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= Os04g0388900 Os04g0388900|AK063224
         (97 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os04g0388900  Similar to U6 snRNA-associated Sm-like protein...   168   7e-43
Os02g0510100  Similar to U6 snRNA-associated Sm-like protein...   166   3e-42
Os11g0657300  Similar to Small nuclear ribonucleoprotein F (...    75   9e-15
Os02g0177500  Similar to Small nuclear ribonucleoprotein F (...    75   1e-14

>Os04g0388900 Similar to U6 snRNA-associated Sm-like protein LSm6 (Sm protein
          F)
          Length = 97

 Score =  168 bits (426), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 84/97 (86%), Positives = 84/97 (86%)

Query: 1  MSTXXXXXXXXXXXXXAVKTPSDFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQ 60
          MST             AVKTPSDFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQ
Sbjct: 1  MSTGGGADKSGGGGGGAVKTPSDFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQ 60

Query: 61 TEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTLTDDA 97
          TEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTLTDDA
Sbjct: 61 TEEYVNGQLKNKYGDAFIRGNNVLYISTSKRTLTDDA 97



>Os02g0510100 Similar to U6 snRNA-associated Sm-like protein LSm6 (Sm protein
          F)
          Length = 96

 Score =  166 bits (420), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 80/81 (98%), Positives = 80/81 (98%)

Query: 17 AVKTPSDFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDA 76
          AVKTPSDFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDA
Sbjct: 16 AVKTPSDFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDA 75

Query: 77 FIRGNNVLYISTSKRTLTDDA 97
          FIRGNNVLYISTSKRTLTD A
Sbjct: 76 FIRGNNVLYISTSKRTLTDGA 96



>Os11g0657300 Similar to Small nuclear ribonucleoprotein F (snRNP-F) (Sm
          protein F) (Sm-F) (SmF)
          Length = 86

 Score = 75.1 bits (183), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 34/77 (44%), Positives = 50/77 (64%), Gaps = 4/77 (5%)

Query: 21 PSDFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRG 80
          P  FL ++ G+PV+VKL  G++Y+G L  +D YMN+ +  TEEY++GQ     G+  IR 
Sbjct: 8  PKPFLNNLTGKPVIVKLKWGMEYKGYLVSVDSYMNLQLANTEEYIDGQFSGNLGEILIRC 67

Query: 81 NNVLYISTSKRTLTDDA 97
          NNVLY+    R + +DA
Sbjct: 68 NNVLYL----RGVPEDA 80



>Os02g0177500 Similar to Small nuclear ribonucleoprotein F (snRNP-F) (Sm
          protein F) (Sm-F) (SmF)
          Length = 86

 Score = 75.1 bits (183), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 34/78 (43%), Positives = 50/78 (64%), Gaps = 1/78 (1%)

Query: 21 PSDFLKSIRGRPVVVKLNSGVDYRGILACLDGYMNIAMEQTEEYVNGQLKNKYGDAFIRG 80
          P  FL ++ G+PV+VKL  G++Y+G L  +D YMN+ +  TEEY++GQ     G+  IR 
Sbjct: 8  PKPFLNNLTGKPVIVKLKWGMEYKGYLVSVDSYMNLQLANTEEYIDGQFSGNLGEILIRC 67

Query: 81 NNVLYI-STSKRTLTDDA 97
          NNVLY+    + T  +DA
Sbjct: 68 NNVLYLRGVPEDTEIEDA 85



  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
   0.317    0.134    0.377 

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: 2,505,705
Number of extensions: 79294
Number of successful extensions: 147
Number of sequences better than 1.0e-10: 4
Number of HSP's gapped: 147
Number of HSP's successfully gapped: 4
Length of query: 97
Length of database: 17,035,801
Length adjustment: 66
Effective length of query: 31
Effective length of database: 13,589,677
Effective search space: 421279987
Effective search space used: 421279987
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 149 (62.0 bits)