Some apparently functional Rpn4p-binding sites are not conserved. (a) The MONKEY p-values (points) of all putatively functional Rpn4p-binding sites at varying evolutionary distances, along with the expected values under the HB and HKY models (solid traces). The majority of sites behave as expected for conserved binding sites (lower trace). Several, however, behave as expected for unconstrained sites (upper trace). (b) The predicted binding site (indicated by a box) in REH1, which encodes a protein of unknown function in S. cerevisiae, is not conserved, whereas a binding site with a lower score is conserved (indicated by a black bar). (c) A very poorly conserved match upstream of PTC3; in this case no other sites can be found in the region.