TBLASTN 2.2.17 [Aug-26-2007]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
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 composition-based statistics:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= SPP00000012_1.0 # Prot # Methionine sulfoxide reductase A
(MsrA) # Hs
         (235 letters)

Database: genome.fa 
           4921 sequences; 228,543,505 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

supercont1.39 of Phytophthora infestans                               149   1e-35

>supercont1.39 of Phytophthora infestans
          Length = 1432524

 Score =  149 bits (375), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 77/168 (45%), Positives = 101/168 (60%)
 Frame = -3

Query: 67     MAVFGMGCFWGAERKFWVLKGVYSTQVGFAGGYTSNPTYKEVCSEKTGHAEVVRVVYQPE 126
              +A F  GCFWG +  F  + GV  T VG+  G   +P+Y++VC+ +T HAE +R+V+   
Sbjct: 628717 VATFAAGCFWGVQLAFDRIPGVLETSVGYTQGNVGSPSYRQVCTGRTNHAEAIRIVFDES 628538

Query: 127    HMSFEELLKVFWENHDPTQGMRQGNDHGTQYRSAIYPTSAKQMEAALSSKENYQKVLSEH 186
                S+E LL  FW  HDPT   RQ ND GTQYRS IY  S  Q ++AL+SKE +QK LS+ 
Sbjct: 628537 QTSYESLLNKFWAIHDPTTLNRQKNDKGTQYRSGIYYHSEDQRKSALASKEEHQKTLSK- 628361

Query: 187    GFGPITTDIREGQTFYYAEDYHQQYLSKNPNGYCGLGGTGVSCPVGIK 234
                 PI T+I E + F+ AED HQ+YL K   G C   G    C V I+
Sbjct: 628360 ---PIVTEIMEAKQFWDAEDNHQKYLEK--GGQCADKG----CDVAIR 628244



 Score = 87.4 bits (215), Expect(2) = 1e-28,   Method: Composition-based stats.
 Identities = 48/98 (48%), Positives = 62/98 (63%)
 Frame = +2

Query: 132    ELLKVFWENHDPTQGMRQGNDHGTQYRSAIYPTSAKQMEAALSSKENYQKVLSEHGFGPI 191
              +LLKVFW  HDPT   RQ +D GTQYRS IY  + +Q + AL+SKE +QK L +    PI
Sbjct: 698477 DLLKVFWAIHDPTSLNRQEDDVGTQYRSGIYYQNEEQHKIALTSKEEHQKTLIK----PI 698644

Query: 192    TTDIREGQTFYYAEDYHQQYLSKNPNGYCGLGGTGVSC 229
               T+I E + F+ AE+ HQ+YL K   G C   G+ V C
Sbjct: 698645 VTEIEEAKEFWDAEEAHQKYLEK--GGSCSDKGSDVQC 698752



 Score = 59.7 bits (143), Expect(2) = 1e-28,   Method: Composition-based stats.
 Identities = 24/57 (42%), Positives = 36/57 (63%)
 Frame = +3

Query: 67     MAVFGMGCFWGAERKFWVLKGVYSTQVGFAGGYTSNPTYKEVCSEKTGHAEVVRVVY 123
              +A F  GCFW  +R F  + GV  T VG+  G T+NPTY+ V + +T HAE +++ +
Sbjct: 698292 IATFAAGCFWAVQRAFDRVPGVIETSVGY*QGNTNNPTYRTVVTGRTNHAEAIKIAF 698462


  Database: genome.fa
    Posted date:  Feb 28, 2008 11:00 AM
  Number of letters in database: 228,543,505
  Number of sequences in database:  4921
  
Lambda     K      H
   0.317    0.133    0.411 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4921
Number of Hits to DB: 73,129,724
Number of extensions: 1144778
Number of successful extensions: 4404
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4403
Number of HSP's successfully gapped: 3
Length of query: 235
Length of database: 76,181,168
Length adjustment: 110
Effective length of query: 125
Effective length of database: 75,639,858
Effective search space: 9454982250
Effective search space used: 9454982250
Neighboring words threshold: 13
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: 50 (23.9 bits)