The Lawrence Livermore National Laboratory in the San Francisco Bay area operates a multi-site UHF trunked system with sites all over. The system info was removed from the RadioReference web site at the request of the LLNL.
On a recent trip through San Francisco I found that there appears to be a site on this system located in or near downtown San Francisco. It is a Motorola Type II UHF system that is using P-25 voice. The system ID is 5434 and I found Site 6 to be coming in full strength with no antenna on the radio while I was at AT&T Park. Here is the site info:
406.1500 MHz - Control Channel, System 5434, Site 6
407.8625 MHz - Voice Channel
408.3875 MHz - Voice Channel
416.8625 MHz - Input to 407.8625
417.3875 MHz - Input to 408.3875
UPDATE: I have been informed that Site 6 of this system is in fact located at the Lawrence Berkley Lab, across the bay from San Francisco.