can I identify the function of cluster with high identity of one gene?
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3.0 years ago
jth6974 ▴ 10

Let's say there is a secondary metabolites biosynthesis cluster in fungi A. and I just found out a homologous gene B(identitiy>=50% with nrps gene located in the cluster) from fungi B using blastp and also found that gene B is located in some gene cluster in fungi B genome using antiSMASH. My question is, with these two proofs can I say the gene cluster including gene B is doing same function with a secondary metabolites biosynthesis cluster in fungi A? (Sorry for bad explanation)

gene antismash cluster genecluster Tutorial • 604 views
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3.0 years ago
Joe 19k

In short: I don’t think so, no.

I would say that’s not enough evidence to say that they are doing the same thing. You haven’t said how much higher than 50% the identity is but I’ll hazard a guess and say that its not much higher, which doesn’t make for a very similar sequence IMO. On this note, it would be better to compare the protein sequence identity rather than the gene identity if you want to argue that they are doing a similar role. If you can find orthologies between other genes in the Gene A cluster and genes in the Gene B cluster, that would provide some more compelling evidence. Additionally, if you know the active site of Gene A in the cluster, and you can find an equivalent site in the protein sequence of Gene B, then thats a much more compelling argument too.

From what little I know about NRPSs, modules can look very similar, but carry out subtly different modifications (as a contrived example: the switch from a kinase to a phosphatase may not require much of a change to the structure since they would both interact with phosphate groups). This could entirely change the products that are made, and is therefore a significant difference.

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Really thanks for your kind advice.

I will try to find orthologies between other genes in the Gene A cluster and genes in the Gene B cluster first. If there is some problem can I ask your advice next time?

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Feel free to post more questions sure. I wouldn’t say that I’m particularly an expert in this specific area, but happy to help if I can. Just make sure any questions you ask are well defined and answerable in a specific manner ideally.

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