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= Os06g0697400 Os06g0697400|AK068912
         (82 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os06g0697400  RNA polymerase Rpb8 family protein                  170   2e-43
Os03g0845700  Similar to RPB17 (Fragment)                         124   1e-29

>Os06g0697400 RNA polymerase Rpb8 family protein
          Length = 82

 Score =  170 bits (430), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 82/82 (100%), Positives = 82/82 (100%)

Query: 1  MYMQLDVATEVYPMRAGDRFTMVLAPTLNLDGTPDTGFYTQAGRKTLADKFDYVMHGKLY 60
          MYMQLDVATEVYPMRAGDRFTMVLAPTLNLDGTPDTGFYTQAGRKTLADKFDYVMHGKLY
Sbjct: 1  MYMQLDVATEVYPMRAGDRFTMVLAPTLNLDGTPDTGFYTQAGRKTLADKFDYVMHGKLY 60

Query: 61 KISEDSSSGQATKVYGFYEFQI 82
          KISEDSSSGQATKVYGFYEFQI
Sbjct: 61 KISEDSSSGQATKVYGFYEFQI 82



>Os03g0845700 Similar to RPB17 (Fragment)
          Length = 148

 Score =  124 bits (312), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 61/82 (74%), Positives = 68/82 (82%), Gaps = 2/82 (2%)

Query: 1   MYMQLDVATEVYPMRAGDRFTMVLAPTLNLDGTPDTGFYTQAGRKTLADKFDYVMHGKLY 60
           MYMQLDVAT+VYPM  GDRFTMVL PTLNLDGTPD+ F+TQAGRKTLADK++YVMHGKLY
Sbjct: 37  MYMQLDVATDVYPMHPGDRFTMVLVPTLNLDGTPDSAFFTQAGRKTLADKYEYVMHGKLY 96

Query: 61  KISE--DSSSGQATKVYGFYEF 80
           KISE  D+S   A KV  +  F
Sbjct: 97  KISEDKDTSDQNAKKVEMYASF 118



  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
   0.320    0.136    0.396 

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: 2,658,933
Number of extensions: 91442
Number of successful extensions: 145
Number of sequences better than 1.0e-10: 2
Number of HSP's gapped: 145
Number of HSP's successfully gapped: 2
Length of query: 82
Length of database: 17,035,801
Length adjustment: 52
Effective length of query: 30
Effective length of database: 14,320,673
Effective search space: 429620190
Effective search space used: 429620190
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)