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= psy9230
         (361 letters)

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

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



>pdb|2YEV|A Chain A, Structure Of Caa3-Type Cytochrome Oxidase
 pdb|2YEV|D Chain D, Structure Of Caa3-Type Cytochrome Oxidase
          Length = 791

 Score = 30.4 bits (67), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 27/99 (27%), Positives = 40/99 (40%), Gaps = 21/99 (21%)

Query: 214 YHLQYLLSCPQRNNDDDMQLPTRASEEFRPFIR----------------RLPEFKFWYSV 257
           Y L++L + P + ++ D++LPT    E RP                    LP   FW   
Sbjct: 502 YTLEWLTASPPKAHNFDVKLPTEFPSE-RPLYDWKKKGVELKPEDPAHIHLPNSSFWPFY 560

Query: 258 MKSTLFATFFTLFDCFNIPVFWPILVLYFITLFIITMKR 296
             +TLFA FF       +P  W   +  F+ LF   + R
Sbjct: 561 SAATLFA-FFVAVAALPVPNVW---MWVFLALFAYGLVR 595


  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
   0.330    0.143    0.466 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,013,585
Number of Sequences: 62578
Number of extensions: 382490
Number of successful extensions: 787
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: 787
Number of HSP's gapped (non-prelim): 4
length of query: 361
length of database: 14,973,337
effective HSP length: 100
effective length of query: 261
effective length of database: 8,715,537
effective search space: 2274755157
effective search space used: 2274755157
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 52 (24.6 bits)