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= 025146
         (257 letters)

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

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



>pdb|3ZRH|A Chain A, Crystal Structure Of The Lys29, Lys33-Linkage-Specific
           Trabid Otu Deubiquitinase Domain Reveals An
           Ankyrin-Repeat Ubiquitin Binding Domain (Ankubd)
          Length = 454

 Score = 28.5 bits (62), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 22/43 (51%)

Query: 137 SASKQISAAISPDQNTSAFKEVAIIRHPRLGEYAFGFITSSVV 179
            A+K I A + P+      +E+A   H R G++A  F+T  V 
Sbjct: 95  QAAKCIPAMVCPELTEQIRREIAASLHQRKGDFACYFLTDLVT 137


  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
   0.324    0.138    0.429 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,458,660
Number of Sequences: 62578
Number of extensions: 287248
Number of successful extensions: 785
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 784
Number of HSP's gapped (non-prelim): 12
length of query: 257
length of database: 14,973,337
effective HSP length: 97
effective length of query: 160
effective length of database: 8,903,271
effective search space: 1424523360
effective search space used: 1424523360
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 50 (23.9 bits)