Using InterPro to search for protein motifs

In this exercise we will analyse some example protein sequences for motifs as an exercise in getting the hang of using InterPro.

Step 1: Click here to bring up a window containing some protein sequences. The sequences are mystery sequences – see if you can assign a putative function to them based on the motifs that you find.

The example presented here uses the first of these sequences. If you aren’t sure what your doing then its probably better to use the first sequence. However, if you are feeling adventurous then pick any of them.

Copy the protein sequence to the clipboard.

Step 2: Click here to bring up the InterPro web interface page. Paste your sequence in to the text box labelled ‘Enter or cut and paste protein sequence here’.

Scrolling down the page you will a number of different sections.

Enter your email address into section 3.

In section 4, make sure ‘Include Smith & Waterman?’ is left unchecked. (This performs a similarity search of the sequence databases using you sequence – it will slow you down)

Click on the grey submit button to start the job (show me)

The process may take some time so please be patient.

Step 3:  You will now be presented with a screen that summarises the results of searching InterPro with the sequence you sent, in a tabular format.

 Since InterPro is an amalgamation of different databases you can see the results of searching these individual databases as well.

How do I interpret the output?