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Retrieving Motif Information of a Protein Using Prosite
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Procedure

 

There are many websites which provides access to Prosite.  

Figure 1 shows the home page of EBI (European Bioinformatics Institute) Prosite database. 

For info on accessing the database please go to simulator tab.

 

Figure 1:  Home page of EBI

 

Enter your computationally represented protein sequence in the text box or upload a file which contains a valid protein sequence. It can be in any sequence format. The particular way of recording sequence in a computer is called sequence format.  For different databases the format will be different.  For example FASTA format is a simplest sequence format which starts with a ‘>’ symbol followed by the sequence ID, other comments and computationally represented protein sequence. Here in PPsearch one can use GCG, FASTA, PIR, NBRF, Phylip or Swiss-Port format. 

 

 

 Figure 5: Paste the FASTA sequence of Ck2 protein

 

 Now click on the Run button to see the results for motif search (figure 6).

 

 

Figure 6: Results for motif search

 

The result shows the query has 2 matching patterns named PS00107 and PS00108. Both these patterns are present only once in the sequence. These are patterns for the PROTEIN_KINASE_ATP and PROTEIN_KINASE_ST. Protein kinase is an enzyme which helps in the phosphorylation of other proteins. The process of adding a phosphate (a chemical) group is called phosphorylation. So the result shows that the entered query sequence is a PROTEIN_KINASE family member. In the beginning of each matching patterns, its position also has shown.

 Now click on PS00107 to see the pattern (Figure 7).

 

 

 

Figure 7: Click on PS00107 to see the pattern

 

Figure 8 shows the pattern for PS00107.

 

 

 Figure 8: The pattern for PS00107

 

 

 There are three other parameters which we can change before run the PPsearch. They are:

 

  • Include abundant patterns:  Short patterns found many in the sequence. Abundant patterns are short patterns that are found in large amount that match with amidation, phosphorylation, glycosylation etc. Amide is a compound derived from ammonia. It is through the substitution of an acyl radical for hydrogen or from acid by replacing the hydroxyl group by an amine group. The formation of ammonia is called amidation. The adidition of a phosphate group to an organic molecule is called phosphorylation. The chemical reaction to form a glycoside is called glycosylation. Glycoside is a compound that has a carbohydrate part which is attached to a non-carbohydrate part. Since the abundant patterns are found in a lot of sequence it gives very few information about the entered query. We cannot predict in which family the new sequence belongs to.

 

  •  View results in ASCII graphics: gives a graphical representation of the matches’ positions.

 

  • View results using a java viewer:  The graphical representation of matches can be viewed using java based viewer..

 

Figure 9 shows the three other parameters ( Include abundant patterns,View results in ASCII graphics and View results using a java viewer) that one could change.

 

 

 

 Figure 9: Shows the three parameters; Include abundant patterns,View results in ASCII graphics and View results using a java viewer

 

 The result for ASCII Graphics is shwon in the figure 10.

 

 

 

Figure 10: result for ASCII Graphic

 

The result in Java a Viewer is shown in figure 11.

 

 

Figure 11:  Result in Java a Viewer

 

 The result showing abundant patterns is shwon in figure 12.

 

 

 Figure 12: Result showing abundant patterns

 

 

This experiment uses: NCBI database, on http://www.ncbi.nlm.nih.gov/, PPSearch - Protein motifs Search from EBI(European Bioinformatics Institute),  http://www.ebi.ac.uk/Tools/ppsearch/

  

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