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= Os08g0169600 Os08g0169600|AK067305
         (104 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os08g0169600  RNA polymerase II transcription factor SIII su...   217   2e-57

>Os08g0169600 RNA polymerase II transcription factor SIII subunit A family
           protein
          Length = 104

 Score =  217 bits (552), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 104/104 (100%), Positives = 104/104 (100%)

Query: 1   MEYGRRKPISLLELCIRTTMDNLRYVDNVDGVEMDLLQRILPHCKMEDLTRIENNTEMDL 60
           MEYGRRKPISLLELCIRTTMDNLRYVDNVDGVEMDLLQRILPHCKMEDLTRIENNTEMDL
Sbjct: 1   MEYGRRKPISLLELCIRTTMDNLRYVDNVDGVEMDLLQRILPHCKMEDLTRIENNTEMDL 60

Query: 61  TPVTDKLWKLFYTRQFGEENANQVVKRMSMSGARYKWKDLFDVK 104
           TPVTDKLWKLFYTRQFGEENANQVVKRMSMSGARYKWKDLFDVK
Sbjct: 61  TPVTDKLWKLFYTRQFGEENANQVVKRMSMSGARYKWKDLFDVK 104



  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    0.137    0.413 

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: 3,310,846
Number of extensions: 112311
Number of successful extensions: 206
Number of sequences better than 1.0e-10: 1
Number of HSP's gapped: 206
Number of HSP's successfully gapped: 1
Length of query: 104
Length of database: 17,035,801
Length adjustment: 72
Effective length of query: 32
Effective length of database: 13,276,393
Effective search space: 424844576
Effective search space used: 424844576
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: 149 (62.0 bits)