Thursday, September 10, 2015

Linking proteins via pathways

Proteins in UniProt are now linked and connected by pathways! When looking at your protein of interest, you will now be able to see if it is involved in any known pathway and then be able to follow links to other proteins involved at different stages of the pathway hierarchy. This allows you to traverse the world of proteins through the pathways that connect them!

Let's follow the example of protein 3-hydroxyanthranilate 3,4-dioxygenase in Baker's yeast. This protein catalyses the oxidative ring opening of 3-hydroxyanthranilate. When looking at the protein in UniProt, I see the 'Pathway' comment in the 'Function' section. Let's look at this comment more closely.

I can see the main pathway title that my protein is involved in, in this case NAD(+) biosynthesis. I see exactly which step of which subpathway my protein is involved in. I then see all steps of the subpathway listed out. My protein is involved in Step 3 but I can also see links to the proteins that are involved in the first two steps.

The subpathway, its parent pathway and superpathway are all linked to UniPathway for more information. The final line in the 'Pathway' comment provides links to all proteins involved in the same subpathway (from the same organism) as my protein, its parent pathway and even the superpathway another level up from the parent pathway. In this example, if I follow the link to Cofactor biosynthesis, I see all 63 proteins involved in this pathway listed out.

Try this out and let us know what you think! Your feedback and suggestions are always welcome. 

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