BLASTP 2.2.23 [Feb-03-2010]


Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, 
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. Schäffer, and Yi-Kuo Yu (2005) "Protein database
searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= Os12g0561000 Os12g0561000|AB027123
         (63 letters)

Database: rap3 
           52,214 sequences; 17,035,801 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os12g0561000  Cytochrome c oxidase polypeptide Vc (EC 1.9.3....   130   2e-31

>Os12g0561000 Cytochrome c oxidase polypeptide Vc (EC 1.9.3.1) (Cytochrome c
          oxidase subunit 5c)
          Length = 63

 Score =  130 bits (328), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 63/63 (100%), Positives = 63/63 (100%)

Query: 1  MAGGRIAHATLKGPSVVKEICIGLTLGLVAGGLWKMHHWNEQRKTRSFYDMLEKGQISVV 60
          MAGGRIAHATLKGPSVVKEICIGLTLGLVAGGLWKMHHWNEQRKTRSFYDMLEKGQISVV
Sbjct: 1  MAGGRIAHATLKGPSVVKEICIGLTLGLVAGGLWKMHHWNEQRKTRSFYDMLEKGQISVV 60

Query: 61 VEE 63
          VEE
Sbjct: 61 VEE 63



  Database: rap3
    Posted date:  Nov 19, 2010  6:03 PM
  Number of letters in database: 17,035,801
  Number of sequences in database:  52,214
  
Lambda     K      H
   0.321    0.137    0.423 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 52214
Number of Hits to DB: 2,364,530
Number of extensions: 77187
Number of successful extensions: 124
Number of sequences better than 1.0e-10: 1
Number of HSP's gapped: 124
Number of HSP's successfully gapped: 1
Length of query: 63
Length of database: 17,035,801
Length adjustment: 35
Effective length of query: 28
Effective length of database: 15,208,311
Effective search space: 425832708
Effective search space used: 425832708
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 149 (62.0 bits)