Because your pup spent virtually all her puppyhood within the confines of the shelter, she is most likely undersocialized. That would explain her overall fear and skittishness. Keep in mind, she's also very new and trying to cope with the drastic change of environment!

A lot of dogs don't know how to cope with their fear, so, if they're cornered, they can turn to aggression. It's that whole "fight or flight" mentality. If your pup normally avoids the cat and seems to act scared in its presence, I wouldn't be surprised if your pup was acting "fear aggressive" towards the cat. The most logical prescription for a fear aggressive dog is to desensitize and countercondition the trigger. For more reading, see Patricia McConnell's The Cautious Canine. In the meantime, I would also monitor the dog and cat at all times to ensure that the cat isn't being too pushy and that the pup has an escape route so that she never feels obligated to attack. Kudos to you for adopting!