Members of the broadly distributed Rid/YER057c/UK114 protein family have imine/enamine deaminase activity, notably on 2-aminoacrylate (2AA). Strains of Salmonella enterica, and other organisms lacking RidA, have diverse growth phenotypes, attributed to the accumulation of 2AA. In S. enterica, 2AA inactivates a number of pyridoxal 5'-phosephate(PLP)-dependent enzymes, some of which have been linked to the growth phenotypes of a ridA mutant. This study used transcriptional differences between S. enterica wild-type and ridA strains to explore the breadth of the cellular consequences that resulted from accumulation of 2AA. Accumulation of endogenously generated 2AA in a ridA mutant resulted in lower expression of genes encoding many flagellar assembly components, which led to a motility defect. qRT-PCR results were consistent with the motility phenotype of a ridA mutant resulting from a defect in FlhD4C2 activity. In total, the results of comparative transcriptomics correctly predicted a 2AA-dependent motility defect and identified additional areas of metabolism impacted by the metabolic stress of 2AA in Salmonella enterica. Further, the data emphasized the value of integrating global approaches with biochemical genetic approaches to understand the complex system of microbial metabolism.