The plasmids found in Acinetobacter species are unique and are not found in other bacterial species. The predominant type encode a Rep_3 family initiation protein and many of these carry their accessory genes in dif modules. Analysis of 78 Rep_3 plasmid types (repA DNA identity <95%) revealed that carriage of dif modules was strongly associated with the presence of a specific open reading frame encoding a protein of unknown function, named orfX, located downstream of repA (n=35). The OrfX proteins in different types are related but diverse with pairwise identities ranging from 21.85%-100% aa identity but plasmid types that encode closely related RepA proteins did not necessarily have a closely related OrfX and vice versa. The predicted structure of OrfX proteins includes a helix-turn-helix motif and a long alpha helix but also includes a large disordered region. The backbone of plasmids carrying an orfX is bounded by inversely oriented pdif sites with the XerC binding sites internal, making it a C type dif module. Therefore, at least one module with internal XerD binding sites must be present i.e. it is not possible to generate a plasmid lacking dif modules. The backbone content upstream of the iterons varies between different plasmids types but often includes mobilisation genes.

How dif modules relocate is not understood although OrfX may be involved.However, recombination can occur between pdif sites with identical bases between the XerCand XerD binding sites. One way that exchange of a single dif module or multiple modules could occur is via cointegration of two different plasmids by recombination at similar pdifsites followed by resolution at a different pair of matched pdif sites. At least 33 cointegrate plasmids where both repA genes were associated with orfX were identified supporting this option for dif module relocation.