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= Os04g0309400 Os04g0309400|AK120707
         (89 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os04g0309400  Conserved hypothetical protein                       84   2e-17
Os09g0129301  Conserved hypothetical protein                       66   6e-12

>Os04g0309400 Conserved hypothetical protein
          Length = 89

 Score = 84.3 bits (207), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 46/63 (73%)

Query: 27 SSFLQRRATATACASSERRRWPAPTAGDGLGGAVXXXXXXXXXXXXXXXXXGFEVELAST 86
          SSFLQRRATATACASSERRRWPAPTAGDGLGGAV                 GFEVELAST
Sbjct: 27 SSFLQRRATATACASSERRRWPAPTAGDGLGGAVPRPIRRRRSSSAWIQRRGFEVELAST 86

Query: 87 PPR 89
          PPR
Sbjct: 87 PPR 89



>Os09g0129301 Conserved hypothetical protein
          Length = 95

 Score = 65.9 bits (159), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 32/34 (94%), Positives = 33/34 (97%)

Query: 27 SSFLQRRATATACASSERRRWPAPTAGDGLGGAV 60
          SSFL+RRATATACASSERRRWPAPT GDGLGGAV
Sbjct: 43 SSFLRRRATATACASSERRRWPAPTVGDGLGGAV 76



  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
   0.316    0.127    0.385 

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: 2,036,315
Number of extensions: 60043
Number of successful extensions: 267
Number of sequences better than 1.0e-10: 2
Number of HSP's gapped: 266
Number of HSP's successfully gapped: 2
Length of query: 89
Length of database: 17,035,801
Length adjustment: 59
Effective length of query: 30
Effective length of database: 13,955,175
Effective search space: 418655250
Effective search space used: 418655250
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 149 (62.0 bits)