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= 026365
         (239 letters)

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

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



>pdb|3NEP|X Chain X, 1.55a Resolution Structure Of Malate Dehydrogenase From
           Salinibacter Ruber
          Length = 314

 Score = 29.6 bits (65), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 30/66 (45%), Gaps = 12/66 (18%)

Query: 69  YEACGRTVNPVNGAVGLLWTGNW--------HVCQAAVETVLRGG---TLRPVPELLNSC 117
           YEA G   N V G  G+L TG +         V    V+ +L GG   T+ P+P    + 
Sbjct: 129 YEASGFPTNRVMGMAGVLDTGRFRSFIAEELDVSVRDVQALLMGGHGDTMVPLPR-YTTV 187

Query: 118 GGSPTP 123
           GG P P
Sbjct: 188 GGIPVP 193


  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
   0.318    0.133    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,515,590
Number of Sequences: 62578
Number of extensions: 237802
Number of successful extensions: 759
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: 759
Number of HSP's gapped (non-prelim): 1
length of query: 239
length of database: 14,973,337
effective HSP length: 96
effective length of query: 143
effective length of database: 8,965,849
effective search space: 1282116407
effective search space used: 1282116407
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)