Patenting an invention in the U.S. that may be patented elsewhere

Not usually. There may be some differences between your invention and what has already been patented, but if they are substantially the same, you cannot normally get a patent here in the US - there are some exceptions, dates come into play, inventors come into play, but normally if A has a patent in Japan, and B wants to patent the same invention here in the US, and A's patent is already more than one year old, you cannot obtain your patent here in the US.