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= Os02g0670400 Os02g0670400|AB079636
         (145 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os02g0670400  Similar to HMGc1 protein                            155   7e-39
Os08g0101100  High mobility group box domain containing protein    81   2e-16
Os06g0728000  HMG1 protein (HMGB1)                                 76   9e-15
Os04g0564600  Similar to HMG1 protein                              74   5e-14
Os09g0551600  Similar to HMGd1 protein (Nucleasome/chromatin...    66   9e-12

>Os02g0670400 Similar to HMGc1 protein
          Length = 145

 Score =  155 bits (393), Expect = 7e-39,   Method: Compositional matrix adjust.
 Identities = 83/126 (65%), Positives = 83/126 (65%)

Query: 1   MKGKADASXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXFFVFMSEFRQEYQAAHPDNKS 60
           MKGKADAS                               FFVFMSEFRQEYQAAHPDNKS
Sbjct: 1   MKGKADASKKGEGRLKAAGGAGKRKKAAASGKPKRPPSAFFVFMSEFRQEYQAAHPDNKS 60

Query: 61  VAAVSKAAGEKWRAMSEQEKAPYVDKAGQKKQDYEKTKANFDXXXXXXXXXXXXHDDGEG 120
           VAAVSKAAGEKWRAMSEQEKAPYVDKAGQKKQDYEKTKANFD            HDDGEG
Sbjct: 61  VAAVSKAAGEKWRAMSEQEKAPYVDKAGQKKQDYEKTKANFDKKESTSSKKAKTHDDGEG 120

Query: 121 SDKSKS 126
           SDKSKS
Sbjct: 121 SDKSKS 126



>Os08g0101100 High mobility group box domain containing protein
          Length = 203

 Score = 81.3 bits (199), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 33/55 (60%), Positives = 48/55 (87%)

Query: 40  FFVFMSEFRQEYQAAHPDNKSVAAVSKAAGEKWRAMSEQEKAPYVDKAGQKKQDY 94
           FF+FMS+FR+EY+A HPDNKSV+AV+K  GE+W++MS+++K PY+DKA + K +Y
Sbjct: 99  FFLFMSDFRKEYKAEHPDNKSVSAVAKEGGERWKSMSDEDKKPYLDKAAELKAEY 153



>Os06g0728000 HMG1 protein (HMGB1)
          Length = 157

 Score = 75.9 bits (185), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 34/63 (53%), Positives = 49/63 (77%)

Query: 40  FFVFMSEFRQEYQAAHPDNKSVAAVSKAAGEKWRAMSEQEKAPYVDKAGQKKQDYEKTKA 99
           FFVFM EFR+E++  +P NKSVAAV KAAG++W++++E +KAPYV KA + K +Y K  A
Sbjct: 49  FFVFMEEFRKEFKEKNPKNKSVAAVGKAAGDRWKSLTEADKAPYVAKANKLKAEYNKAIA 108

Query: 100 NFD 102
            ++
Sbjct: 109 AYN 111



>Os04g0564600 Similar to HMG1 protein
          Length = 132

 Score = 73.6 bits (179), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 45/91 (49%), Positives = 53/91 (58%), Gaps = 8/91 (8%)

Query: 40  FFVFMSEFRQEYQAAHPDNKSVAAVSKAAGEKWRAMSEQEKAPYVDKAGQKKQDYEKTKA 99
           FF F++EFR +Y   HP+ K VAAV+KAAGEKWRAMS++EKA Y    G KK D E   A
Sbjct: 32  FFAFLAEFRPQYMEKHPNTKGVAAVTKAAGEKWRAMSDEEKAQY----GGKKPDGESKPA 87

Query: 100 NFDXXXXXXXXXXXXHD----DGEGSDKSKS 126
                           D    +GEGSDKSKS
Sbjct: 88  AASKKKESTSSKKAKTDGAEQEGEGSDKSKS 118



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

 Score = 65.9 bits (159), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 27/57 (47%), Positives = 43/57 (75%)

Query: 40 FFVFMSEFRQEYQAAHPDNKSVAAVSKAAGEKWRAMSEQEKAPYVDKAGQKKQDYEK 96
          FFVFM +FR++Y+  HP+ K V+ + KA G+KW++M++ +KAP+V KA + K +Y K
Sbjct: 35 FFVFMEQFRKDYKEKHPNVKQVSVIGKAGGDKWKSMTDADKAPFVTKAEKLKAEYTK 91



  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
   0.306    0.121    0.337 

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: 2,582,271
Number of extensions: 67005
Number of successful extensions: 198
Number of sequences better than 1.0e-10: 6
Number of HSP's gapped: 196
Number of HSP's successfully gapped: 6
Length of query: 145
Length of database: 17,035,801
Length adjustment: 91
Effective length of query: 54
Effective length of database: 12,284,327
Effective search space: 663353658
Effective search space used: 663353658
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 151 (62.8 bits)