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= 008470
         (564 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 = 29.6 bits (65), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 21/92 (22%), Positives = 39/92 (42%), Gaps = 7/92 (7%)

Query: 277  PESLHAQPNVFGELMRVLISPSEDVEEAVKWVLGNGVDPDISLHMRMLTNRSVRAVQAAV 336
            PE L A   V  +  R +  P  D+++ V       +  ++S H R  TN+ +  +    
Sbjct: 962  PEGLQAFGAVLVDAHRRITDPERDIQDFV-------LTAELSRHPRAYTNKRLAHLTVYY 1014

Query: 337  KCIRKVVNSLNLTSRPKTVIVSDTPSFAKTIT 368
            K + +     ++  R   VIV+ T    +T+ 
Sbjct: 1015 KLMARRAQVPSIKDRIPYVIVAQTREVEETVA 1046


  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
   0.322    0.136    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,589,193
Number of Sequences: 62578
Number of extensions: 600163
Number of successful extensions: 1260
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1260
Number of HSP's gapped (non-prelim): 2
length of query: 564
length of database: 14,973,337
effective HSP length: 104
effective length of query: 460
effective length of database: 8,465,225
effective search space: 3894003500
effective search space used: 3894003500
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: 54 (25.4 bits)