Loss of the T3SS PAI occurs by least four distinct routes.
(A) Recombination sites leading to loss of the PAI in CR- colonies showing the sizes of deleted fragments and ISs (hatched boxes). ORFs are shown according to their predicted functions: (in cyan blue) TA systems; (in purple) hypothetical proteins; (in green) virulence-associated proteins; (in grey) homologues of ISs; (in brown) IS components; (in turquoise) homologues of proteins involved in plasmid partitioning; (hatched boxes) ISs involved in the deletion. (B) Alignment of the four PAI deletions with pWR100 (inner black ring). Image created using BRIG v0.95 and BLAST v2.2.29.