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= Os12g0194700 Os12g0194700|AK121912
         (108 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os12g0194700  DNA-directed RNA polymerase, 13 to 16 kDa subu...   226   2e-60
Os11g0218100  RNA polymerase, RBP11-like domain containing p...    98   2e-21

>Os12g0194700 DNA-directed RNA polymerase, 13 to 16 kDa subunit family protein
          Length = 108

 Score =  226 bits (577), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 108/108 (100%), Positives = 108/108 (100%)

Query: 1   MEHGSVTDSTASTFSIVEEDHTLANSVRFVLNQDPRVAFCGYSIPHPADNKVNIRVQTTG 60
           MEHGSVTDSTASTFSIVEEDHTLANSVRFVLNQDPRVAFCGYSIPHPADNKVNIRVQTTG
Sbjct: 1   MEHGSVTDSTASTFSIVEEDHTLANSVRFVLNQDPRVAFCGYSIPHPADNKVNIRVQTTG 60

Query: 61  DPAKDVLKDSLQDLMVMCQHVRGTFDTAVTQFRQNNPTGMNIDQNKKK 108
           DPAKDVLKDSLQDLMVMCQHVRGTFDTAVTQFRQNNPTGMNIDQNKKK
Sbjct: 61  DPAKDVLKDSLQDLMVMCQHVRGTFDTAVTQFRQNNPTGMNIDQNKKK 108



>Os11g0218100 RNA polymerase, RBP11-like domain containing protein
          Length = 143

 Score = 97.8 bits (242), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 48/62 (77%), Positives = 50/62 (80%), Gaps = 1/62 (1%)

Query: 43  SIPHPADNKVNIRVQTTGDPAKDVLKDSLQDLMVMCQHVRGTFDTAVTQFRQNNPT-GMN 101
           SIPHPADNKVNIRVQTTGDPA DV KD LQDL+VMCQHVRGTFD AV  FR   P   M+
Sbjct: 80  SIPHPADNKVNIRVQTTGDPAIDVFKDGLQDLIVMCQHVRGTFDNAVVDFRSKVPAQQMD 139

Query: 102 ID 103
           ID
Sbjct: 140 ID 141



  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
   0.316    0.130    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: 3,552,303
Number of extensions: 126184
Number of successful extensions: 199
Number of sequences better than 1.0e-10: 2
Number of HSP's gapped: 199
Number of HSP's successfully gapped: 2
Length of query: 108
Length of database: 17,035,801
Length adjustment: 76
Effective length of query: 32
Effective length of database: 13,067,537
Effective search space: 418161184
Effective search space used: 418161184
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 (21.7 bits)
S2: 149 (62.0 bits)