We investigate the mobility of polyampholytes consisting of both negatively and positively charged sections. The simulations are carried out using molecular dynamics simulations with electrohydrodynamical effects taken into account via a simple coupling scheme to a lattice-Boltzmann fluid. Our results show a previously predicted mobility reversal of the polyampholytes as the applied electric field is increased due to stretching of the polyampholytes. Further, we show that a similar mobility reversal can be induced due to confinement between parallel plates. At high electric field strengths, the polyampholytes' electrophoretic mobility is a non-monotonic function of the distance between the plates. These results help to clarify the role of deformation and confinement on the electrophoretic mobility of polyampholytes.