Clustering enzymes into functional categories
2
0
Entering edit mode
5 days ago

Hello,

I have a huge list of enzymes for predicted metagenome. Enzyme list

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

Thanks in advance.

metagenomics • 192 views
ADD COMMENT
2
Entering edit mode
5 days ago
Mensur Dlakic ★ 20k

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.

ADD COMMENT
0
Entering edit mode
5 days ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 2271 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6