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= 025285
         (255 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 = 90.9 bits (224), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 38/73 (52%), Positives = 54/73 (73%), Gaps = 5/73 (6%)

Query: 30  YGNNVEIQALCEMYNRPIHIYSYTT-----EPINIFHGSYNTDNPPIRLSYHHGNHYNSL 84
           +GN++E+QA+ EMYNRP+ +Y Y+T     EPIN FHG +  ++ PIR+SYH   HYNS+
Sbjct: 112 HGNHIEMQAMAEMYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSYHRNIHYNSV 171

Query: 85  VDPRRMTVGAGLG 97
           V+P + T+G GLG
Sbjct: 172 VNPNKATIGVGLG 184


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

 Score = 85.9 bits (211), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 37/73 (50%), Positives = 51/73 (69%), Gaps = 5/73 (6%)

Query: 30  YGNNVEIQALCEMYNRPIHIYSYTT-----EPINIFHGSYNTDNPPIRLSYHHGNHYNSL 84
           +GN++E QA  E YNRP+ +Y Y+T     EPIN FHG +  ++ PIR+SYH   HYNS+
Sbjct: 112 HGNHIEXQAXAEXYNRPVEVYQYSTGTSAVEPINTFHGIHQNEDEPIRVSYHRNIHYNSV 171

Query: 85  VDPRRMTVGAGLG 97
           V+P + T+G GLG
Sbjct: 172 VNPNKATIGVGLG 184


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

 Score = 80.1 bits (196), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 32/60 (53%), Positives = 45/60 (75%)

Query: 30  YGNNVEIQALCEMYNRPIHIYSYTTEPINIFHGSYNTDNPPIRLSYHHGNHYNSLVDPRR 89
           +GN++E QA  E YNRP+ +Y Y+TEPIN FHG +  ++ PIR+SYH   HYNS+V+P +
Sbjct: 125 HGNHIEXQAXAEXYNRPVEVYQYSTEPINTFHGIHQNEDEPIRVSYHRNIHYNSVVNPNK 184


>pdb|3BED|A Chain A, MannoseSORBOSE SPECIFIC IIA SUBUNIT OF PHOSPHOTRANSFERASE
           SYSTEM FROM Enterococcus Faecalis
 pdb|3BED|B Chain B, MannoseSORBOSE SPECIFIC IIA SUBUNIT OF PHOSPHOTRANSFERASE
           SYSTEM FROM Enterococcus Faecalis
          Length = 142

 Score = 27.7 bits (60), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 15/56 (26%), Positives = 25/56 (44%)

Query: 192 LEGGKGCELSDTVLSNSMQMVLSMGFSYLQVIEAYSIFGDDVDSMVCYLLETGSSS 247
           L GG  C ++        Q+ +  G +    IEA     ++VD +  YL + G S+
Sbjct: 70  LXGGTPCNVAXXAXGTYPQLRVVAGLNLAXAIEAAVSPVENVDELAAYLTQIGQSA 125


  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
   0.320    0.134    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,711,535
Number of Sequences: 62578
Number of extensions: 239913
Number of successful extensions: 616
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 610
Number of HSP's gapped (non-prelim): 4
length of query: 255
length of database: 14,973,337
effective HSP length: 97
effective length of query: 158
effective length of database: 8,903,271
effective search space: 1406716818
effective search space used: 1406716818
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)