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= 041672
         (127 letters)

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

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



>pdb|1WR5|A Chain A, Three Dimensional Structure Of The E41k Mutant Of
          Tetraheme Cytochrome C3 From Desulfovibrio Vulgaris
          Miyazaki F
          Length = 108

 Score = 25.4 bits (54), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 11/40 (27%), Positives = 18/40 (45%)

Query: 44 GSIESLKCSACNCHRNFHRKEIGCDAHYHHLHQQAMMMLS 83
          G  +  KC+   CH N  +K+     +YH +H +     S
Sbjct: 40 GKKDYQKCATAGCHDNMDKKDKSAKGYYHAMHDKGTKFKS 79


  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
   0.317    0.129    0.404 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,701,712
Number of Sequences: 62578
Number of extensions: 138182
Number of successful extensions: 490
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 474
Number of HSP's gapped (non-prelim): 20
length of query: 127
length of database: 14,973,337
effective HSP length: 87
effective length of query: 40
effective length of database: 9,529,051
effective search space: 381162040
effective search space used: 381162040
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)