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= 027723
         (219 letters)

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

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



>pdb|2AGA|A Chain A, De-Ubiquitinating Function Of Ataxin-3: Insights From The
           Solution Structure Of The Josephin Domain
          Length = 190

 Score = 30.8 bits (68), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 11/32 (34%), Positives = 21/32 (65%)

Query: 131 PVIISDNFVPPFFEILNWESFAVFVLERDIPN 162
           P +ISD ++  F   L  E +++FV++ D+P+
Sbjct: 145 PELISDTYLALFLAQLQQEGYSIFVVKGDLPD 176


>pdb|2JRI|A Chain A, Solution Structure Of The Josephin Domain Of Ataxin-3 In
           Complex With Ubiquitin Molecule.
 pdb|1YZB|A Chain A, Solution Structure Of The Josephin Domain Of Ataxin-3
          Length = 182

 Score = 30.4 bits (67), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 11/32 (34%), Positives = 21/32 (65%)

Query: 131 PVIISDNFVPPFFEILNWESFAVFVLERDIPN 162
           P +ISD ++  F   L  E +++FV++ D+P+
Sbjct: 140 PELISDTYLALFLAQLQQEGYSIFVVKGDLPD 171


>pdb|2DOS|A Chain A, Structural Basis For The Recognition Of Lys48-Linked
           Polyubiquitin Chain By The Josephin Domain Of Ataxin-3,
           A Putative Deubiquitinating Enzyme
          Length = 176

 Score = 30.4 bits (67), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 11/32 (34%), Positives = 21/32 (65%)

Query: 131 PVIISDNFVPPFFEILNWESFAVFVLERDIPN 162
           P +ISD ++  F   L  E +++FV++ D+P+
Sbjct: 145 PELISDTYLALFLAQLQQEGYSIFVVKGDLPD 176


>pdb|3O65|A Chain A, Crystal Structure Of A Josephin-Ubiquitin Complex:
           Evolutionary Restraints On Ataxin-3 Deubiquitinating
           Activity
 pdb|3O65|C Chain C, Crystal Structure Of A Josephin-Ubiquitin Complex:
           Evolutionary Restraints On Ataxin-3 Deubiquitinating
           Activity
 pdb|3O65|E Chain E, Crystal Structure Of A Josephin-Ubiquitin Complex:
           Evolutionary Restraints On Ataxin-3 Deubiquitinating
           Activity
 pdb|3O65|G Chain G, Crystal Structure Of A Josephin-Ubiquitin Complex:
           Evolutionary Restraints On Ataxin-3 Deubiquitinating
           Activity
          Length = 191

 Score = 27.3 bits (59), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 11/34 (32%), Positives = 22/34 (64%)

Query: 131 PVIISDNFVPPFFEILNWESFAVFVLERDIPNLK 164
           P +ISD  +  F   L  ++++VFV++ D+P+ +
Sbjct: 141 PELISDTCLANFLARLQQQAYSVFVVKGDLPDCE 174


  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    0.141    0.458 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,519,908
Number of Sequences: 62578
Number of extensions: 239431
Number of successful extensions: 581
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 577
Number of HSP's gapped (non-prelim): 4
length of query: 219
length of database: 14,973,337
effective HSP length: 95
effective length of query: 124
effective length of database: 9,028,427
effective search space: 1119524948
effective search space used: 1119524948
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: 49 (23.5 bits)