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. 

Wednesday, September 2, 2015

Have you tried our new Beta UniProtJAPI?

A new Beta version of the UniProtJAPI is now available! It aims to improve several issues encountered by the current version such as frequent library updates, retrieval speeds and server availability. We invite you to try the Beta JAPI and share your feedback via a short survey so we can provide the best service for your needs.

Please try the Beta UniProtJAPI for your tasks at and then fill out this short 5 minute survey:

Here are some examples of tasks you could try on the JAPI (or simply use your own tasks):

  1. Create a UniProt, UniRef and UniParc service, and use each of these to find out the number of entries in the release.
  2. Retrieve entries containing keywords “Kinase” or “Amyloidosis”.
  3. Retrieve entries that have been updated in the last six months, and then filter only those that are reviewed (Swiss-Prot).
  4. Given the PFAM signature “PM00228”, find the associated reviewed (Swiss-Prot) and non-reviewed (TrEMBL) entries.

We hope you will find our new JAPI useful!