The new IS1595 family, its relation to IS1 and the frontier between insertion sequences and transposons.

A picture of insertion sequence (IS) diversity is emerging in which previously well-defined groups or families, while remaining tightly clustered, no longer have defined borders but tend to be joined by ISs with partially shared characteristics. This is to some extent due to the presence or absence of different structurally defined transposase domains (and their spacing) and sequence similarities between IS ends. A surprising result arising from the detailed analysis of ISs in various bacterial genomes is the presence of close relatives carrying passenger genes (e.g. antibiotic resistances, methyltransferases, or transcriptional regulators as well as unknown functions). This is beginning to obscure the previously defined line between ISs (no additional orfs) and transposons. We include the lowercase prefix "t" to distinguish them from classical ISs. This is illustrated here by the IS1595 family, distantly related to IS1, which can be subdivided into several groups based on BLAST analysis of transposases, the genetic organization (number and position of the orfs) and the inverted repeats at their ends. The classification was subsequently confirmed using MCL (Markov cluster algorithm) software with parameters derived from the well-defined IS3 family. Many new ISs were identified from the public databases using a reiterative BLAST approach.