Clustering enzymes into functional categories

Question

[dharitrisaikia162]

Hello,

I have a huge list of enzymes for predicted metagenome.

Is there any way to cluster those enzymes into different functional categories?

Thanks in advance.

Answer 1

[Mensur Dlakic]

Your table already has functional categories in the first column. Those are EC numbers corresponding to major chemical reactions performed by enzymes. It is all explained at BRENDA database:

https://www.brenda-enzymes.org/

Briefly, if two enzymes have the first 3 numbers identical (say, EC 6.1.1), they in most cases perform the same reaction but on a different substrate. If they are the same only on the first two numbers, they probably perform the same reaction and on the same type of bond, but likely on a different set of compounds. Below is a link to ligases where you can see the hierarchy:

https://www.brenda-enzymes.org/enzyme.php?ecno=6.1.1.1

Anyway, sorting your table by the first column will give you a good clustering by function.

Answer 2

[dharitrisaikia162]

Thank you so much for explaining this so nicely @mensur. Have a nice day.