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= psy8401
         (103 letters)

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

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



>pdb|1CMX|A Chain A, Structural Basis For The Specificity Of Ubiquitin C-
           Terminal Hydrolases
 pdb|1CMX|C Chain C, Structural Basis For The Specificity Of Ubiquitin C-
           Terminal Hydrolases
          Length = 235

 Score = 30.0 bits (66), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 11/50 (22%), Positives = 20/50 (40%)

Query: 28  YINRNFSIYNNRNHSMYDNTRNNNRHYSMYINRNHSMYNTRNNNRNHPMY 77
            I  N   ++       + T + N HY  Y+  N  ++     N + P+Y
Sbjct: 141 VIKENVQTFSTGQSEAPEATADTNLHYITYVEENGGIFELDGRNLSGPLY 190


  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
   0.316    0.124    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,539,328
Number of Sequences: 62578
Number of extensions: 137999
Number of successful extensions: 390
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 362
Number of HSP's gapped (non-prelim): 41
length of query: 103
length of database: 14,973,337
effective HSP length: 68
effective length of query: 35
effective length of database: 10,718,033
effective search space: 375131155
effective search space used: 375131155
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)