There is an active effort within the SEED Project to make available public metabolic models for many (eventually, thousands) of organisms. Currently, we have a large and growing collection that have already been constructed. You can explore these models and run flux-balance analysis, using a variety of media conditions in the public model-viewer.
You can also build an initial model for any genome that you submit to RAST. Soon, we will support the abilities described in the diagram below, which depicts our suggested steps for using our tools on your newly-sequenced genome.