The bacterial flagellum is a self-assembling nanomachine that allows bacteria to swim and cause infections. It is assembled through the Type III Secretion System (T3SS), which has been the subject of extensive investigation. The flagellum structure is commonly divided into three parts: the basal body, a membrane-embedded protein that spans from the cytoplasm to the outer membrane; a ~55 nm flexible hook that protrudes from the outer membrane which attaches to the hook filament junction; and the filament, which extends off the hook, propelling the Salmonella enterica cell. A noteworthy characteristic of T3S is its ability to change its secretion-substrate specificity from early-class substrates to late-class substrates. Once the hook reaches the expected length of ~55 nm, the substrate-specificity of the secretion apparatus instigates late substrate configuration. Before HBB completion FlgM binds tightly to Ïƒ28 (FliA). Once HBB is completed, the specificity switch turns on LATE mode, FlgM is secreted freeing Ïƒ 28 to turn on class III promoter genes (Figure 1). Class III promoter gene products are required to complete the construction of the flagellar system. While the composition and function of the flagellum are well understood, how substrates are recognized and targeted for export in an orderly manner is still poorly understood. It is known that T3S substrates require an N-terminally encoded secretion signal and that a secretion specificity switch is required to maintain the proper secretion of substrates required early and late in the assembly process. The work presented in this study aims to gain insight into the secretion of one early substrate protein; FlgJ; which is the cap of the proximal rod.