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= Os09g0520100 Os09g0520100|AK119678
         (131 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os09g0520100  DNA polymerase delta, subunit 4 family protein      176   4e-45

>Os09g0520100 DNA polymerase delta, subunit 4 family protein
          Length = 131

 Score =  176 bits (446), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 90/131 (68%), Positives = 90/131 (68%)

Query: 1   MASGGMKDFYRQXXXXXXXXXXXXXXXXXQHYTGGASVGASDTAQTSALISHGNLDLKDD 60
           MASGGMKDFYRQ                 QHYTGGASVGASDTAQTSALISHGNLDLKDD
Sbjct: 1   MASGGMKDFYRQKKKGGPTKASSSSKKKTQHYTGGASVGASDTAQTSALISHGNLDLKDD 60

Query: 61  FSEQEEQLRLFDMDMKFGPCIGVTRLQRWERASAMGXXXXXXXXXXXXXXXXXXXXXXXX 120
           FSEQEEQLRLFDMDMKFGPCIGVTRLQRWERASAMG                        
Sbjct: 61  FSEQEEQLRLFDMDMKFGPCIGVTRLQRWERASAMGLHPPPHLRDLLLNNTHAGNHNNNG 120

Query: 121 PSLECLWEGKV 131
           PSLECLWEGKV
Sbjct: 121 PSLECLWEGKV 131



  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
   0.318    0.133    0.406 

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: 3,178,571
Number of extensions: 84467
Number of successful extensions: 172
Number of sequences better than 1.0e-10: 1
Number of HSP's gapped: 170
Number of HSP's successfully gapped: 1
Length of query: 131
Length of database: 17,035,801
Length adjustment: 89
Effective length of query: 42
Effective length of database: 12,388,755
Effective search space: 520327710
Effective search space used: 520327710
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 (21.7 bits)
S2: 150 (62.4 bits)