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= psy13485
         (152 letters)

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

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



>pdb|2Y6E|A Chain A, Ubiquitin Specific Protease 4 Is Inhibited By Its
           Ubiquitin- Like Domain
 pdb|2Y6E|B Chain B, Ubiquitin Specific Protease 4 Is Inhibited By Its
           Ubiquitin- Like Domain
 pdb|2Y6E|C Chain C, Ubiquitin Specific Protease 4 Is Inhibited By Its
           Ubiquitin- Like Domain
 pdb|2Y6E|D Chain D, Ubiquitin Specific Protease 4 Is Inhibited By Its
           Ubiquitin- Like Domain
 pdb|2Y6E|E Chain E, Ubiquitin Specific Protease 4 Is Inhibited By Its
           Ubiquitin- Like Domain
 pdb|2Y6E|F Chain F, Ubiquitin Specific Protease 4 Is Inhibited By Its
           Ubiquitin- Like Domain
          Length = 367

 Score = 27.7 bits (60), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 4/63 (6%)

Query: 27  NAAASTPLHQLVGVVTYYGK----HYSTFFFHTKLKVWIYFDDATVREVGPRWEQVRSAF 82
           N +A   ++ L+ V  +YG     HY+ +  +     W YFDD+ V          ++A+
Sbjct: 292 NLSARPYVYDLIAVSNHYGAMGVGHYTAYAKNKLNGKWYYFDDSNVSLASEDQIVTKAAY 351

Query: 83  YFF 85
             F
Sbjct: 352 VLF 354


>pdb|3A1I|A Chain A, Crystal Structure Of Rhodococcus Sp. N-771 Amidase
           Complexed With Benzamide
          Length = 521

 Score = 27.7 bits (60), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 12/21 (57%), Positives = 16/21 (76%)

Query: 62  YFDDATVREVGPRWEQVRSAF 82
           +FDDATV  VG  +E++R AF
Sbjct: 484 HFDDATVLRVGRAFEKLRGAF 504


>pdb|3A1K|A Chain A, Crystal Structure Of Rhodococcus Sp. N771 Amidase
          Length = 521

 Score = 27.7 bits (60), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 12/21 (57%), Positives = 16/21 (76%)

Query: 62  YFDDATVREVGPRWEQVRSAF 82
           +FDDATV  VG  +E++R AF
Sbjct: 484 HFDDATVLRVGRAFEKLRGAF 504


  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
   0.325    0.141    0.472 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,577,819
Number of Sequences: 62578
Number of extensions: 157123
Number of successful extensions: 301
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 296
Number of HSP's gapped (non-prelim): 11
length of query: 152
length of database: 14,973,337
effective HSP length: 90
effective length of query: 62
effective length of database: 9,341,317
effective search space: 579161654
effective search space used: 579161654
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 47 (22.7 bits)