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= psy13491
         (69 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of
          Hypothetical Polyadenylate-Binding Protein (Pabpn1)
          From Homo Sapiens At 1.95 A Resolution
          Length = 89

 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)

Query: 3  AKRDEVQTAMAMDESLFRGRQIKVNPKRTNRPGI 36
          + ++ V+T++A+DESLFRGRQIKV PKRTNRPGI
Sbjct: 56 SDKESVRTSLALDESLFRGRQIKVIPKRTNRPGI 89


>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
 pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
 pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
 pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
 pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
          Length = 96

 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 24/34 (70%), Positives = 31/34 (91%)

Query: 3  AKRDEVQTAMAMDESLFRGRQIKVNPKRTNRPGI 36
          + ++ V+T++A+DESLFRGRQIKV PKRTNRPGI
Sbjct: 55 SDKESVRTSLALDESLFRGRQIKVIPKRTNRPGI 88


>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
           Xenopus Laevis Epabp2
 pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
           Xenopus Laevis Epabp2
          Length = 124

 Score = 55.5 bits (132), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 25/38 (65%), Positives = 32/38 (84%)

Query: 3   AKRDEVQTAMAMDESLFRGRQIKVNPKRTNRPGISTTN 40
           A+R+ V  A+AMDE++FRGR IKV PKRTN PGIS+T+
Sbjct: 86  AERNSVDAAVAMDETVFRGRTIKVLPKRTNMPGISSTD 123


>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
 pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
           With 5'- Uccagu-3'
 pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
           With 5'- Uggagu-3'
          Length = 135

 Score = 25.4 bits (54), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 4   KRDEVQTAMAMDESLFRGRQIKVNPKRTNRP 34
           KRD      AMD ++  GR+++V   R  RP
Sbjct: 99  KRDAEDAMDAMDGAVLDGRELRVQMARYGRP 129


  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
   0.319    0.130    0.366 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,313,656
Number of Sequences: 62578
Number of extensions: 24975
Number of successful extensions: 42
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 37
Number of HSP's gapped (non-prelim): 5
length of query: 69
length of database: 14,973,337
effective HSP length: 39
effective length of query: 30
effective length of database: 12,532,795
effective search space: 375983850
effective search space used: 375983850
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)