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= Os08g0119800 Os08g0119800|AK060602
         (205 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os08g0119800  Similar to Photosystem II core complex protein...   124   3e-29

>Os08g0119800 Similar to Photosystem II core complex proteins psbY, chloroplast
           precursor (L- arginine metabolising enzyme) (L-AME)
           [Contains: Photosystem II protein psbY-1 (psbY-A1)
          Length = 205

 Score =  124 bits (312), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 65/98 (66%), Positives = 65/98 (66%)

Query: 108 WVLYNILQPALNQLNRMRSEQVLVXXXXXXXXXXXXXXFPPXXXXXXXXXXXXXXXXXXX 167
           WVLYNILQPALNQLNRMRSEQVLV              FPP                   
Sbjct: 108 WVLYNILQPALNQLNRMRSEQVLVAGLGLGAAAGAGLAFPPEASAAQEVARLAAEAAAAE 167

Query: 168 GGDNRGLLLLFVVAPAIAWVLYNILQPALNQLNRMRSD 205
           GGDNRGLLLLFVVAPAIAWVLYNILQPALNQLNRMRSD
Sbjct: 168 GGDNRGLLLLFVVAPAIAWVLYNILQPALNQLNRMRSD 205




 Score = 69.7 bits (169), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 36/36 (100%), Positives = 36/36 (100%)

Query: 1  MATTIAAMAMLKPSKIVARSSPAPSGSGRVPSISLK 36
          MATTIAAMAMLKPSKIVARSSPAPSGSGRVPSISLK
Sbjct: 1  MATTIAAMAMLKPSKIVARSSPAPSGSGRVPSISLK 36




 Score = 63.5 bits (153), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/35 (85%), Positives = 32/35 (91%)

Query: 171 NRGLLLLFVVAPAIAWVLYNILQPALNQLNRMRSD 205
           NRGL LL  +APAIAWVLYNILQPALNQLNRMRS+
Sbjct: 93  NRGLALLLPIAPAIAWVLYNILQPALNQLNRMRSE 127



  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
   0.322    0.134    0.395 

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: 3,270,369
Number of extensions: 70347
Number of successful extensions: 263
Number of sequences better than 1.0e-10: 1
Number of HSP's gapped: 261
Number of HSP's successfully gapped: 3
Length of query: 205
Length of database: 17,035,801
Length adjustment: 96
Effective length of query: 109
Effective length of database: 12,023,257
Effective search space: 1310535013
Effective search space used: 1310535013
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 (21.9 bits)
S2: 153 (63.5 bits)