Catalyzes the transfer of a farnesyl or geranyl-geranyl moiety from farnesyl or geranyl-geranyl diphosphate to a cysteine at the fourth position from the C-terminus of several proteins having the C-terminal sequence Cys-aliphatic-aliphatic-X. The alpha subunit is thought to participate in a stable complex with the substrate. The beta subunit binds the peptide substrate (By similarity). (2E,6E)-farnesyl diphosphate + L-cysteinyl-[protein] = diphosphate + S-(2E,6E)-farnesyl-L-cysteinyl-[protein] geranylgeranyl diphosphate + L-cysteinyl-[protein] = diphosphate + S-geranylgeranyl-L-cysteinyl-[protein] Heterodimer of fntA and fntB (farnesyltransferase). Heterodimer of an alpha and a beta subunit (By similarity). Belongs to the protein prenyltransferase subunit alpha family.