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= 025076
         (258 letters)

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

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



>pdb|2J1P|A Chain A, Geranylgeranyl Diphosphate Synthase From Sinapis Alba In
           Complex With Ggpp
 pdb|2J1P|B Chain B, Geranylgeranyl Diphosphate Synthase From Sinapis Alba In
           Complex With Ggpp
          Length = 293

 Score = 30.4 bits (67), Expect = 0.88,   Method: Compositional matrix adjust.
 Identities = 17/64 (26%), Positives = 33/64 (51%)

Query: 9   IGMVVGVIAIIREVSKHYGFGFDKDTGIKAIREWSDRLGVWAIPVFVGFHTLTIALCLPY 68
           IG++  V+  I +V+K     + K  G++  RE++++L   A    +GF +  +A  L  
Sbjct: 225 IGLLFQVVDDILDVTKSSKLTYPKLXGLEKSREFAEKLNTEARDQLLGFDSDKVAPLLAL 284

Query: 69  AVFF 72
           A + 
Sbjct: 285 ANYI 288


  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
   0.327    0.141    0.440 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,624,542
Number of Sequences: 62578
Number of extensions: 235521
Number of successful extensions: 585
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: 584
Number of HSP's gapped (non-prelim): 1
length of query: 258
length of database: 14,973,337
effective HSP length: 97
effective length of query: 161
effective length of database: 8,903,271
effective search space: 1433426631
effective search space used: 1433426631
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 50 (23.9 bits)