (non-prelim): 17
length of query: 194
length of database: 14,973,337
effective HSP length: 94
effective length of query: 100
effective length of database: 9,091,005
effective search space: 909100500
effective search space used: 909100500
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: 49 (23.5 bits)