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= psy13242
         (76 letters)

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

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



>pdb|3SY2|A Chain A, Crystal Structure Of The Salmonella E3 Ubiquitin Ligase
           Sopa In Complex With The Human E2 Ubch7
 pdb|3SY2|B Chain B, Crystal Structure Of The Salmonella E3 Ubiquitin Ligase
           Sopa In Complex With The Human E2 Ubch7
          Length = 621

 Score = 25.8 bits (55), Expect = 6.8,   Method: Composition-based stats.
 Identities = 12/39 (30%), Positives = 21/39 (53%)

Query: 5   GSRLSITLDSSLGENEQDANSALAELEKGLRSSKIGEQC 43
           G  + +T+DS   +  Q+   A+ +L K LR  ++ E C
Sbjct: 192 GKSILMTIDSLPDKYSQEKVQAMEDLVKSLRGGRLTEAC 230


>pdb|2QYU|A Chain A, Crystal Structure Of Salmonella Effector Protein Sopa
          Length = 627

 Score = 25.8 bits (55), Expect = 7.2,   Method: Composition-based stats.
 Identities = 12/39 (30%), Positives = 21/39 (53%)

Query: 5   GSRLSITLDSSLGENEQDANSALAELEKGLRSSKIGEQC 43
           G  + +T+DS   +  Q+   A+ +L K LR  ++ E C
Sbjct: 198 GKSILMTIDSLPDKYSQEKVQAMEDLVKSLRGGRLTEAC 236


  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    0.136    0.373 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,919,105
Number of Sequences: 62578
Number of extensions: 57340
Number of successful extensions: 139
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 137
Number of HSP's gapped (non-prelim): 4
length of query: 76
length of database: 14,973,337
effective HSP length: 45
effective length of query: 31
effective length of database: 12,157,327
effective search space: 376877137
effective search space used: 376877137
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)