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= 022689
         (293 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 = 0.036,   Method: Compositional matrix adjust.
 Identities = 36/153 (23%), Positives = 62/153 (40%), Gaps = 33/153 (21%)

Query: 144 VNDIKPDGHCLYRAVEDQLAHLSGGASPYNFQQLRQMVAAYMRDH---SSDFLPFYLSEN 200
           +  +K DG CL+RAV DQ+         Y  Q + ++V  +  D+   ++D+   Y++E+
Sbjct: 48  IKQMKEDGACLFRAVADQV---------YGDQDMHEVVRKHCMDYLMKNADYFSNYVTED 98

Query: 201 MIGEESAQSQVERFENYCKEVESTAAWGGELELRALTHCLRKHIMI--YSGSFPDVEMGK 258
                        F  Y          G  +E++A+     + + +  YS     VE   
Sbjct: 99  -------------FTTYINRKRKNNCHGNHIEMQAMAEMYNRPVEVYQYSTGTSAVEPIN 145

Query: 259 EYXXXXXXXXXXXIILSYHRHAFGLGEHYNSVI 291
            +           I +SYHR+      HYNSV+
Sbjct: 146 TF-HGIHQNEDEPIRVSYHRNI-----HYNSVV 172


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

 Score = 32.3 bits (72), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 34/147 (23%), Positives = 55/147 (37%), Gaps = 34/147 (23%)

Query: 148 KPDGHCLYRAVEDQLAHLSGGASPYNFQQLRQMVAAYMRDH---SSDFLPFYLSENMIGE 204
           K DG CL+RAV DQ+         Y  Q   ++V  +  D+   ++D+   Y++E+    
Sbjct: 65  KEDGACLFRAVADQV---------YGDQDXHEVVRKHCXDYLXKNADYFSNYVTED---- 111

Query: 205 ESAQSQVERFENYCKEVESTAAWGGELELRALTHCLRKHIMIYSGSFPDVEMGKEYXXXX 264
                    F  Y          G  +E +A      + + +Y  S   +          
Sbjct: 112 ---------FTTYINRKRKNNCHGNHIEXQAXAEXYNRPVEVYQYSTEPINT----FHGI 158

Query: 265 XXXXXXXIILSYHRHAFGLGEHYNSVI 291
                  I +SYHR+      HYNSV+
Sbjct: 159 HQNEDEPIRVSYHRNI-----HYNSVV 180


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

 Score = 30.8 bits (68), Expect = 0.90,   Method: Compositional matrix adjust.
 Identities = 36/149 (24%), Positives = 57/149 (38%), Gaps = 33/149 (22%)

Query: 148 KPDGHCLYRAVEDQLAHLSGGASPYNFQQLRQMVAAYMRDH---SSDFLPFYLSENMIGE 204
           K DG CL+RAV DQ+         Y  Q   ++V  +  D+   ++D+   Y++E+    
Sbjct: 52  KEDGACLFRAVADQV---------YGDQDXHEVVRKHCXDYLXKNADYFSNYVTED---- 98

Query: 205 ESAQSQVERFENYCKEVESTAAWGGELELRALTHCLRKHIMI--YSGSFPDVEMGKEYXX 262
                    F  Y          G  +E +A      + + +  YS     VE    +  
Sbjct: 99  ---------FTTYINRKRKNNCHGNHIEXQAXAEXYNRPVEVYQYSTGTSAVEPINTF-H 148

Query: 263 XXXXXXXXXIILSYHRHAFGLGEHYNSVI 291
                    I +SYHR+      HYNSV+
Sbjct: 149 GIHQNEDEPIRVSYHRNI-----HYNSVV 172


  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
   0.315    0.130    0.368 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,372,220
Number of Sequences: 62578
Number of extensions: 198104
Number of successful extensions: 410
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 410
Number of HSP's gapped (non-prelim): 3
length of query: 293
length of database: 14,973,337
effective HSP length: 98
effective length of query: 195
effective length of database: 8,840,693
effective search space: 1723935135
effective search space used: 1723935135
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)