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= 025960
         (245 letters)

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

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



>pdb|3AL8|B Chain B, Plexin A2  SEMAPHORIN 6A COMPLEX
 pdb|3AL9|A Chain A, Mouse Plexin A2 Extracellular Domain
 pdb|3AL9|B Chain B, Mouse Plexin A2 Extracellular Domain
          Length = 539

 Score = 26.9 bits (58), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 9/30 (30%), Positives = 14/30 (46%)

Query: 128 RKCNQLKPPRCHHCSVCGRCILKMDHHCVW 157
           R+  ++    C   + CG C+   D HC W
Sbjct: 471 RQVTRVPVESCEQYTTCGECLSSGDPHCGW 500


  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    0.140    0.466 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,543,573
Number of Sequences: 62578
Number of extensions: 208396
Number of successful extensions: 449
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 444
Number of HSP's gapped (non-prelim): 10
length of query: 245
length of database: 14,973,337
effective HSP length: 96
effective length of query: 149
effective length of database: 8,965,849
effective search space: 1335911501
effective search space used: 1335911501
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: 50 (23.9 bits)