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= psy8527
(209 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1DMU|A Chain A, Crystal Structure Of The Restriction Endonuclease Bgli
(E.C.3.1.21.4) Bound To Its Dna Recognition Sequence
Length = 299
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 31/64 (48%), Gaps = 11/64 (17%)
Query: 58 TEVVTATIPPQEILAEMTSTSTVAPTIFPFIQPVHPIFLQTKTAQG-------LASAFVG 110
+++ TIPP IL S T+AP + FI+P++ + TK G LAS G
Sbjct: 188 SQIFLPTIPPLYIL----SDGTIAPVVHLFIKPIYAMRSLTKGDTGQSLYKIKLASVPNG 243
Query: 111 AALF 114
LF
Sbjct: 244 LGLF 247
>pdb|2RQG|B Chain B, Structure Of Gspt1ERF3A-Pabc
pdb|2RQH|B Chain B, Structure Of Gspt1ERF3A-Pabc
Length = 83
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 6/41 (14%)
Query: 55 RPLTEVVTATIPPQEILAEMTSTSTVAPTIFPFIQPVHPIF 95
PLT + A+ PPQE + +FP IQ +HP
Sbjct: 3 EPLTASMLASAPPQE------QKQMLGERLFPLIQAMHPTL 37
>pdb|3PTH|A Chain A, The Pabc1 Mlle Domain Bound To The Variant Pam2 Motif Of
Larp4b
Length = 82
Score = 28.5 bits (62), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 6/41 (14%)
Query: 55 RPLTEVVTATIPPQEILAEMTSTSTVAPTIFPFIQPVHPIF 95
PLT + A+ PPQE + +FP IQ +HP
Sbjct: 4 EPLTASMLASAPPQE------QKQMLGERLFPLIQAMHPTL 38
>pdb|3KUS|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUS|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUT|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KUT|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(a)-binding
Protein In Complex With The Binding Region Of Paip2
pdb|3KTP|A Chain A, Structural Basis Of Gw182 Recognition By Poly(a)-binding
Protein
pdb|3KTR|A Chain A, Structural Basis Of Ataxin-2 Recognition By
Poly(A)-Binding
pdb|3KUI|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
Complex Binding Region Of Erf3a
pdb|3KUJ|A Chain A, Crystal Structure Of C-Terminal Domain Of Pabpc1 In
Complex With Binding Region Of Erf3a
pdb|3PKN|A Chain A, Crystal Structure Of Mlle Domain Of Poly(A) Binding
Protein In Complex With Pam2 Motif Of La-Related
Protein 4 (Larp4)
Length = 88
Score = 28.1 bits (61), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 6/40 (15%)
Query: 56 PLTEVVTATIPPQEILAEMTSTSTVAPTIFPFIQPVHPIF 95
PLT + A+ PPQE + +FP IQ +HP
Sbjct: 6 PLTASMLASAPPQE------QKQMLGERLFPLIQAMHPTL 39
>pdb|3KUR|A Chain A, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|B Chain B, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|C Chain C, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|D Chain D, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|E Chain E, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|F Chain F, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|G Chain G, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
pdb|3KUR|H Chain H, Crystal Structure Of The Mlle Domain Of Poly(A)-Binding
Protein
Length = 79
Score = 27.7 bits (60), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 6/42 (14%)
Query: 54 ARPLTEVVTATIPPQEILAEMTSTSTVAPTIFPFIQPVHPIF 95
PLT + A+ PPQE + +FP IQ +HP
Sbjct: 4 GSPLTASMLASAPPQE------QKQMLGERLFPLIQAMHPTL 39
>pdb|1JGN|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of
Human Poly(A)-Binding Protein In Complex With The
Peptide From Paip2
pdb|1JH4|A Chain A, Solution Structure Of The C-Terminal Pabc Domain Of
Human Poly(A)-Binding Protein In Complex With The
Peptide From Paip1
Length = 98
Score = 27.3 bits (59), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 6/42 (14%)
Query: 54 ARPLTEVVTATIPPQEILAEMTSTSTVAPTIFPFIQPVHPIF 95
PLT + A+ PPQE + +FP IQ +HP
Sbjct: 4 GSPLTASMLASAPPQE------QKQMLGERLFPLIQAMHPTL 39
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
0.328 0.141 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,064,014
Number of Sequences: 62578
Number of extensions: 146882
Number of successful extensions: 530
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 528
Number of HSP's gapped (non-prelim): 9
length of query: 209
length of database: 14,973,337
effective HSP length: 94
effective length of query: 115
effective length of database: 9,091,005
effective search space: 1045465575
effective search space used: 1045465575
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 49 (23.5 bits)