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= Os08g0260400 Os08g0260400|Os08g0260400
         (192 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os08g0260400  Helix-loop-helix DNA-binding domain containing...   260   5e-70

>Os08g0260400 Helix-loop-helix DNA-binding domain containing protein
          Length = 192

 Score =  260 bits (664), Expect = 5e-70,   Method: Compositional matrix adjust.
 Identities = 139/192 (72%), Positives = 139/192 (72%)

Query: 1   MHAPRKFKKAFMERLLLSLQVAGLTSKSMGLRERRDAVRLSSDVAMASARGRAAPWARAL 60
           MHAPRKFKKAFMERLLLSLQVAGLTSKSMGLRERRDAVRLSSDVAMASARGRAAPWARAL
Sbjct: 1   MHAPRKFKKAFMERLLLSLQVAGLTSKSMGLRERRDAVRLSSDVAMASARGRAAPWARAL 60

Query: 61  VARHAAERRNEPLLRRIMGGDVYEXXXXXXXXXXXXXXXXXXXXXXXXCSSRRKXXXXXX 120
           VARHAAERRNEPLLRRIMGGDVYE                        CSSRRK      
Sbjct: 61  VARHAAERRNEPLLRRIMGGDVYERAVSSAGAAVARSRRIVRRSQRVACSSRRKRRSLAM 120

Query: 121 XXXXXXXXXXXXXXXVKGXXXXXXXXVPGGEALRGFSLLSETLDYVVCLKTQVELMHSLC 180
                          VKG        VPGGEALRGFSLLSETLDYVVCLKTQVELMHSLC
Sbjct: 121 AAASGGGGALAARRMVKGRLRLLRRLVPGGEALRGFSLLSETLDYVVCLKTQVELMHSLC 180

Query: 181 KGSQQKLHLQLG 192
           KGSQQKLHLQLG
Sbjct: 181 KGSQQKLHLQLG 192



  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    0.384 

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: 4,054,229
Number of extensions: 105360
Number of successful extensions: 391
Number of sequences better than 1.0e-10: 1
Number of HSP's gapped: 391
Number of HSP's successfully gapped: 1
Length of query: 192
Length of database: 17,035,801
Length adjustment: 95
Effective length of query: 97
Effective length of database: 12,075,471
Effective search space: 1171320687
Effective search space used: 1171320687
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 (22.0 bits)
S2: 153 (63.5 bits)