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= psy8057
         (243 letters)

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

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



>pdb|1VGO|A Chain A, Crystal Structure Of Archaerhodopsin-2
 pdb|1VGO|B Chain B, Crystal Structure Of Archaerhodopsin-2
 pdb|2EI4|A Chain A, Trimeric Complex Of Archaerhodopsin-2
 pdb|2Z55|A Chain A, Bacterioruberin In The Trimeric Structure Of
           Archaerhodopsin-2
 pdb|2Z55|B Chain B, Bacterioruberin In The Trimeric Structure Of
           Archaerhodopsin-2
 pdb|2Z55|D Chain D, Bacterioruberin In The Trimeric Structure Of
           Archaerhodopsin-2
 pdb|2Z55|E Chain E, Bacterioruberin In The Trimeric Structure Of
           Archaerhodopsin-2
          Length = 253

 Score = 27.7 bits (60), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 114 LFINCLFLIMIMWVLITKLRSANTVETQQYRKATKALVVLIPLLGITY-ILVIAGPTEGP 172
           LF    FL  +++ L+T LRSA    +++ R     L  L+ +L   Y IL I G TEG 
Sbjct: 144 LFSTIAFL-FVLYYLLTSLRSAAAKRSEEVRSTFNTLTALVAVLWTAYPILWIVG-TEGA 201

Query: 173 YV 174
            V
Sbjct: 202 GV 203


  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
   0.328    0.140    0.465 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,228,177
Number of Sequences: 62578
Number of extensions: 269362
Number of successful extensions: 480
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: 479
Number of HSP's gapped (non-prelim): 1
length of query: 243
length of database: 14,973,337
effective HSP length: 96
effective length of query: 147
effective length of database: 8,965,849
effective search space: 1317979803
effective search space used: 1317979803
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 50 (23.9 bits)