Difference between revisions of "CD task2 protocol"

From Bioinformatikpedia
(HHBlits)
(PsiBlast)
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<b>2 iterations, more strict E-value cutoff of 10E-10 </b>
 
<b>2 iterations, more strict E-value cutoff of 10E-10 </b>
 
<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>
 
<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>
  +
  +
<b>GO Term Enrichment (all terms represented more than once)</b>
  +
hydrolase activity, acting on ester bonds 766
  +
metabolic process 665
  +
hydrolase activity 507
  +
metal ion binding 488
  +
zinc ion binding 294
  +
arginine catabolic process to glutamate 234
  +
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides 176
  +
aspartoacylase activity 158
  +
arginine metabolic process 132
  +
succinylglutamate desuccinylase activity 132
  +
cytoplasm 30
  +
arginine catabolic process to succinate 24
  +
proteolysis 23
  +
metallocarboxypeptidase activity 22
  +
apical plasma membrane 12
  +
carboxypeptidase activity 9
  +
nucleus 8
  +
aminoacylase activity 8
  +
membrane 8
  +
identical protein binding 6
  +
oxidation-reduction process 6
  +
plasma membrane 6
  +
oxidoreductase activity 5
  +
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 2
  +
  +
   
   

Revision as of 12:59, 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)

hydrolase activity, acting on ester bonds	766
metabolic process	665
hydrolase activity	507
metal ion binding	488
zinc ion binding	294
arginine catabolic process to glutamate	234
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	176
aspartoacylase activity	158
arginine metabolic process	132
succinylglutamate desuccinylase activity	132
cytoplasm	30
arginine catabolic process to succinate	24
proteolysis	23
metallocarboxypeptidase activity	22
apical plasma membrane	12
carboxypeptidase activity	9
nucleus	8
aminoacylase activity	8
membrane	8
identical protein binding	6
oxidation-reduction process	6
plasma membrane	6
oxidoreductase activity	5
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	2


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>