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= 021398
         (313 letters)

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

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



>pdb|1BVU|A Chain A, Glutamate Dehydrogenase From Thermococcus Litoralis
 pdb|1BVU|B Chain B, Glutamate Dehydrogenase From Thermococcus Litoralis
 pdb|1BVU|C Chain C, Glutamate Dehydrogenase From Thermococcus Litoralis
 pdb|1BVU|D Chain D, Glutamate Dehydrogenase From Thermococcus Litoralis
 pdb|1BVU|E Chain E, Glutamate Dehydrogenase From Thermococcus Litoralis
 pdb|1BVU|F Chain F, Glutamate Dehydrogenase From Thermococcus Litoralis
          Length = 418

 Score = 28.1 bits (61), Expect = 6.7,   Method: Compositional matrix adjust.
 Identities = 12/22 (54%), Positives = 14/22 (63%)

Query: 38  NPRELRSWAKKTGFVSDFSGET 59
           N  E+ +W KKTG V DF G T
Sbjct: 255 NADEVLAWKKKTGSVKDFPGAT 276


  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
   0.316    0.137    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,913,874
Number of Sequences: 62578
Number of extensions: 359059
Number of successful extensions: 310
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 309
Number of HSP's gapped (non-prelim): 1
length of query: 313
length of database: 14,973,337
effective HSP length: 99
effective length of query: 214
effective length of database: 8,778,115
effective search space: 1878516610
effective search space used: 1878516610
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)