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= psy17940
         (81 letters)

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

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



>pdb|3PPC|A Chain A, Crystal Structure Of The Candida Albicans Methionine
           Synthase By Surface Entropy Reduction, Tyrosine Variant
           With Zinc
 pdb|3PPC|B Chain B, Crystal Structure Of The Candida Albicans Methionine
           Synthase By Surface Entropy Reduction, Tyrosine Variant
           With Zinc
          Length = 789

 Score = 25.8 bits (55), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 13/30 (43%), Positives = 18/30 (60%)

Query: 13  QKAKEKPGHKVQPDDPISFLELSSARGSEF 42
           QK KE    +VQ D+P+  L+L  A  S+F
Sbjct: 227 QKLKEAGAEQVQIDEPVLVLDLPEAVQSKF 256


>pdb|3PPH|A Chain A, Crystal Structure Of The Candida Albicans Methionine
           Synthase By Surface Entropy Reduction, Threonine Variant
 pdb|3PPH|B Chain B, Crystal Structure Of The Candida Albicans Methionine
           Synthase By Surface Entropy Reduction, Threonine Variant
          Length = 789

 Score = 25.4 bits (54), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 13/30 (43%), Positives = 18/30 (60%)

Query: 13  QKAKEKPGHKVQPDDPISFLELSSARGSEF 42
           QK KE    +VQ D+P+  L+L  A  S+F
Sbjct: 227 QKLKEAGAEQVQIDEPVLVLDLPEAVQSKF 256


>pdb|3PPF|A Chain A, Crystal Structure Of The Candida Albicans Methionine
           Synthase By Surface Entropy Reduction, Alanine Variant
           Without Zinc
 pdb|3PPG|A Chain A, Crystal Structure Of The Candida Albicans Methionine
           Synthase By Surface Entropy Reduction, Alanine Variant
           With Zinc
          Length = 789

 Score = 25.4 bits (54), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 13/30 (43%), Positives = 18/30 (60%)

Query: 13  QKAKEKPGHKVQPDDPISFLELSSARGSEF 42
           QK KE    +VQ D+P+  L+L  A  S+F
Sbjct: 227 QKLKEAGAEQVQIDEPVLVLDLPEAVQSKF 256


  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
   0.302    0.120    0.316 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,161,727
Number of Sequences: 62578
Number of extensions: 65184
Number of successful extensions: 83
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 80
Number of HSP's gapped (non-prelim): 3
length of query: 81
length of database: 14,973,337
effective HSP length: 50
effective length of query: 31
effective length of database: 11,844,437
effective search space: 367177547
effective search space used: 367177547
T: 11
A: 40
X1: 17 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.8 bits)
S2: 45 (21.9 bits)