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= 004476
         (751 letters)

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

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



>pdb|1V33|A Chain A, Crystal Structure Of Dna Primase From Pyrococcus
           Horikoshii
 pdb|1V34|A Chain A, Crystal Structure Of Pyrococcus Horikoshii Dna Primase-utp
           Complex
          Length = 366

 Score = 29.6 bits (65), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 4/57 (7%)

Query: 232 DAHVSTSGLGDRILKMKEERLKKNSEGAPEILSWVNRSRKIEQIKNVEKKKALQLSK 288
           D H+  SG G  I  + E  LK +S+    ILS+V+ S    +I++VE+ + L L+K
Sbjct: 160 DIHIIYSGRGYHIRVLDEWALKLDSKSRERILSFVSAS----EIEDVEEFRKLLLNK 212


  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
   0.308    0.129    0.352 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,588,883
Number of Sequences: 62578
Number of extensions: 560179
Number of successful extensions: 1056
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1056
Number of HSP's gapped (non-prelim): 4
length of query: 751
length of database: 14,973,337
effective HSP length: 106
effective length of query: 645
effective length of database: 8,340,069
effective search space: 5379344505
effective search space used: 5379344505
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 55 (25.8 bits)