jeanrjc
commented
2 years ago Hello,
Inverted integron-integrases have already been described before IntegronFinder came out (https://www.sciencedirect.com/science/article/abs/pii/S0966842X07001023). In the original paper for IF, we describe that we found some of them across the integrase tree :
a group of integrons displaying an integron-integrase in the same orientation as the attC sites (inverted integron-integrase group) was previously described as a monophyletic group (7), but in our analysis it was clearly paraphyletic (Supplementary Figure S2, column F). Notably, in addition to the previously identified inverted integron-integrase group of certain Treponema spp., a class 1 integron present in the genome of Acinetobacter baumannii 1656-2 had an inverted integron-integrase.
They are true integron in the sense that they have an integrases and attC sites. They might or might not be as effective as other integrons, or maybe they don't even recombine at all, I'm not sure if they were experimentally tested. Anyway, you can still filter them out easily if you don't want to include them in your analysis.
jiarong
Hi, I noticed a few cases in IF2 (v2.0.2) results that have IntI and gene cassettes on the same strand. All examples I seen in literature has integrase on the opposite strand of gene cassettes. Should these cases with IntI and gene cassettes on the same strand be kept as true integron? Thanks!