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= 041629
         (362 letters)

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

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



>pdb|3UTW|A Chain A, Crystal Structure Of Bacteriorhodopsin Mutant P50aY57F
          Length = 249

 Score = 28.1 bits (61), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 11/63 (17%)

Query: 216 QRIWLIRGLSCHLFGTLEYLLKSLGISAFGFNVTSKVVDDEQSKIYSQEMLDFGVPSPMF 275
           + IWL  G +    GTL +L+K +G+S           D +  K Y+   L   +   MF
Sbjct: 9   EWIWLALGTALMGLGTLYFLVKGMGVS-----------DPDAKKFYAITTLVAAIAFTMF 57

Query: 276 VTL 278
           +++
Sbjct: 58  LSM 60


>pdb|1S53|A Chain A, Thr46ser Bacteriorhodopsin
 pdb|1S53|B Chain B, Thr46ser Bacteriorhodopsin
          Length = 227

 Score = 28.1 bits (61), Expect = 8.5,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 29/58 (50%), Gaps = 3/58 (5%)

Query: 216 QRIWLIRGLSCHLFGTLEYLLKSLGIS---AFGFNVTSKVVDDEQSKIYSQEMLDFGV 270
           + IWL  G +    GTL +L+K +G+S   A  F   S +V      +Y   +L +G+
Sbjct: 5   EWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAISTLVPAIAFTMYLSMLLGYGL 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
   0.325    0.140    0.452 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,303,224
Number of Sequences: 62578
Number of extensions: 339111
Number of successful extensions: 958
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 958
Number of HSP's gapped (non-prelim): 3
length of query: 362
length of database: 14,973,337
effective HSP length: 100
effective length of query: 262
effective length of database: 8,715,537
effective search space: 2283470694
effective search space used: 2283470694
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)