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= 033361
         (121 letters)

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

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



>pdb|3TMP|A Chain A, The Catalytic Domain Of Human Deubiquitinase Duba In
           Complex With Ubiquitin Aldehyde
 pdb|3TMP|C Chain C, The Catalytic Domain Of Human Deubiquitinase Duba In
           Complex With Ubiquitin Aldehyde
 pdb|3TMP|E Chain E, The Catalytic Domain Of Human Deubiquitinase Duba In
           Complex With Ubiquitin Aldehyde
 pdb|3TMP|G Chain G, The Catalytic Domain Of Human Deubiquitinase Duba In
           Complex With Ubiquitin Aldehyde
          Length = 184

 Score = 35.4 bits (80), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 25/114 (21%), Positives = 47/114 (41%), Gaps = 4/114 (3%)

Query: 1   MYKSPEYHKHVRKEVVKQLKDCRSMYEGYVPMKYKRYYKNMAKVGEWGDHVTLQAAADKF 60
           +Y   + H+ VRK  +  L      +  YV   +  Y     K    G+H+ +QA A+ +
Sbjct: 66  VYGDQDMHEVVRKHCMDYLMKNADYFSNYVTEDFTTYINRKRKNNCHGNHIEMQAMAEMY 125

Query: 61  AAKICLLTSFRDTCFIEIMPQ----HQAPKRELWLSFWSEVHYNSLYDIRDAPV 110
              + +      T  +E +      HQ     + +S+   +HYNS+ +   A +
Sbjct: 126 NRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSYHRNIHYNSVVNPNKATI 179


>pdb|3TMO|A Chain A, The Catalytic Domain Of Human Deubiquitinase Duba
          Length = 184

 Score = 35.0 bits (79), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 25/114 (21%), Positives = 45/114 (39%), Gaps = 4/114 (3%)

Query: 1   MYKSPEYHKHVRKEVVKQLKDCRSMYEGYVPMKYKRYYKNMAKVGEWGDHVTLQAAADKF 60
           +Y   + H+ VRK     L      +  YV   +  Y     K    G+H+  QA A+ +
Sbjct: 66  VYGDQDXHEVVRKHCXDYLXKNADYFSNYVTEDFTTYINRKRKNNCHGNHIEXQAXAEXY 125

Query: 61  AAKICLLTSFRDTCFIEIMPQ----HQAPKRELWLSFWSEVHYNSLYDIRDAPV 110
              + +      T  +E +      HQ     + +S+   +HYNS+ +   A +
Sbjct: 126 NRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSYHRNIHYNSVVNPNKATI 179


>pdb|3PFY|A Chain A, The Catalytic Domain Of Human Otud5
          Length = 185

 Score = 30.8 bits (68), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 22/102 (21%), Positives = 39/102 (38%), Gaps = 1/102 (0%)

Query: 1   MYKSPEYHKHVRKEVVKQLKDCRSMYEGYVPMKYKRYYKNMAKVGEWGDHVTLQAAADKF 60
           +Y   + H+ VRK     L      +  YV   +  Y     K    G+H+  QA A+ +
Sbjct: 79  VYGDQDXHEVVRKHCXDYLXKNADYFSNYVTEDFTTYINRKRKNNCHGNHIEXQAXAEXY 138

Query: 61  AAKICLLTSFRDTCFIEIMPQHQAPKRELWLSFWSEVHYNSL 102
              + +   +           HQ     + +S+   +HYNS+
Sbjct: 139 NRPVEVY-QYSTEPINTFHGIHQNEDEPIRVSYHRNIHYNSV 179


  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
   0.323    0.136    0.449 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,029,481
Number of Sequences: 62578
Number of extensions: 145969
Number of successful extensions: 257
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 250
Number of HSP's gapped (non-prelim): 5
length of query: 121
length of database: 14,973,337
effective HSP length: 83
effective length of query: 38
effective length of database: 9,779,363
effective search space: 371615794
effective search space used: 371615794
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)