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= 039620
         (486 letters)

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

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



>pdb|3SUA|D Chain D, Crystal Structure Of The Intracellular Domain Of Plexin-B1
           In Complex With Rac1
 pdb|3SUA|E Chain E, Crystal Structure Of The Intracellular Domain Of Plexin-B1
           In Complex With Rac1
 pdb|3SUA|F Chain F, Crystal Structure Of The Intracellular Domain Of Plexin-B1
           In Complex With Rac1
          Length = 633

 Score = 29.3 bits (64), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 2/27 (7%)

Query: 414 GGLRPWILYKPENHTAPDPPCHRAMSM 440
           GG+RPW L KP +   P+PP  R  S+
Sbjct: 377 GGIRPWHLVKPSDE--PEPPRPRRGSL 401


>pdb|3HM6|X Chain X, Crystal Structure Of The Cytoplasmic Domain Of Human
           Plexin B1
          Length = 644

 Score = 29.3 bits (64), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 2/27 (7%)

Query: 414 GGLRPWILYKPENHTAPDPPCHRAMSM 440
           GG+RPW L KP +   P+PP  R  S+
Sbjct: 388 GGIRPWHLVKPSDE--PEPPRPRRGSL 412


>pdb|3SU8|X Chain X, Crystal Structure Of A Truncated Intracellular Domain Of
           Plexin-B1 In Complex With Rac1
          Length = 611

 Score = 29.3 bits (64), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 2/27 (7%)

Query: 414 GGLRPWILYKPENHTAPDPPCHRAMSM 440
           GG+RPW L KP +   P+PP  R  S+
Sbjct: 355 GGIRPWHLVKPSDE--PEPPRPRRGSL 379


  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
   0.321    0.137    0.433 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,618,717
Number of Sequences: 62578
Number of extensions: 589461
Number of successful extensions: 1051
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1050
Number of HSP's gapped (non-prelim): 6
length of query: 486
length of database: 14,973,337
effective HSP length: 103
effective length of query: 383
effective length of database: 8,527,803
effective search space: 3266148549
effective search space used: 3266148549
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: 53 (25.0 bits)