Data source.

Complete genomes of Y. pestis (Supplemental Table 3) and the NR database were downloaded from the NCBI. Strain 91001, which is avirulent to humans,⁴ was isolated from a Brandt's vole (Microtus brandti) in Inner Mongolia, China. MS data from this strain were acquired by the TMT method³⁰ in 2015. The 91001 sample was labeled by stable isotope labeling by amino acids in cell culture (SILAC) method.³¹ Heavy isotope labeled amino acids were Lys (CNLM-291-H-0.25) and Arg (CNLM-539-H-0.25). The expression profile data were obtained from microarray hybridization experiments,³² and the sRNA data were obtained from RNA-seq results.¹⁸ In addition, data from related literatures, including MS data from the KIM, CO92, and PestoidesF strains, and sRNA data from the 91001 and KIM strains,^33,34 were collected manually.