Annotation result with lots of Hypothetical protein
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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...