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= 009572
         (532 letters)

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

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



>pdb|3HD4|A Chain A, Mhv Nucleocapsid Protein Ntd
          Length = 139

 Score = 29.3 bits (64), Expect = 6.0,   Method: Composition-based stats.
 Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 279 FRGVTVEVQKFEDFKWLNASYVPVLKQLQDSETQSYYFSGNSDGGRTP 326
           F G+T + QK ++F++     VP+   +  SE + Y++  N    +TP
Sbjct: 11  FSGIT-QFQKGKEFQFAEGQGVPIANGIPASEQKGYWYRHNRRSFKTP 57


  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    0.137    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,797,120
Number of Sequences: 62578
Number of extensions: 580820
Number of successful extensions: 1205
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 1202
Number of HSP's gapped (non-prelim): 4
length of query: 532
length of database: 14,973,337
effective HSP length: 103
effective length of query: 429
effective length of database: 8,527,803
effective search space: 3658427487
effective search space used: 3658427487
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)