The Amtrak California network map has a gap. The system is made up of three state-supported rail lines, some long-distance rail lines, and a network of buses to connect cities that do not get rail (thruway buses). Many years ago (at least a decade) you could take an Amtrak bus from the Central Valley to San Jose, via Los Banos and Gilroy. Once that bus line was cancelled, Amtrak riders had to take the train all the way up and around the Bay Area.
Greyhound used to provide buses across to San Jose, but they have continued to cut their routes and no longer do so. BoltBus never provided a route like that, but instead of expanding, they cancelled their entire California network. Flixbus only connects Fresno to LA, and Megabus doesn’t serve the Central Valley at all.