While it might be a naive question, but I really need your help if possible. I want to predict whether some type strains (like Methanofollis liminatans GKZPZ) has a certain type of enzyme (anaerobic carbon-monoxide dehydrogenase)
There are several aspects I considered:
Blast the certain sequence in another type strain from a different but more studied genus. Maybe that's more determined.
Take all the sequences in the NCBI gene/protein subdatabase encoding this enzyme I can find and do redundancy by CD-HIT, just like to create a local customized database. Then, blast them with my strain genome.
Are these two methods feasible, which one is better? Or another common method?
Another question: Is there any way to predict if there is a certain enzyme in the type strain that has the same function as the enzyme I want?
I would really appreciate it if you could give me some advice. Thanks so much.