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= 022861
         (291 letters)

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

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



>pdb|1NO7|A Chain A, Structure Of The Large Protease Resistant Upper Domain Of
           Vp5, The Major Capsid Protein Of Herpes Simplex Virus-1
 pdb|1NO7|B Chain B, Structure Of The Large Protease Resistant Upper Domain Of
           Vp5, The Major Capsid Protein Of Herpes Simplex Virus-1
          Length = 604

 Score = 29.3 bits (64), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 1/68 (1%)

Query: 2   RRITGMPLNSSSSEFGTVLTSWWAEINESSQWQDGIFYSLCAAYALVSSVALIQLIRIEL 61
           R++  +P    ++ F ++       + ES+  ++ + Y+L A Y  +S VAL   ++  L
Sbjct: 535 RQVPLVPPALGANYFSSIRQPVVQHVRESAAGENALTYALMAGYFKISPVALHHQLKTGL 594

Query: 62  RVPEYGWT 69
             P +G+T
Sbjct: 595 H-PGFGFT 601


  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
   0.331    0.142    0.448 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,134,931
Number of Sequences: 62578
Number of extensions: 234812
Number of successful extensions: 446
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 445
Number of HSP's gapped (non-prelim): 2
length of query: 291
length of database: 14,973,337
effective HSP length: 98
effective length of query: 193
effective length of database: 8,840,693
effective search space: 1706253749
effective search space used: 1706253749
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 51 (24.3 bits)