They started the project by selecting a microbe, Mycoplasma genitalium, that has only has 482 genes. They then introduced crippling mutations into each gene to figure out which ones are dispensable and which can't be done without. In January last year they reported that 382 were essential. In the patent, the number drops to 381. As the application explains, it would be theoretically possible to synthesize a 381-gene genome and plug it into a genome-free cell, and--voila--boot up a new organism. This artificial genome could be engineered so that it can easily accept other genes to carry out new functions--such as producing cheap hydrogen fuel.
There's no evidence in the patent that Venter has actually booted up a synthetic organism, but it's worth bearing in mind that the patent was filed in October and is only now coming available. So at this point, Venter is claiming a patent for something he has yet to build.