Plasmid Annotation

New plasmid sequences need to be annotated well before submission to one of the databases.  Plasmid gene naming based on the top hit in a BLAST search can be misleading.  For example, the Type IV secretion system genes of many plasmid conjugation systems show high similarity to the vir genes of Agrobacterium. Naming these genes vir could be misinterpreted by suggesting a role in true virulence. ISPB recommends that plasmid gene names reflect their function either by using standard names such as tra, trb, mob,rlx, par, rep, inc, or unique names such as prg (E. faecalis) or trw (IncW plasmids). For advice on annotation we suggest you look at::

Christopher M.Thomas, Nicholas R.Thomson, Anna M. Cerdeño-Tárraga, Celeste J. Brown, Eva M Top and Laura S. Frost (2017) Annotation of plasmid genes. Plasmid 91, 61-67.