Our current knowledge of solute carrier (SLC) transporter proteins comes from decades of detailed functional studies and more recent structural analyses. However, it remains problematic to accurately predict function of uncharacterised SLC proteins from across all kingdoms of life. Many animals have nutritional symbiotic partnerships with microbes which are intrinsically dependent on directional transport of nutrients between species. Such microbial symbionts can aid food digestion or synthesise nutrients missing from the host animal’s diet. For example, sap feeding insects such as aphids, and blood feeding insects such as lice, have intracellular symbionts who provide their host insect with essential amino acids and vitamins. For these relationships to be maintained, specific transporters must function at multiple membranes in both species, yet little is known as to the identity and function of the proteins involved. We have used knowledge of bacterial and mammalian SLC transporters to accurately predict the function of aphid transporters involved in facilitating nutritional symbiosis. By doing so we are not only advancing knowledge of the molecular mechanisms central to a fundamental aspect of invertebrate pest biology but also of how an archetypal transporter binding pocket has evolved to produce a multitude of protein functions.