Mediates GPI anchoring in the endoplasmic reticulum, by replacing a protein's C-terminal GPI attachment signal peptide with a pre-assembled GPI. During this transamidation reaction, the GPI transamidase forms a carbonyl intermediate with the substrate protein (By similarity). Glycolipid biosynthesis; glycosylphosphatidylinositol-anchor biosynthesis. Belongs to the peptidase C13 family.