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= psy8255
         (117 letters)

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

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



>pdb|1JMT|B Chain B, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
          Length = 28

 Score = 49.3 bits (116), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 19/27 (70%), Positives = 23/27 (85%)

Query: 59 RRKASLYWDVPPPGFEHVSPSQYKAMQ 85
          ++K   YWDVPPPGFEH++P QYKAMQ
Sbjct: 1  KKKVRKYWDVPPPGFEHITPMQYKAMQ 27


>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
          Length = 172

 Score = 35.4 bits (80), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 14/15 (93%), Positives = 15/15 (100%)

Query: 103 ARRLYVGNIPFGVTE 117
           ARRLYVGNIPFG+TE
Sbjct: 4   ARRLYVGNIPFGITE 18


>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
           U2af65 Tandem Rrm1 And Rrm2 Domains
 pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains  With
           Eight-Site Uridine Binding
          Length = 198

 Score = 35.4 bits (80), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 14/15 (93%), Positives = 15/15 (100%)

Query: 103 ARRLYVGNIPFGVTE 117
           ARRLYVGNIPFG+TE
Sbjct: 4   ARRLYVGNIPFGITE 18


>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
 pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
 pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
 pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
 pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
 pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
 pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
 pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
 pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
 pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
 pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
 pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
 pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
 pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
 pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
 pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
 pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
 pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
          Length = 174

 Score = 35.4 bits (80), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 14/15 (93%), Positives = 15/15 (100%)

Query: 103 ARRLYVGNIPFGVTE 117
           ARRLYVGNIPFG+TE
Sbjct: 6   ARRLYVGNIPFGITE 20


>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
           Subunit
          Length = 87

 Score = 35.0 bits (79), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 14/15 (93%), Positives = 15/15 (100%)

Query: 103 ARRLYVGNIPFGVTE 117
           ARRLYVGNIPFG+TE
Sbjct: 6   ARRLYVGNIPFGITE 20


>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
           Hu2af65
          Length = 90

 Score = 35.0 bits (79), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 14/15 (93%), Positives = 15/15 (100%)

Query: 103 ARRLYVGNIPFGVTE 117
           ARRLYVGNIPFG+TE
Sbjct: 1   ARRLYVGNIPFGITE 15


  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    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,777,419
Number of Sequences: 62578
Number of extensions: 46546
Number of successful extensions: 77
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 71
Number of HSP's gapped (non-prelim): 6
length of query: 117
length of database: 14,973,337
effective HSP length: 80
effective length of query: 37
effective length of database: 9,967,097
effective search space: 368782589
effective search space used: 368782589
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: 45 (21.9 bits)