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= 020890
         (320 letters)

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

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



>pdb|1NY7|2 Chain 2, Cowpea Mosaic Virus (Cpmv)
 pdb|2BFU|L Chain L, X-Ray Structure Of Cpmv Top Component
          Length = 369

 Score = 27.7 bits (60), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 13/36 (36%), Positives = 22/36 (61%), Gaps = 2/36 (5%)

Query: 143 DLQFELTKLSTPWGYVSAIVLCVATFGTIAIMSGLF 178
           +L FE+TK+S+P  Y+ A V  +  FG ++   G +
Sbjct: 245 ELHFEVTKMSSP--YIKATVTFLIAFGNLSDAFGFY 278


  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
   0.323    0.140    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,610,541
Number of Sequences: 62578
Number of extensions: 328069
Number of successful extensions: 774
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 772
Number of HSP's gapped (non-prelim): 4
length of query: 320
length of database: 14,973,337
effective HSP length: 99
effective length of query: 221
effective length of database: 8,778,115
effective search space: 1939963415
effective search space used: 1939963415
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)