The PB1 (Phox and Bem1) domain, comprising about 80 amino acid residues, is conserved among animals, fungi, amoebas, and plants. It functions as a protein binding module through PB1-mediated heterodimerization or homo-oligomerization [1,2,3,4]. The PB1 domain is found in several signaling proteins including:

• Mammalian MEK5, a MAP kinase kinase implicated in epidermal growth factor- induced cell proliferation.
• Mammalian Sequestosome-1 (Sqstm1) or p62/ZIP, a protein linking the zeta isoform of protein kinase C to RIP and/or potassium channels.
• Mammalian neutrophil cytosol factor 4 (NCF-4) or p40(phox), a cytosolic factor of the superoxide-generating NADPH oxidase in phagocytes.
• Mammalian neutrophil cytosol factor 2 (NCF-2) or p67(phox), an oxidase activator.
• Yeast bud emergence protein 1 (Bem1), necessary for cell polarization during vegetative growth.
• Yeast cell division control protein 24 (CDC24), a guanine nucleotide exchange factor (GEF) for the small GTPase CDC42.
• Plant AUXIN RESPONSE FACTOR (ARF) transcription factor family, regulates gene expression in response to auxin.
• Plant AUXIN/INDOLE 3-ACETIC ACID (Aux/IAA) repressor proteins, repress ARF transcription factors via direct interaction under low auxin concentrations.

The PB1 domains adopt an ubiquitin-like β-grasp fold, containing two α helices and a mixed five-stranded β sheet (see <PDB:1WMH>). The β-sheet has a convex surface, and α1 fits into the cavity formed by the sheet. PB1 domains may display an acidic surface (type I), a basic surface (tape II), or both surfaces (type I/II) on opposite faces of the domain structure to allow for front-to-back orientation of multiple PB1 domains [1,2,3,4].

The profile we developed covers the entire PB1 domain.