The final mix of reforms could very well benefit companies that are currently paying more than 15 or 20 percent, while driving up taxes for companies that already have low rates thanks to loopholes. Trump's strategy for keeping the tax cuts revenue-neutral depends in part on eliminating some "special interest loopholes."

"You can make the basic observation that companies like Exxon Mobil that are routinely able to reduce their tax bill will likely benefit much less than companies in the retail sector, which traditionally pay a lot closer to 35 percent," said Matthew Gardner, senior fellow at CTJ. "Congress has enacted special tax breaks for a number of different industries, but retailers are generally unaffected and there aren't a lot of breaks designed for them."

Take a company like Amazon, which has paid 11 percent in taxes on its domestic income over the last eight years. According to the company's annual report, that rate was reached using a number of special deductions, including stock-based compensation deductions, accelerated depreciation deductions, research and development credits, and the domestic production activities deduction. Companies like Boeing (-1 percent from 2008 to 2012) and Honeywell (8 percent) use similar deductions and credits.

"The companies that tend to do the best tend to be companies that make a lot of capital investments, like utilities or manufacturers because the accelerated depreciation rules have been so generous over the last couple of decades," said Gardner. "They give big rewards to anyone investing in factories or machinery."

Generally, the biggest deductions are more useful for companies in utilities, telecommunications, oil and gas, manufacturing and some pharmaceutical companies, while retailers, financial services, food companies and health-care companies tend to pay closer to the statutory rate. Take a look at all the profitable Fortune 500 companies below: