Place masking tape over the drain to prevent errant sealant from clogging it.
Insert the tip of your putty knife in the sealant at the bottom of the shower door, where it attaches to the shower pan.
Work your way around the base of the shower door, removing the caulking sealant as you go. Discard the old caulking sealant.
Apply a line of silicone caulk at the base of the shower door, using the caulking gun to cover the length of the bottom of the door.
Wait overnight for the caulk to dry.