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= Os01g0889200 Os01g0889200|AK066619
         (198 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os01g0889200  RNA polymerase III RPC4 family protein              376   e-105
Os04g0394500  RNA polymerase III RPC4 family protein              132   1e-31

>Os01g0889200 RNA polymerase III RPC4 family protein
          Length = 198

 Score =  376 bits (966), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 184/198 (92%), Positives = 184/198 (92%)

Query: 1   HCHSQEGTTKANWKKKPFHITRAVPLDAIPGFLYXXXXXXXXXXXXXXNNVELEEIRPSS 60
           HCHSQEGTTKANWKKKPFHITRAVPLDAIPGFLY              NNVELEEIRPSS
Sbjct: 1   HCHSQEGTTKANWKKKPFHITRAVPLDAIPGFLYDDEDDDDDDDDEGDNNVELEEIRPSS 60

Query: 61  TECESSIHPAEELNLLEQGDTRRMLLFQLPKSLPLPRISAAVERNGKARDKEVKEGSNLK 120
           TECESSIHPAEELNLLEQGDTRRMLLFQLPKSLPLPRISAAVERNGKARDKEVKEGSNLK
Sbjct: 61  TECESSIHPAEELNLLEQGDTRRMLLFQLPKSLPLPRISAAVERNGKARDKEVKEGSNLK 120

Query: 121 ELPQGYLGKMVVYKSGKIKMKLGDVMFDVNPGEECRMAQHVAAINTKEKHCCLLGEIESR 180
           ELPQGYLGKMVVYKSGKIKMKLGDVMFDVNPGEECRMAQHVAAINTKEKHCCLLGEIESR
Sbjct: 121 ELPQGYLGKMVVYKSGKIKMKLGDVMFDVNPGEECRMAQHVAAINTKEKHCCLLGEIESR 180

Query: 181 HVVVTPDVDSLLLNDNRG 198
           HVVVTPDVDSLLLNDNRG
Sbjct: 181 HVVVTPDVDSLLLNDNRG 198



>Os04g0394500 RNA polymerase III RPC4 family protein
          Length = 276

 Score =  132 bits (333), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 69/141 (48%), Positives = 91/141 (64%), Gaps = 19/141 (13%)

Query: 70  AEELNLLEQGDTRRMLLFQLPKSLPLPRI--SAAVERNGKARDKE-----VKE------- 115
           AEEL L+ + D  ++L FQ+P SLPLP+   S A    G   D E      KE       
Sbjct: 129 AEELGLMHRSDKAQLLFFQMPASLPLPKQPDSVAETDKGDGVDAEPTSTSSKEMHAGTRP 188

Query: 116 ----GSNLKELPQGYLGKMVVYKSGKIKMKLGDVMFDVNPGEECRMAQHVAAINTKEKHC 171
               GS LK+LP+G++GK++VY+SGK+KMK+GD +FDV+PG  C   Q VAAIN +EKHC
Sbjct: 189 PKVLGSKLKDLPEGFMGKILVYRSGKVKMKIGDSLFDVSPGSNCMFVQEVAAINAREKHC 248

Query: 172 CLLGEIESRHVVVTPDVDSLL 192
           C LGEI S+  +VTPD++ LL
Sbjct: 249 CTLGEI-SKRAIVTPDIEHLL 268



  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    0.134    0.394 

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: 6,403,470
Number of extensions: 238187
Number of successful extensions: 449
Number of sequences better than 1.0e-10: 2
Number of HSP's gapped: 447
Number of HSP's successfully gapped: 2
Length of query: 198
Length of database: 17,035,801
Length adjustment: 96
Effective length of query: 102
Effective length of database: 12,023,257
Effective search space: 1226372214
Effective search space used: 1226372214
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: 153 (63.5 bits)