Capital gains...

I recently liquidated my negative cash flowing money pit investment property and am now experiencing added heartburn as a result of the outrageous tax bill that will be levied by the IRS. Now I'm no expert when it comes to financial matters, but I was under the impression that I would be taxed on the gains from the sale of an investment property, instead of the total sales amount. While I depreciated many of the improvements over the years (roof, appliances, flooring, etc.), I never depreciated the property. My accountant seems to be unable to explain why I'm being taxed so heavily, so I thought I would throw it out there to the financial experts in the BP community to help me understand how it's possible. 

Here are some of the specifics:

Purchase date: 9/2004

Purchase price: $375,900

Expenses to date: approx. $55,000

Sale date: 10/2015

Sale price: $410,000

Proceeds (after expenses): approx. $134,000