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= 044735
         (183 letters)

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

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



>pdb|1WP5|A Chain A, Crystal Structure Of The C-Terminal Domain Of Dna
           Topoisomerase Iv
          Length = 323

 Score = 28.9 bits (63), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 37/74 (50%), Gaps = 8/74 (10%)

Query: 45  PHFIS---PTHKAEKLPPCIQKGFMTTIMASRIAVRNFSRRFSSSGKVLSEEEKAAENVY 101
           PH IS       ++ +    +K F+ TI    I    FS R+S+   VL EEE     + 
Sbjct: 246 PHRISGFVVAQDSDTIYLQTEKSFIETIKVGDI---RFSDRYSNGSFVLDEEEN-GRVIS 301

Query: 102 IKKVE-QEKLEKMA 114
           + KVE ++K EK+A
Sbjct: 302 VWKVEAEDKTEKLA 315


>pdb|3N3K|A Chain A, The Catalytic Domain Of Usp8 In Complex With A Usp8
           Specific Inhibitor
          Length = 396

 Score = 27.7 bits (60), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 17/60 (28%), Positives = 27/60 (45%), Gaps = 2/60 (3%)

Query: 48  ISPTHKAEKLPPCIQKGFMTTIMASRIAVRNFSRRFSSSGKVLSEEEKAAENVYIKKVEQ 107
           ++PT   E  P C  K  ++ + AS+I  RN +  F  SG  L+         Y+  + Q
Sbjct: 22  VTPTVNRENKPTCYPKAEISRLSASQI--RNLNPVFGGSGPALTGLRNLGNTCYMNSILQ 79


>pdb|2GFO|A Chain A, Structure Of The Catalytic Domain Of Human Ubiquitin
           Carboxyl-terminal Hydrolase 8
          Length = 396

 Score = 26.6 bits (57), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 2/60 (3%)

Query: 48  ISPTHKAEKLPPCIQKGFMTTIMASRIAVRNFSRRFSSSGKVLSEEEKAAENVYIKKVEQ 107
           ++PT   E  P C  K  ++ + AS+I  RN +  F  SG  L+         Y   + Q
Sbjct: 22  VTPTVNRENKPTCYPKAEISRLSASQI--RNLNPVFGGSGPALTGLRNLGNTCYXNSILQ 79


  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
   0.312    0.127    0.356 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,016,292
Number of Sequences: 62578
Number of extensions: 182036
Number of successful extensions: 386
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 386
Number of HSP's gapped (non-prelim): 8
length of query: 183
length of database: 14,973,337
effective HSP length: 93
effective length of query: 90
effective length of database: 9,153,583
effective search space: 823822470
effective search space used: 823822470
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)