How do scientists determine that a particular gene, such as those found in the mimivirus in this case, came from a bacterium? Do bacterial genes (or at least some of them) have specific signatures that identify them as being of bacterial origin? And the same question applies to "viral genes" and "eukaryotic genes". What are these specific signatures? Any experts here have the answer to this?
They mean that they have sequences (actually I think they mean proteins, presumed to have been coded by genes - I don't believe a gene sequence has been established) that have previously only been found in these groups.