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= Os05g0400700 Os05g0400700|AK072739
         (177 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Os05g0400700  Similar to DNA-directed RNA polymerase II 19 k...   360   e-100
Os05g0157100  RNA polymerase Rpb7, N-terminal domain contain...    88   4e-18
Os05g0224700  RNA polymerase Rpb7, N-terminal domain contain...    79   1e-15

>Os05g0400700 Similar to DNA-directed RNA polymerase II 19 kDa polypeptide (EC
           2.7.7.6) (RNA polymerase II subunit 5)
          Length = 177

 Score =  360 bits (923), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 177/177 (100%), Positives = 177/177 (100%)

Query: 1   MFFHIVLERNMQLHPRHFGPHLRDKLVSKLIKDVEGTCSGRHGFVVAITGVEDVGKGLIR 60
           MFFHIVLERNMQLHPRHFGPHLRDKLVSKLIKDVEGTCSGRHGFVVAITGVEDVGKGLIR
Sbjct: 1   MFFHIVLERNMQLHPRHFGPHLRDKLVSKLIKDVEGTCSGRHGFVVAITGVEDVGKGLIR 60

Query: 61  EGTGYVTFPVKYQCVVFRPFKGEILEAVVTMVNKMGFFAEAGPVQIFVSNHLIPDDMEFQ 120
           EGTGYVTFPVKYQCVVFRPFKGEILEAVVTMVNKMGFFAEAGPVQIFVSNHLIPDDMEFQ
Sbjct: 61  EGTGYVTFPVKYQCVVFRPFKGEILEAVVTMVNKMGFFAEAGPVQIFVSNHLIPDDMEFQ 120

Query: 121 SGDVPNYTTSDGSVKIQKDSEVRLKIIGTRVDATEIFCIGTIKDDFLGVISDPGAAV 177
           SGDVPNYTTSDGSVKIQKDSEVRLKIIGTRVDATEIFCIGTIKDDFLGVISDPGAAV
Sbjct: 121 SGDVPNYTTSDGSVKIQKDSEVRLKIIGTRVDATEIFCIGTIKDDFLGVISDPGAAV 177



>Os05g0157100 RNA polymerase Rpb7, N-terminal domain containing protein
          Length = 175

 Score = 87.8 bits (216), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 53/175 (30%), Positives = 98/175 (56%), Gaps = 10/175 (5%)

Query: 1   MFFHIVLERNMQLHPRHFGPH---LRDKLVSKLIKDVEG-TCSGRHGFVVAITGVEDVGK 56
           +F  + +  N+ + P    P    LR  ++ +L++D+     S  HG+ +A++ ++ + +
Sbjct: 2   VFLKVEMSLNVLISPSQLSPQGLLLRKAVIVRLLEDIANRKASKDHGYYIAVSELKAISE 61

Query: 57  GLIREGTGYVTFPVKYQCVVFRPFKGEILEAVVTMVNKMGFFAEAGPVQ-IFVSNHLIPD 115
           G +RE TG V FPV + C+  +P KGE+L   V  + K G F ++GP++ IF+S   +  
Sbjct: 62  GKVRELTGDVLFPVTFTCITQKPMKGEVLVGSVDKILKHGIFLKSGPIESIFLSEKTM-S 120

Query: 116 DMEFQSGDVPNYTTSDGSVKIQKDSEVRLKIIGTR-VDATEIF-CIGTIKDDFLG 168
           D ++  G+  N    +   K++KD+ VR K++G R ++A   F  + T+  D+LG
Sbjct: 121 DFKYIGGE--NAVFMNEHSKLEKDTVVRFKVMGFRWMEADRQFQLLATLAGDYLG 173



>Os05g0224700 RNA polymerase Rpb7, N-terminal domain containing protein
          Length = 782

 Score = 79.3 bits (194), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 45/150 (30%), Positives = 82/150 (54%), Gaps = 8/150 (5%)

Query: 1   MFFHIVLERNMQLHPRHFGPH---LRDKLVSKLIKDVEG-TCSGRHGFVVAITGVEDVGK 56
           +F  + +  N+ + P    P    LR  ++  L++++     S  HG+ +A++ ++ + +
Sbjct: 2   VFLKVDMSWNVLISPSELSPKGLLLRKAVIVSLLEEIANRKASKDHGYYIAVSELKAISE 61

Query: 57  GLIREGTGYVTFPVKYQCVVFRPFKGEILEAVVTMVNKMGFFAEAGPVQ-IFVSNHLIPD 115
           G +RE TG V FPV + C+  +P KGEIL   V  + K G F ++GP++ IF+S   +  
Sbjct: 62  GKVRELTGDVLFPVTFTCITQKPTKGEILVGSVDKILKHGVFLKSGPIESIFLSEKTL-S 120

Query: 116 DMEFQSGDVPNYTTSDGSVKIQKDSEVRLK 145
           D ++  G+ P +       K++KD+ VR K
Sbjct: 121 DYKYIGGENPMFMNDHS--KLEKDTAVRFK 148



  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
   0.324    0.143    0.427 

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: 6,133,611
Number of extensions: 242463
Number of successful extensions: 489
Number of sequences better than 1.0e-10: 3
Number of HSP's gapped: 489
Number of HSP's successfully gapped: 3
Length of query: 177
Length of database: 17,035,801
Length adjustment: 94
Effective length of query: 83
Effective length of database: 12,127,685
Effective search space: 1006597855
Effective search space used: 1006597855
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 152 (63.2 bits)