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= psy12163
         (88 letters)

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

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



>pdb|2OTN|A Chain A, Crystal Structure Of The Catalytically Active Form Of
           Diaminopimelate Epimerase From Bacillus Anthracis
 pdb|2OTN|B Chain B, Crystal Structure Of The Catalytically Active Form Of
           Diaminopimelate Epimerase From Bacillus Anthracis
          Length = 308

 Score = 26.2 bits (56), Expect = 4.4,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 26/49 (53%), Gaps = 2/49 (4%)

Query: 39  DNPFLREETVYSSTTSTLIGYVLFNPTGILMIQFLQS--ITCLGGVVKT 85
           + PF+RE  +Y++         + NP  ++ +  ++   +T LG V++T
Sbjct: 162 ETPFIRENFLYNNHRYAFTAVSMGNPHAVIFVDDVEQAPLTTLGPVLET 210


  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
   0.324    0.140    0.473 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,465,872
Number of Sequences: 62578
Number of extensions: 78975
Number of successful extensions: 106
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 106
Number of HSP's gapped (non-prelim): 1
length of query: 88
length of database: 14,973,337
effective HSP length: 56
effective length of query: 32
effective length of database: 11,468,969
effective search space: 367007008
effective search space used: 367007008
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 45 (21.9 bits)