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= 040837
         (276 letters)

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

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



>pdb|1JB0|B Chain B, Crystal Structure Of Photosystem I: A Photosynthetic
           Reaction Center And Core Antenna System From
           Cyanobacteria
 pdb|3PCQ|B Chain B, Femtosecond X-Ray Protein Nanocrystallography
 pdb|4FE1|B Chain B, Improving The Accuracy Of Macromolecular Structure
           Refinement At 7 A Resolution
          Length = 740

 Score = 31.2 bits (69), Expect = 0.63,   Method: Compositional matrix adjust.
 Identities = 20/68 (29%), Positives = 28/68 (41%), Gaps = 8/68 (11%)

Query: 27  LDRFRNHPSRRTCKFTCL-LHVGFEDIAQVVHNKVLIAAG-------VSAAIGQLSKPVT 78
           LDR   H        + + L +GF  +   VHN V++A G       +     Q  +   
Sbjct: 411 LDRVLQHKEAIISHLSWVSLFLGFHTLGLYVHNDVVVAFGTPEKQILIEPVFAQFIQAAH 470

Query: 79  GSLLYGKD 86
           G LLYG D
Sbjct: 471 GKLLYGFD 478


  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    0.131    0.369 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,079,227
Number of Sequences: 62578
Number of extensions: 261874
Number of successful extensions: 533
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 533
Number of HSP's gapped (non-prelim): 2
length of query: 276
length of database: 14,973,337
effective HSP length: 97
effective length of query: 179
effective length of database: 8,903,271
effective search space: 1593685509
effective search space used: 1593685509
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: 51 (24.3 bits)