Chemotactic bacteria couple their motility to environmental signals using a dedicated protein infrastructure that couples sensory behavior of chemoreceptor arrays to the motility supplied by the flagellar motor through a two-component signaling system comprised of a dedicated histidine kinase CheA and a response regulator CheY that affects flagellar rotation. Binding of attractant and repellant molecules to sensory chemoreceptors leads to modulation of CheA autophosphorylation activity. Binding events trigger conformational changes that travel along the length of the receptor through its kinase control domain to the point of contact with CheA. This mechanism is responsible for correlation of swimming behavior to chemoreceptor binding events.Energy taxis, intimately related to chemotaxis, relies on special chemoreceptors that monitor changes in respiration internal to the cell. In E. coli, the primary energy sensor for motility is Aer, the aerotaxis receptor, which binds a redox-sensitive flavin adenine dinucleotide (FAD) cofactor. Aer monitors the redox activity of respiratory complexes and detects changes to the flux of reducing equivalents travelling through the respiratory chain. The work presented here sheds light on three key areas of signal transduction in bacterial chemotaxis and energy taxis. First, the domain orientating role of interdomain linkers flanking the CheA kinase domain is explored. Secondly, Aer's sensitivity to respiration is explored and the reduction potential of Aer-bound FAD is reported, shedding light on Aer's mechanism of energy sensing. Finally, the conformational transitions in the Aer kinase control domain upon switching signaling states are investigated.