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= psy5317
         (101 letters)

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

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



>pdb|2PB9|A Chain A, Crystal Structure Of C-Terminal Domain Of
           Phosphomethylpyrimidine Kinase
 pdb|2PB9|B Chain B, Crystal Structure Of C-Terminal Domain Of
           Phosphomethylpyrimidine Kinase
          Length = 195

 Score = 27.7 bits (60), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 18/39 (46%)

Query: 34  AVLTSGLTCAFSSLQEAPRVFRHLSKDGLYPYIGWFGRG 72
           A +  G+  A   ++E P +  HL   G  P I  FGR 
Sbjct: 137 ATIPWGIETAIKRIKERPDIIYHLGDVGKEPXILVFGRN 175


>pdb|2I7A|A Chain A, Domain Iv Of Human Calpain 13
          Length = 174

 Score = 25.4 bits (54), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 10/22 (45%), Positives = 13/22 (59%)

Query: 40  LTCAFSSLQEAPRVFRHLSKDG 61
           L C    L+   + FR+LSKDG
Sbjct: 136 LVCFLMRLEAMAKTFRNLSKDG 157


  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    0.406 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,737,542
Number of Sequences: 62578
Number of extensions: 94277
Number of successful extensions: 261
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 260
Number of HSP's gapped (non-prelim): 2
length of query: 101
length of database: 14,973,337
effective HSP length: 67
effective length of query: 34
effective length of database: 10,780,611
effective search space: 366540774
effective search space used: 366540774
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)