Anubis's Mothership is more powerful then your ordinary Mothership, it has advanced shields and weaponry constructed from the knowledge of the Ancients that Anubis got from ascending.
It is capable of obliterating entire land masses from orbit. It is made even more powerful with the help of 6 "eyes" that each make the ship powerful, and when joined turn the ship into a huge super-weapon. The weapon requires cooling, and to do this a ventilation shaft is located on the ship. If the ventilation shaft is destroyed the weapon would also be destroyed.
The ship however has a another flaw, when in atmospheric flight the ship can only have a maximum of 40 percent shields making it a target for the enemy, however even at that it may take a huge fleet to defeat.