A model for Mu genome immunity. The model proposes that segregation of Mu into a separate domain on the E. coli chromosome is aided by the centrally located SGS, which initiates loop formation, and is sealed by either the Mu transpososome assembled on the ends or NAPs. Several NAPs are shown stabilizing this structure, hypothesized to promote formation of MuB filaments, which provide a barrier against self-integration. Fis and H-NS may be expected to reside at the SGS and Mu ends because these proteins prefer A/T rich regions (see Additional file 2). SMCs have been proposed to be involved in the creation of large topological loops by bridging two DNAs at the base of the stem of such loops [29, 39].