Annotation result with lots of Hypothetical protein

Question

[Leo]

Hi everyone, I have treated a megaplasmid sequence with RAST annoation tools, and the result return with many hypothetical proteins, is that normal? Is it a good or bad thing? 600 genes out of 756 are hypothetical proteins.

Thanks for reply.

[Fabio Marroni]

I suggest you to give a look at this article in wikipedia and references within to get started with the world of "hypotetical proteins"! Good or bad, you ask? It depends. If you characterized a novel "exotic" megaplasmid for which you want to show how many new fucntions it has, it's good. If you are screening a very famous megaplasmid, for which most of the genes are already annotated, it's bad...