PATRIC: Pathosystems Research Integration Center. Good source for microbial genomes, as well as metadata (microbial habitat, optimal growth temperature, how the genome was sequenced, etc)

EcoCyc: Comprehensive encyclopedia of E. coli genes, gene regulation, proteins and enzymes, and metabolism.

NCBI: National Center for Biotechnology Information

BRENDA: comprehensive enzyme database. You can search enzymes by pathway, organisms, or E.C. number, and get information on Km, Kcat, of your favorites.

Microbes Online: A browser for microbial genome content.