Germination protease (GPR) plays an important role in the germination of spores of Bacillus and Clostridium species. A few very similar GPRs form a singleton group without significant sequence similarities to any other proteins. Their active site locations and catalytic mechanisms are unclear, despite the recent 3-D structure determination of Bacillus megaterium GPR. Using structural comparison and sequence analysis, we show that GPR is homologous to bacterial hydrogenase maturation protease (HybD). HybD's activity relies on the recognition and binding of metal ions in Ni-Fe hydrogenase, its substrate. Two highly conserved motifs are shared among GPRs, hydrogenase maturation proteases, and another group of hypothetical proteins. Conservation of two acidic residues in all these homologs indicates that metal binding is important for their function. Our analysis helps localize the active site of GPRs and provides insight into the catalytic mechanisms of a superfamily of putative metal-regulated proteases.