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= Os09g0568400 Os09g0568400|AK059386
         (44 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os09g0568400  Similar to 60S ribosomal protein L40 (CEP52)         91   2e-19
Os03g0234200  Ubiquitin                                            69   7e-13
AK064604                                                           62   6e-11

>Os09g0568400 Similar to 60S ribosomal protein L40 (CEP52)
          Length = 44

 Score = 90.9 bits (224), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 44/44 (100%), Positives = 44/44 (100%)

Query: 1  VQHVNTFRLFSCRCYARLHPRAVNCRKKKCGHSNQLRPKKKIKN 44
          VQHVNTFRLFSCRCYARLHPRAVNCRKKKCGHSNQLRPKKKIKN
Sbjct: 1  VQHVNTFRLFSCRCYARLHPRAVNCRKKKCGHSNQLRPKKKIKN 44



>Os03g0234200 Ubiquitin
          Length = 129

 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 32/40 (80%), Positives = 35/40 (87%)

Query: 5   NTFRLFSCRCYARLHPRAVNCRKKKCGHSNQLRPKKKIKN 44
           N  ++   +CYARLHPRAVNCRKKKCGHSNQLRPKKKIKN
Sbjct: 90  NQDKMICRKCYARLHPRAVNCRKKKCGHSNQLRPKKKIKN 129



>AK064604 
          Length = 128

 Score = 62.4 bits (150), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 29/43 (67%), Positives = 34/43 (79%)

Query: 1   VQHVNTFRLFSCRCYARLHPRAVNCRKKKCGHSNQLRPKKKIK 43
            Q  N  ++   +CYARLHPRAVNCRKKKCGH+N LRPKKK+K
Sbjct: 86  AQKYNCDKMICRKCYARLHPRAVNCRKKKCGHTNNLRPKKKVK 128



  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
   0.329    0.137    0.460 

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: 1,581,358
Number of extensions: 35858
Number of successful extensions: 113
Number of sequences better than 1.0e-10: 3
Number of HSP's gapped: 113
Number of HSP's successfully gapped: 3
Length of query: 44
Length of database: 17,035,801
Length adjustment: 18
Effective length of query: 26
Effective length of database: 16,095,949
Effective search space: 418494674
Effective search space used: 418494674
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 bits)
S2: 149 (62.0 bits)