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 # Protein # Methionine sulfoxide reductase A
(MsrA) # Homo sapiens # Complete
         (235 letters)

Database: genome.fa 
           23,491 sequences; 86,045,674 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gb|AAXJ01000112.1| Perkinsus marinus ATCC 50983 strain ATCC 5098...    94   5e-28
gb|AAXJ01005342.1| Perkinsus marinus ATCC 50983 strain ATCC 5098...    94   9e-28
gb|AAXJ01000524.1| Perkinsus marinus ATCC 50983 strain ATCC 5098...    28   9.5  

>gb|AAXJ01000112.1| Perkinsus marinus ATCC 50983 strain ATCC 50983 gcontig_1104296679972,
             whole genome shotgun sequence
          Length = 64280

 Score = 94.0 bits (232), Expect(2) = 5e-28,   Method: Composition-based stats.
 Identities = 71/201 (35%), Positives = 90/201 (44%), Gaps = 63/201 (31%)
 Frame = -1

Query: 93    VGFAGGYTSNPTYKEVCSEKTGHAEVVRVVYQPEHMSFEELL----------------KV 136
             VG+A G T NPTY+EVCS +T H+EVVR++Y P+ +++++LL                KV
Sbjct: 17582 VGYAQGKTPNPTYEEVCSGQTNHSEVVRIIYNPKTITYKDLLKVTHSSLRSSSMMMYSKV 17403

Query: 137   FWENHDPTQGMRQGNDHGTQ-------------------YRSAIYPTSAKQMEAA----- 172
             FW  HDPT  M QGND G+Q                   Y   +    A+   A+     
Sbjct: 17402 FWSGHDPTVPMAQGNDCGSQ*VHMAGRWSSPSWSGIGVVYIIIMRSRRARHWRASERVND 17223

Query: 173   ------LSSKENYQKVLSEHGFGP-ITTDIREGQTFYYAEDYHQQY-------------- 211
                    S +E YQ  LS+ G    I T+I     FYYAEDYHQQY              
Sbjct: 17222 SSVSSFSSFREEYQAALSKAGMKKTIVTEIEPAGEFYYAEDYHQQYGSTLLLPPSAFYAR 17043

Query: 212   LSKNPNG--YCGLGGTGVSCP 230
              S  P    YCGL   GV  P
Sbjct: 17042 YSSKPGSRQYCGLRPLGVDFP 16980



 Score = 49.3 bits (116), Expect(2) = 5e-28,   Method: Composition-based stats.
 Identities = 22/42 (52%), Positives = 28/42 (66%)
 Frame = -3

Query: 52    VNGNRTVEPFPEGTQMAVFGMGCFWGAERKFWVLKGVYSTQV 93
             V GN    P+P   + A+FGMGCFW +E  F  +KGV+STQV
Sbjct: 17760 VTGNPMYGPWPVAMEQALFGMGCFWCSEALFVDMKGVFSTQV 17635


>gb|AAXJ01005342.1| Perkinsus marinus ATCC 50983 strain ATCC 50983 gcontig_1104296309956,
            whole genome shotgun sequence
          Length = 2780

 Score = 94.0 bits (232), Expect(2) = 9e-28,   Method: Composition-based stats.
 Identities = 63/169 (37%), Positives = 82/169 (48%), Gaps = 48/169 (28%)
 Frame = -1

Query: 93   VGFAGGYTSNPTYKEVCSEKTGHAEVVRVVYQPEHMSFEELL----------------KV 136
            VG+A G T NPTY+EVCS +T H+EVVR++Y P+ +++++LL                KV
Sbjct: 2024 VGYAQGKTPNPTYEEVCSGQTNHSEVVRIIYNPKTITYKDLLKVTHRSLRSSSMMMYRKV 1845

Query: 137  FWENHDPTQGMRQGNDHGTQ-------------------YRSAIYPTSAKQMEAA----- 172
            FW  HDPT  M QGND G+Q                   Y   +    A+   A+     
Sbjct: 1844 FWSGHDPTVPMAQGNDCGSQ*VHMAGRWSSPSWSGIGVVYIIIMRSRRARHWRASERVNN 1665

Query: 173  ------LSSKENYQKVLSEHGF--GPITTDIREGQTFYYAEDYHQQYLS 213
                   S +E YQ  LS+ G     I T+I     FYYAEDYHQQY S
Sbjct: 1664 SSVSIFSSFREEYQAALSKAGMKEKTIVTEIEPAGEFYYAEDYHQQYGS 1518



 Score = 48.5 bits (114), Expect(2) = 9e-28,   Method: Composition-based stats.
 Identities = 21/42 (50%), Positives = 28/42 (66%)
 Frame = -3

Query: 52   VNGNRTVEPFPEGTQMAVFGMGCFWGAERKFWVLKGVYSTQV 93
            V GN    P+P   + A+FGMGCFW +E  F  +KG++STQV
Sbjct: 2202 VTGNPMYGPWPVAMEQALFGMGCFWCSEALFVDMKGIFSTQV 2077


>gb|AAXJ01000524.1| Perkinsus marinus ATCC 50983 strain ATCC 50983 gcontig_1104296718546,
            whole genome shotgun sequence
          Length = 26511

 Score = 28.5 bits (62), Expect = 9.5,   Method: Composition-based stats.
 Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 5/85 (5%)
 Frame = -1

Query: 58   VEPFPEGTQMAVFGMGCFWGAERKFWVL-KGVYSTQVGF----AGGYTSNPTYKEVCSEK 112
            V+P PEG  + + G G  W   RK W   +  + TQVG     A  + S  T  + C   
Sbjct: 3489 VKPKPEGMAIQILGAGKNWVGGRKTWARGR*SWVTQVGCPRDEANVHPSRET--KTCHSA 3316

Query: 113  TGHAEVVRVVYQPEHMSFEELLKVF 137
            T  ++++  +  P  +    L+ VF
Sbjct: 3315 TLRSKILTGIRSPMPVRLLALVYVF 3241


  Database: genome.fa
    Posted date:  Jan 16, 2009 12:51 PM
  Number of letters in database: 86,045,674
  Number of sequences in database:  23,491
  
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: 23491
Number of Hits to DB: 27,792,086
Number of extensions: 426637
Number of successful extensions: 1881
Number of sequences better than 10.0: 4
Number of HSP's gapped: 1879
Number of HSP's successfully gapped: 8
Length of query: 235
Length of database: 28,681,891
Length adjustment: 103
Effective length of query: 132
Effective length of database: 26,262,318
Effective search space: 3466625976
Effective search space used: 3466625976
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: 40 (20.0 bits)
