Difference between revisions of "CD task2 protocol"

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(PsiBlast)
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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>
hydrolase activity, acting on ester bonds 766
+
766 hydrolase activity, acting on ester bonds
metabolic process 665
+
665 metabolic process
hydrolase activity 507
+
507 hydrolase activity
metal ion binding 488
+
488 metal ion binding
zinc ion binding 294
+
294 zinc ion binding
arginine catabolic process to glutamate 234
+
234 arginine catabolic process to glutamate
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides 176
+
176 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
aspartoacylase activity 158
+
158 aspartoacylase activity
arginine metabolic process 132
+
132 arginine metabolic process
succinylglutamate desuccinylase activity 132
+
132 succinylglutamate desuccinylase activity
  +
30 cytoplasm
cytoplasm 30
 
arginine catabolic process to succinate 24
+
24 arginine catabolic process to succinate
  +
23 proteolysis
proteolysis 23
 
metallocarboxypeptidase activity 22
+
22 metallocarboxypeptidase activity
apical plasma membrane 12
+
12 apical plasma membrane
carboxypeptidase activity 9
+
9 carboxypeptidase activity
  +
8 nucleus
nucleus 8
 
aminoacylase activity 8
+
8 aminoacylase activity
  +
8 membrane
membrane 8
 
identical protein binding 6
+
6 identical protein binding
oxidation-reduction process 6
+
6 oxidation-reduction process
plasma membrane 6
+
6 plasma membrane
oxidoreductase activity 5
+
5 oxidoreductase activity
malate synthase activity 2
+
2 malate synthase activity
glyoxylate cycle 2
+
2 glyoxylate cycle
exonuclease activity 2
+
2 exonuclease activity
nucleotide binding 2
+
2 nucleotide binding
acetate metabolic process 2
+
2 acetate metabolic process
arginine catabolic process 2
+
2 arginine catabolic process
cell adhesion 2
+
2 cell adhesion
virus-host interaction 2
+
2 virus-host interaction
integral to membrane 2
+
2 integral to membrane
transferase activity 2
+
2 transferase activity
  +
 
 
   

Revision as of 13:00, 24 August 2012

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>