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= Os06g0618600 Os06g0618600|AK060212
         (378 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os06g0618600  RNA polymerase subunit, RPB5/RPB6-like domain ...   704   0.0  

>Os06g0618600 RNA polymerase subunit, RPB5/RPB6-like domain containing protein
          Length = 378

 Score =  704 bits (1816), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 347/378 (91%), Positives = 347/378 (91%)

Query: 1   SIVLGNGDQNIAPVNTAVQLEARVPLQICVSQKSSNLLNEEVNFPLPIEQPDIFWREKDE 60
           SIVLGNGDQNIAPVNTAVQLEARVPLQICVSQKSSNLLNEEVNFPLPIEQPDIFWREKDE
Sbjct: 1   SIVLGNGDQNIAPVNTAVQLEARVPLQICVSQKSSNLLNEEVNFPLPIEQPDIFWREKDE 60

Query: 61  DSEWSKANDNTDLEEGYXXXXXXXXXXXXYNKANPEXXXXXXXXXXXXXXXXXXXEPLYS 120
           DSEWSKANDNTDLEEGY            YNKANPE                   EPLYS
Sbjct: 61  DSEWSKANDNTDLEEGYDSSKDEVSSVSSYNKANPESSLRSSVSMHSLSSRLSTSEPLYS 120

Query: 121 RERPSFPSYSPIPRLSVSEISDDHGGGVVSPQRKLNHLLSDHHPSNGQMFSLDPDRSNDD 180
           RERPSFPSYSPIPRLSVSEISDDHGGGVVSPQRKLNHLLSDHHPSNGQMFSLDPDRSNDD
Sbjct: 121 RERPSFPSYSPIPRLSVSEISDDHGGGVVSPQRKLNHLLSDHHPSNGQMFSLDPDRSNDD 180

Query: 181 AGPPLTPKYVEPAGSEGFMRGRSYNIRIDDQVLLRFSPKNSDSTYYFGDMIGGALTFFHG 240
           AGPPLTPKYVEPAGSEGFMRGRSYNIRIDDQVLLRFSPKNSDSTYYFGDMIGGALTFFHG
Sbjct: 181 AGPPLTPKYVEPAGSEGFMRGRSYNIRIDDQVLLRFSPKNSDSTYYFGDMIGGALTFFHG 240

Query: 241 SGTRRCLEVSVTLETSETVNPRVIHPSRRSSPSITKVHSEHYEVVADLHQTSFLFSVPID 300
           SGTRRCLEVSVTLETSETVNPRVIHPSRRSSPSITKVHSEHYEVVADLHQTSFLFSVPID
Sbjct: 241 SGTRRCLEVSVTLETSETVNPRVIHPSRRSSPSITKVHSEHYEVVADLHQTSFLFSVPID 300

Query: 301 GPMSFSTSKVSVQWSLRFEFFTTPEGIDSSRYEHPLLVEKREKGDWVLPITVYAPPLRRQ 360
           GPMSFSTSKVSVQWSLRFEFFTTPEGIDSSRYEHPLLVEKREKGDWVLPITVYAPPLRRQ
Sbjct: 301 GPMSFSTSKVSVQWSLRFEFFTTPEGIDSSRYEHPLLVEKREKGDWVLPITVYAPPLRRQ 360

Query: 361 AIHGRNDRSVLVGNLFNS 378
           AIHGRNDRSVLVGNLFNS
Sbjct: 361 AIHGRNDRSVLVGNLFNS 378



  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
   0.315    0.134    0.400 

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: 13,716,540
Number of extensions: 615117
Number of successful extensions: 1083
Number of sequences better than 1.0e-10: 1
Number of HSP's gapped: 1082
Number of HSP's successfully gapped: 1
Length of query: 378
Length of database: 17,035,801
Length adjustment: 103
Effective length of query: 275
Effective length of database: 11,657,759
Effective search space: 3205883725
Effective search space used: 3205883725
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: 42 (22.0 bits)
S2: 157 (65.1 bits)