Eukaryote-like serine/threonine kinases (STKs) and cognate phosphatases (STPs) comprise an important regulatory system in many bacterial pathogens. The complexity of this regulatory system has not been fully understood due to the presence of multiple STKs/STPs in many bacteria and their multiple substrates involved in many different physiological and pathogenetic processes. are the best materials for the study due to a single copy of the gene encoding STK and its cognate STP. Although several studies have been done to investigate the roles of STK and STP in zoonotic , respectively, few studies were performed on the coordinated regulatory roles of this system. In this study, we carried out a systemic study on STK/STP in by using a comparative phenotypic, proteomic, and phosphoproteomic analysis. Mouse infection assays revealed that STK played a much more important role in pathogenesis than STP. The ∆ and ∆∆ strains, but not ∆, showed severe growth retardation. Moreover, both ∆ and ∆ strains displayed defects in cell division, but they were abnormal in different ways. The comparative proteomics and phosphoproteomics revealed that deletion of or had a significant influence on protein expression. Interestingly, more virulence factors were found to be downregulated in ∆ than ∆. In ∆ strain, a substantial number of the proteins with a reduced phosphorylation level were involved in cell division, energy metabolism, and protein translation. However, only a few proteins showed increased phosphorylation in ∆, which also included some proteins related to cell division. Collectively, our results show that both STP and STK are critical regulatory proteins for and that STK seems to play more important roles in growth, cell division, and pathogenesis.