This dataset repository contains the following items: Source data file (zip file) containing spreadsheets with the data used to make all the plots in the paper (organized by main figures and extended data figures). The file also contains the statistics results of all comparisons made in the paper. Metabolic modeling information (zip file) containing the codes used during the analysis. Tn-seq files (zip file) containing all the wig files used in the analysis with TRANSIT (raw and aBGC-normalized) and the annotation table. Imaging data (zip file) containing the tiff files for all the images and movies displayed in the manuscript.