The minimum trade profit percentage is the minimal profit percentage for a trade.
If you set it to 1%, then the trade engine will place sell orders such that at at least 1% profit is booked on earlier acquired funds.
This is the net profit after having paid the exchange commissions of both buying and selling the funds.
Note that if you are on the Standard subscription, you pay a GSMG commission from your fuel credits. This is not taken into account when determining the net profit.
Note also that the trade engine regularly places sell orders (much) higher than strictly necessary to obtain the configured minimum trade profit. This has various reasons and is nothing to worry about as you will come to see.