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= 004016
         (779 letters)

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

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



>pdb|2GV9|A Chain A, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna
           Polymerase
 pdb|2GV9|B Chain B, Crystal Structure Of The Herpes Simplex Virus Type 1 Dna
           Polymerase
          Length = 1193

 Score = 31.6 bits (70), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 21/70 (30%), Positives = 35/70 (50%), Gaps = 4/70 (5%)

Query: 124 FFTLSARIDKGIVKKSGKLAIVIGVGA----FIIPLIVSILTTLFIRDGLELDDELRSTL 179
           F TLS R D     ++GK  + I VG     F+   +   L ++ +RD L +  ++RS +
Sbjct: 691 FSTLSLRADAVAHLEAGKDYLEIEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRI 750

Query: 180 PMVATLEATI 189
           P  +  EA +
Sbjct: 751 PQSSPEEAVL 760


  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
   0.327    0.141    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,750,717
Number of Sequences: 62578
Number of extensions: 668764
Number of successful extensions: 1203
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1203
Number of HSP's gapped (non-prelim): 1
length of query: 779
length of database: 14,973,337
effective HSP length: 106
effective length of query: 673
effective length of database: 8,340,069
effective search space: 5612866437
effective search space used: 5612866437
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 55 (25.8 bits)