After buying a boat (for the business) for 5K, I want to sell it for 5K, but it depreciated for example by 1K it is worth 4k. Do I pay taxes on the 4K or the 1K?

Your adjusted basis is $4k, which means you have $1k of Section 1245 gain, which is taxed at ordinary income tax rates.

In Turbotax (TT), you enter the sale price of $5K and the cost basis of $5K.  You will then be asked if you claimed (or should have claimed) any depreciation. You enter $1K.  Based on those inputs, TT will enter the numbers, in the proper places, on the forms.

Great, and after selling, what do you do with the 4k that was collected from the selling of the equipment/boat? How is it taxed? I understand now that the 1k from the gain is taxed but the rest becomes what?... 

The $4k is not subject to taxation; it is your adjusted basis in the property (i.e, your adjusted cost).