Yes, you can use the standard mileage rate, because your car allowance is taxed. But, because the standard mileage rate includes allowances for tires and other repairs, you must subtract any non-taxed reimbursements or repairs that are paid for without being added to your taxable wages. (You do not subtract taxable reimbursements.) After entering the mileage, keep going in the interview and you will be asked about non-taxed reimbursements.
Note that the ability to deduct work expenses was eliminated in the tax cut bill starting 1/1/2018. You may want to discuss moving more of your car expenses to non-taxed reimbursements under an accountable expense plan.