Difference between revisions of "Canavan Task 2 - Sequence alignments"
(→PSIBLAST) |
|||
| Line 39: | Line 39: | ||
** 197 results |
** 197 results |
||
** best E-Value: E^-164 |
** best E-Value: E^-164 |
||
| − | ** 93 results with EValue < e^-15 of which most are (probable or putative)Aspartoacylases |
+ | ** 93 results with EValue < e^-15 of which most are (probable or putative) Aspartoacylases |
** proteins > EValue e^-15 are often Succinylglutamate Desuccinylases |
** proteins > EValue e^-15 are often Succinylglutamate Desuccinylases |
||
** results similar to blastp run |
** results similar to blastp run |
||
| Line 52: | Line 52: | ||
*10 iterations, default Evalue 0.002 |
*10 iterations, default Evalue 0.002 |
||
| − | **<code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it10_p45381_wt_big80.out -j 10</code> |
+ | ** <code> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it10_p45381_wt_big80.out -j 10</code> |
| − | **time: ~10m |
+ | ** time: ~10m |
| − | ** |
+ | ** converged after 8 rounds |
| + | ** 500 results |
||
| + | ** best E-Value 5E^-70 |
||
| + | ** worst E-Value 8E^-38 |
||
| + | ** most significant results include more Succinylglutamate Desuccinylases than Aspartoacylases |
||
Revision as of 18:14, 2 May 2012
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 0.002
blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it2_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 10e-10
- 5 iterations, default Evalue 0.002
blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it5_p45381_wt_big80.out -j 2
- 10 iterations, default Evalue 0.002
blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it10_p45381_wt_big80.out -j 10- time: ~10m
- converged after 8 rounds
- 500 results
- best E-Value 5E^-70
- worst E-Value 8E^-38
- most significant results include more Succinylglutamate Desuccinylases than Aspartoacylases
- 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 10e-10
