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= 031826
         (152 letters)

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

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



>pdb|1P8U|A Chain A, Bacteriorhodopsin N' Intermediate At 1.62 A Resolution
 pdb|3HAN|A Chain A, Crystal Structure Of Bacteriorhodopsin Mutant V49a
           Crystallized From Bicelles
          Length = 249

 Score = 27.3 bits (59), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 21/42 (50%)

Query: 103 GITTLYFYDLGHCSVDNECQKYQASVGLAICCCFTIATSSLI 144
           G+ TLYF   G    D + +K+ A   LA    FT+  S L+
Sbjct: 21  GLGTLYFLVKGMGVSDPDAKKFYAITTLAPAIAFTMYLSMLL 62


>pdb|2I21|A Chain A, BacteriorhodopsinLIPID COMPLEX, T46V MUTANT
          Length = 249

 Score = 27.3 bits (59), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 21/42 (50%)

Query: 103 GITTLYFYDLGHCSVDNECQKYQASVGLAICCCFTIATSSLI 144
           G+ TLYF   G    D + +K+ A V L     FT+  S L+
Sbjct: 21  GLGTLYFLVKGMGVSDPDAKKFYAIVTLVPAIAFTMYLSMLL 62


  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
   0.332    0.140    0.454 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,541,318
Number of Sequences: 62578
Number of extensions: 100567
Number of successful extensions: 365
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 363
Number of HSP's gapped (non-prelim): 2
length of query: 152
length of database: 14,973,337
effective HSP length: 90
effective length of query: 62
effective length of database: 9,341,317
effective search space: 579161654
effective search space used: 579161654
T: 11
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (22.0 bits)
S2: 47 (22.7 bits)