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= 006751
         (632 letters)

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

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



>pdb|2DAI|A Chain A, Solution Structure Of The First Uba Domain In The Human
           Ubiquitin Associated Domain Containing 1 (Ubadc1)
          Length = 83

 Score = 36.6 bits (83), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 21/50 (42%), Positives = 28/50 (56%)

Query: 165 QQLVAMGFSSERATLALMLNEGRVEESVNWLFEVSEEEARNTDPKLESSG 214
           +QL  MGF   RAT AL LN   V +++ WL E +E+   +T     SSG
Sbjct: 34  RQLTEMGFPENRATKALQLNHMSVPQAMEWLIEHAEDPTIDTPLSGPSSG 83


>pdb|2DAK|A Chain A, Solution Structure Of The Second Uba Domain In The Human
           Ubiquitin Specific Protease 5 (Isopeptidase 5)
          Length = 63

 Score = 30.8 bits (68), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 12/30 (40%), Positives = 20/30 (66%)

Query: 167 LVAMGFSSERATLALMLNEGRVEESVNWLF 196
           +V+MGFS ++A  AL      +E +V+W+F
Sbjct: 16  IVSMGFSRDQALKALRATNNSLERAVDWIF 45


>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
 pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
          Length = 854

 Score = 30.8 bits (68), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 12/30 (40%), Positives = 20/30 (66%)

Query: 167 LVAMGFSSERATLALMLNEGRVEESVNWLF 196
           +V+MGFS ++A  AL      +E +V+W+F
Sbjct: 727 IVSMGFSRDQALKALRATNNSLERAVDWIF 756


  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
   0.310    0.127    0.368 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,049,654
Number of Sequences: 62578
Number of extensions: 588699
Number of successful extensions: 973
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 966
Number of HSP's gapped (non-prelim): 18
length of query: 632
length of database: 14,973,337
effective HSP length: 105
effective length of query: 527
effective length of database: 8,402,647
effective search space: 4428194969
effective search space used: 4428194969
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 54 (25.4 bits)