Canavan Task 2 - Sequence alignments

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Task 2 : Canavans Disease

Sequence

Native ASPA sequence:

UniProt: P45381

>hsa:443 ASPA, ACY2, ASP; aspartoacylase; K01437 aspartoacylase [EC:3.5.1.15] (A)
MTSCHIAEEHIQKVAIFGGTHGNELTGVFLVKHWLENGAEIQRTGLEVKPFITNPRAVKK
CTRYIDCDLNRIFDLENLGKKMSEDLPYEVRRAQEINHLFGPKDSEDSYDIIFDLHNTTS
NMGCTLILEDSRNNFLIQMFHYIKTSLAPLPCYVYLIEHPSLKYATTRSIAKYPVGIEVG
PQPQGVLRADILDQMRKMIKHALDFIHHFNEGKEFPPCAIEVYKIIEKVDYPRDENGEIA
AIIHPNLQDQDWKPLHPGDPMFLTLDGKTIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTK
LTLNAKSIRCCLH

BLASTP

Run BlastP on student machines with big_80 database.

Command:

blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out

-p specifies the blast type
-d database
-i input file
-o output file

We got 195 resulting sequences, out of which the last 101 have EValues below E^-15. Most of the resulting proteins are Aspartoacylases of other species. Most of the results with EValue > E^-15 are Succinylglutamate Desuccinylases, which catalyze a reaction similar to Aspartoacylase.

PSIBLAST

  • 2 iterations, default Evalue 10
    • blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 2
    • time: ~2m30
    • 197 results
    • best E-Value: E^-164
    • 93 results with EValue < e^-15 of which most are (probable or putative)Aspartoacylases
    • proteins > EValue e^-15 are often Succinylglutamate Desuccinylases
    • results similar to blastp run
  • 2 iterations, E-value cutoff 10E-10
    • blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 2 -h


  • 10 iterations, default Evalue 10
    • blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 10
  • 10 iterations, E-value cutoff 10E-10
    • blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out -j 10 -h