Difference between revisions of "CD task2 protocol"
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<b>GO Term Enrichment (all terms represented more than once)</b> |
<b>GO Term Enrichment (all terms represented more than once)</b> |
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| − | hydrolase activity, acting on ester bonds |
+ | 766 hydrolase activity, acting on ester bonds |
| − | metabolic process |
+ | 665 metabolic process |
| − | hydrolase activity |
+ | 507 hydrolase activity |
| − | metal ion binding |
+ | 488 metal ion binding |
| − | zinc ion binding |
+ | 294 zinc ion binding |
| − | arginine catabolic process to glutamate |
+ | 234 arginine catabolic process to glutamate |
| − | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides |
+ | 176 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides |
| − | aspartoacylase activity |
+ | 158 aspartoacylase activity |
| − | arginine metabolic process |
+ | 132 arginine metabolic process |
| − | succinylglutamate desuccinylase activity |
+ | 132 succinylglutamate desuccinylase activity |
| + | 30 cytoplasm |
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| − | cytoplasm 30 |
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| − | arginine catabolic process to succinate |
+ | 24 arginine catabolic process to succinate |
| + | 23 proteolysis |
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| − | proteolysis 23 |
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| − | metallocarboxypeptidase activity |
+ | 22 metallocarboxypeptidase activity |
| − | apical plasma membrane |
+ | 12 apical plasma membrane |
| − | carboxypeptidase activity |
+ | 9 carboxypeptidase activity |
| + | 8 nucleus |
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| − | nucleus 8 |
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| − | aminoacylase activity |
+ | 8 aminoacylase activity |
| + | 8 membrane |
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| − | membrane 8 |
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| − | identical protein binding |
+ | 6 identical protein binding |
| − | oxidation-reduction process |
+ | 6 oxidation-reduction process |
| − | plasma membrane |
+ | 6 plasma membrane |
| − | oxidoreductase activity |
+ | 5 oxidoreductase activity |
| − | malate synthase activity |
+ | 2 malate synthase activity |
| − | glyoxylate cycle |
+ | 2 glyoxylate cycle |
| − | exonuclease activity |
+ | 2 exonuclease activity |
| − | nucleotide binding |
+ | 2 nucleotide binding |
| − | acetate metabolic process |
+ | 2 acetate metabolic process |
| − | arginine catabolic process |
+ | 2 arginine catabolic process |
| − | cell adhesion |
+ | 2 cell adhesion |
| − | virus-host interaction |
+ | 2 virus-host interaction |
| − | integral to membrane |
+ | 2 integral to membrane |
| − | transferase activity |
+ | 2 transferase activity |
| + | |||
Revision as of 12:00, 24 August 2012
Contents
Sequence
The 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
We ran BlastP on student machines with the big_80 as a reference database.
<source lang="bash"> blastall -p blastp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o blastp_p45381_wt_big80.out </source>
PsiBlast
PSIBlast was used in the same fashion as BLAST, with the big_80 as the background database.
2 iterations and default E-Value 0.002 <source lang="bash"> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it2_p45381_wt_big80.out -j 2 -v 700</source>
2 iterations, more strict E-value cutoff of 10E-10
<source lang="bash"> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it2_h10e10_p45381_wt_big80.out -j 2 -h 10e-10 </source>
GO Term Enrichment (all terms represented more than once)
766 hydrolase activity, acting on ester bonds 665 metabolic process 507 hydrolase activity 488 metal ion binding 294 zinc ion binding 234 arginine catabolic process to glutamate 176 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides 158 aspartoacylase activity 132 arginine metabolic process 132 succinylglutamate desuccinylase activity 30 cytoplasm 24 arginine catabolic process to succinate 23 proteolysis 22 metallocarboxypeptidase activity 12 apical plasma membrane 9 carboxypeptidase activity 8 nucleus 8 aminoacylase activity 8 membrane 6 identical protein binding 6 oxidation-reduction process 6 plasma membrane 5 oxidoreductase activity 2 malate synthase activity 2 glyoxylate cycle 2 exonuclease activity 2 nucleotide binding 2 acetate metabolic process 2 arginine catabolic process 2 cell adhesion 2 virus-host interaction 2 integral to membrane 2 transferase activity
10 iterations, default Evalue 0.002 <source lang="bash"> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it10_p45381_wt_big80.out -j 10 </source>
10 iterations, E-value cutoff 10E-10
<source lang="bash"> blastpgp -d /mnt/project/pracstrucfunc12/data/big/big_80 -i P45381_wt.fasta -o psiblast_it10_h10e10_p45381_wt_big80.out -j 10 -h 10e-10 </source>
HHBlits
Run HHBlits on student machines with Uniprot20 database.
- 2 iterations
<source lang="bash"> hhblits -i P45381_wt.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -o hhblits_p45381_def.out </source>
- 8 iterations
<source lang="bash"> hhblits -i P45381_wt.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -n 8 -z 1000 -v 1000-o hhblits_p45381_n10.out </source>
- 2 iterations, -e 10e-10
<source lang="bash"> hhblits -i P45381_wt.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -e 10e-10 -o hhblits_p45381_def.out </source>
- 8 iterations, -e 10e-10
<source lang="bash"> hhblits -i P45381_wt.fasta -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -n 8 -e 10e-10 -z 1000 -v 1000 -o hhblits_p45381_n10.out </source>
