Just discovered this paper: MBGD update 2013: the microbial genome database for exploring the diversity of microbial world. Seems to be a useful microbial genomes database with some nice associated tools. Among the potentially useful features:
General Ortholog Table
Select your own organisms for a Custom Ortholog Table
Add your own genome in My MBGD Mode
And more. Anyway - worth checking out.
I note - I found out about this via Google Scholar Updates:
For more on Scholar Updates see here.