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Hi and welcome to Just Answer! According to the IRS publication 544 - http://www.irs.gov/pub/irs-pdf/p544.pdf
Generally, if you sell or exchange property you used partly for business or rental purposes and partly for personal purposes, you must figure the gain or loss on the sale or exchange as though you had sold two separate pieces of property.
So - your first step is to determine the business and personal use percentage. To do so - you should keep track of miles used for personal and business every year - and prorate sale price and basis accordingly.
Assuming you determine that the car was used 60% for business and 30% for personal purposes - thus you will report the sale of car (business portion): -- sale price $1000 * 60% = $600 -- basis $5000 * 60% = $3000 -- when the basis is adjusted by depreciation - it may not be less than zero - so in this example the depreciation adjustment is limited by $3000.
If your basis is reduced to zero (but not below zero) through the use of the standard mileage rate, and you continue to use your car for business, no adjustment (reduction) to the standard mileage rate is needed.
You will report the disposition of the car (business portion only!) on form 4797 - assuming the asset was held more than a year - Part III. Sale price $600, adjusted basis - $3000, depreciation recapture $3000, ordinary income - $600.