The GTP and GTX transceivers have a large number of supplies which need to be provided specific voltages as outlined in the Virtex-5 Data sheet. This answer record discusses the order in which these supplies need to be powered up.
Xilinx does not have an official sequencing recommendation for supplying power to the transceivers on the Virtex 5 devices. The only requirement is that prior to configuration, each supply meet the voltage requirements outlined in DS202, the Virtex-5 Data Sheet. These supplies include MGTAVTTTX, MGTAVTTRX, MGTAVTTRXC, MGTAVCCPLL, MGTAVCC and the reference resistor pin MGTRREF.
The Virtex-5 Data Sheet can be found here: