Difference between revisions of "CD task2 protocol"

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(BlastP)
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<b>GO Term Enrichment (hit more than once)</b>
 
<b>GO Term Enrichment (hit more than once)</b>
   
  +
#hits GO term
GO ID GO name # hits
 
  +
185 metabolic process
GO16788 hydrolase activity, acting on ester bonds 94
 
  +
184 hydrolase activity, acting on ester bonds
GO8152 metabolic process 94
 
GO16811 hydrolase activity... 88
+
133 hydrolase activity
  +
125 metal ion binding
GO16787 hydrolase activity 66
 
  +
88 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
GO46872 metal ion binding 62
 
GO19807 aspartoacylase activity 58
+
60 aspartoacylase activity
GO8270 zinc ion binding 19
+
44 zinc ion binding
  +
24 arginine metabolic process
GO5737 cytoplasm 8
 
  +
24 arginine catabolic process to glutamate
GO16324 apical plasma membrane 4
 
  +
23 succinylglutamate desuccinylase activity
GO4046 aminoacylase activity 4
 
  +
8 cytoplasm
GO5886 plasma membrane 3
 
  +
5 arginine catabolic process to succinate
GO42802 identical protein binding 3
 
  +
4 apical plasma membrane
GO16020 membrane 3
 
  +
4 aminoacylase activity
GO5634 nucleus 2
 
  +
4 membrane
  +
3 plasma membrane
  +
3 identical protein binding
  +
2 nucleus
  +
2 intracellular
  +
2 exonuclease activity
  +
2 nucleotide binding
  +
2 nucleic acid binding
  +
2 oxidoreductase activity
  +
2 oxidation-reduction process
   
 
==PsiBlast==
 
==PsiBlast==

Revision as of 14:27, 29 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>

GO Term Enrichment (hit more than once)

#hits    GO term
185	 metabolic process
184	 hydrolase activity, acting on ester bonds
133	 hydrolase activity
125	 metal ion binding
88	 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides
60	 aspartoacylase activity
44	 zinc ion binding
24	 arginine metabolic process
24	 arginine catabolic process to glutamate
23	 succinylglutamate desuccinylase activity
8	 cytoplasm
5	 arginine catabolic process to succinate
4	 apical plasma membrane
4	 aminoacylase activity
4	 membrane
3	 plasma membrane
3	 identical protein binding
2	 nucleus
2	 intracellular
2	 exonuclease activity
2	 nucleotide binding
2	 nucleic acid binding
2	 oxidoreductase activity
2	 oxidation-reduction process

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>