https://www.genome.jp/dbget-bin/www_bget?K00004
I'm looking into Enzyme Commission (EC) numbers and I've noticed many annotations have the following scenarios:
- Multiple ECs
- An EC without only 3 levels
According to Expasy (https://enzyme.expasy.org/EC/1.1.1.-):
1.-.-.-: Oxidoreductases
1.1.-.-: Acting on the CH-OH group of donors
1.1.1.-: With NAD(+) or NADP(+) as acceptor
I have the following questions:
- Does this mean K00004 can function as both 1.1.1.4 and 1.1.1.303?
- Does this mean K00004 can function as all the enzymes within 1.1.1 level?
- If there is a pathway that requires 1.1.1.2 would a protein annotated as 1.1.1.- be sufficient?
Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using a hypergeometric test. In some pathways, there is a level 3 enzyme like 1.1.1.- and I’m wondering if I can use, for example, a 1.1.1.3 enzyme to fulfill that in my set enrichment? Also vice versa, If there was a 1.1.1.3 in the pathway and the protein was annotate as a 1.1.1.- enzyme. If the answer to either of those is true, then could I just remove the last level on all enzymes when I’m doing pathway enrichment?
Enzymes under the umbrella of
1.1.1.-
workwith NAD(+) or NADP(+) as acceptor
. That only tells you about their cofactors, but not about their substrates.Again, you'll do better by figuring this out on your own. Click randomly on a dozen or so
1.1.1.-
enzymes and see if their functions (meaning substrates) are equivalent. If they are, then you can ignore the fourth number.