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= 025074
         (258 letters)

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

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



>pdb|4GJ1|A Chain A, Crystal Structure Of
           1-(5-Phosphoribosyl)-5-[(5-Phosphoribosylamino)
           Methylideneamino] Imidazole-4-Carboxamide Isomerase
           (Hisa)
          Length = 243

 Score = 31.2 bits (69), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 37/77 (48%), Gaps = 8/77 (10%)

Query: 157 AVEDQLAHLSGGEESAQSQVERFENYCKEVESTAAWGGEL----ELRALTHCLRKHIMIY 212
           A E  L  L+G ++ ++ Q    E   KEV      GG +    E++AL  C  K ++I 
Sbjct: 45  AKELHLVDLTGAKDPSKRQFALIEKLAKEVSVNLQVGGGIRSKEEVKALLDCGVKRVVIG 104

Query: 213 SGSFPD----VEMGKEY 225
           S +  D    +E+ KE+
Sbjct: 105 SXAIKDATLCLEILKEF 121


>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 = 28.9 bits (63), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 30/131 (22%), Positives = 48/131 (36%), Gaps = 24/131 (18%)

Query: 144 VNDIKPDGHCLYRAVEDQLAH----------------LSGGEESAQSQVERFENYCKEVE 187
           +  +K DG CL+RAV DQ+                  +   +  +    E F  Y     
Sbjct: 48  IKQMKEDGACLFRAVADQVYGDQDMHEVVRKHCMDYLMKNADYFSNYVTEDFTTYINRKR 107

Query: 188 STAAWGGELELRALTHCLRKHIMI--YSGSFPDVEMGKEYXXXXXXXXXXXIILSYHRHA 245
                G  +E++A+     + + +  YS     VE    +           I +SYHR+ 
Sbjct: 108 KNNCHGNHIEMQAMAEMYNRPVEVYQYSTGTSAVEPINTF-HGIHQNEDEPIRVSYHRNI 166

Query: 246 FGLGEHYNSVI 256
                HYNSV+
Sbjct: 167 -----HYNSVV 172


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

 Score = 27.3 bits (59), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 31/125 (24%), Positives = 45/125 (36%), Gaps = 25/125 (20%)

Query: 148 KPDGHCLYRAVEDQLAHLSGGEESAQSQ--------VERFENYCKEVESTA--------A 191
           K DG CL+RAV DQ+       E  +           + F NY  E  +T          
Sbjct: 65  KEDGACLFRAVADQVYGDQDXHEVVRKHCXDYLXKNADYFSNYVTEDFTTYINRKRKNNC 124

Query: 192 WGGELELRALTHCLRKHIMIYSGSFPDVEMGKEYXXXXXXXXXXXIILSYHRHAFGLGEH 251
            G  +E +A      + + +Y  S   +                 I +SYHR+      H
Sbjct: 125 HGNHIEXQAXAEXYNRPVEVYQYSTEPINT----FHGIHQNEDEPIRVSYHRNI-----H 175

Query: 252 YNSVI 256
           YNSV+
Sbjct: 176 YNSVV 180


  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
   0.313    0.129    0.363 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,391,072
Number of Sequences: 62578
Number of extensions: 160419
Number of successful extensions: 245
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 245
Number of HSP's gapped (non-prelim): 4
length of query: 258
length of database: 14,973,337
effective HSP length: 97
effective length of query: 161
effective length of database: 8,903,271
effective search space: 1433426631
effective search space used: 1433426631
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: 50 (23.9 bits)