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= Os06g0728000 Os06g0728000|AK062226
         (157 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os06g0728000  HMG1 protein (HMGB1)                                143   5e-35
Os09g0551600  Similar to HMGd1 protein (Nucleasome/chromatin...    78   3e-15

>Os06g0728000 HMG1 protein (HMGB1)
          Length = 157

 Score =  143 bits (361), Expect = 5e-35,   Method: Compositional matrix adjust.
 Identities = 85/122 (69%), Positives = 85/122 (69%)

Query: 1   MKGAKSKGAAKPDAKLAVKSXXXXXXXXXXXXXXXXXDPNKPKRAPSAXXXXXXXXXXXX 60
           MKGAKSKGAAKPDAKLAVKS                 DPNKPKRAPSA            
Sbjct: 1   MKGAKSKGAAKPDAKLAVKSKGAEKPAAKGRKGKAGKDPNKPKRAPSAFFVFMEEFRKEF 60

Query: 61  XXXXXXXXSVAAVGKAAGDRWKSLTEADKAPYVAKANKLKAEYNKAIAAYNKGESTAKKA 120
                   SVAAVGKAAGDRWKSLTEADKAPYVAKANKLKAEYNKAIAAYNKGESTAKKA
Sbjct: 61  KEKNPKNKSVAAVGKAAGDRWKSLTEADKAPYVAKANKLKAEYNKAIAAYNKGESTAKKA 120

Query: 121 PA 122
           PA
Sbjct: 121 PA 122



>Os09g0551600 Similar to HMGd1 protein (Nucleasome/chromatin assembly factor D
           protein NFD101)
          Length = 127

 Score = 78.2 bits (191), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 39/74 (52%), Positives = 45/74 (60%)

Query: 38  DPNKPKRAPSAXXXXXXXXXXXXXXXXXXXXSVAAVGKAAGDRWKSLTEADKAPYVAKAN 97
           DPNKPKR PSA                     V+ +GKA GD+WKS+T+ADKAP+V KA 
Sbjct: 24  DPNKPKRPPSAFFVFMEQFRKDYKEKHPNVKQVSVIGKAGGDKWKSMTDADKAPFVTKAE 83

Query: 98  KLKAEYNKAIAAYN 111
           KLKAEY K I AYN
Sbjct: 84  KLKAEYTKKIDAYN 97



  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
   0.301    0.116    0.315 

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: 2,595,835
Number of extensions: 61018
Number of successful extensions: 88
Number of sequences better than 1.0e-10: 3
Number of HSP's gapped: 86
Number of HSP's successfully gapped: 3
Length of query: 157
Length of database: 17,035,801
Length adjustment: 92
Effective length of query: 65
Effective length of database: 12,232,113
Effective search space: 795087345
Effective search space used: 795087345
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 17 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 43 (21.8 bits)
S2: 152 (63.2 bits)