There are many tools out there for annotating bacterial/archaeal genomes.
My suggestion is to try multiple tools and do a comparison, especially if your analysis is hypothesis-driven.
For quick annotation (in the matter of minutes) - my suggestion would be prokka https://github.com/tseemann/prokka
For fairly quick and ease in visualization in terms of metabolic pathways (in the matter of hours) - I feel like blastkoala http://www.kegg.jp/blastkoala/ is pretty good.
For detailed annotation but may not be as rigorous - RAST is quite neat. http://rast.nmpdr.org/
For rigorous and publication quality - IMG/ER would be my recommendation but the caveat is the time. IMG/ER only does one annotation a month and if you missed the queue, you may have to wait up to a month. https://img.jgi.doe.gov/cgi-bin/mer/main.cgi