Here we report a primary structure conserved between Helicobacter pylori (H. pylori)-tumor necrosis factor-α inducing protein (Tipα) and bacterial penicillin-binding proteins. H. pylori is a Gram-negative bacterium which plays a key part in carcinogenesis in the human stomach. We previously reported that Tipα has a carcinogenic potential as tumor promoter, and that it has no obvious homologue in other species. To investigate the structure–function relationship of Tipα and to predict its ancestral protein, we searched among proteins which have weak homology to Tipα in their primary structures, using Psi-Blast, and we identified numerous Gram-positive bacterial penicillin-binding proteins as weakly homologous to Tipα. Among these, several unique amino acids are conserved and form a motif-like structure. Phylogenic tree analysis indicated that Tipα is closer to the penicillin-binding proteins of Gram-positive bacteria, based on their primary structures, than to H. pylori. This finding suggests that Tipα and penicillin-binding proteins are derived from a common ancestral protein, and that Tipα gene may be transferred horizontally from Gram-positive bacteria to H. pylori.