Step 3: Confirming Your Frame! (Part I)
So you’ve picked out a frame. But is it the right frame? There are a couple of web tools to help you validate your choice. One I like is called InterProScan. Proteins are made up of commonly conserved functional parts called “domains” and “motifs”, like assembling Legos. InterProScan takes advantage of that to check your sequence for known functional bits and predict what your proteins might do. If you picked the right frame, InterProScan should return to you a very clear idea of what you should expect your gene’s protein product to be.
- Put your frame into FASTA format.
- Open InterProScan in a new window.
- Paste your FASTA-formatted sequence into the window and submit it.
If you picked the right frame, InterProScan should have returned a screen that looks like this, from which you should be able to conclude you have the alpha subunit of ATP synthase. Clicking on the links next to each identified domain will give you useful information on each to help you understand your protein better.
