Depending on the type of transmission , there is vacuum supplied to the shift modulator as well , and that may not be a pump your seeing but a vacuum reservoir . Could you post a picture of that too?
EDIT: Unless it's a diesel engine then, it may be a vacuum pump.
99DSDP 3884, Freightliner, XC, CAT 3126B, 300 HP /ALLISON 3060
2000 Caravan toad, Remco & Blue Ox.