The protein sequences of a number of Azospirillaceae strains were investigated that contain the pf00669 domain and belong to a variety of bacterial flagellum systems with unusually large flagellin sizes. A set of tools for the homologous and template-based modeling of protein structures was used to reveal the probability of alternative folding, i.e., generation of two protein models with significantly different 3D structures and functions (flagellin or S-layer protein) for a single amino acid sequence.