proMGE allows the exploration of 2.4 million MGEs that are found across 76k genomes (from species with at least 2 genomes in the proGenomes2 database). At the species level, it is possible to explore different MGE categories, their genomic positions, antibiotic resistance carrying potential and the extent of their horizontal transfer across higher taxonomic levels: family and above (for each species HGT visualisation is provided by iTOL: interactive Tree Of Life). Additionally for Integrons, IS elements and transposons it is possible to explore if they’re nested within other MGE categories (under the 'Nested recombinase' tab in the species search results).

Note: Consider the following points while analysing and interpreting MGE predictions from this resource (i) MGE boundaries represent upper limits of genomic regions that harbour one or more MGEs of same or different types; (ii) all proteins within the MGE boundaries might not be sufficiently annotated, so that some of our gene context-based approaches for MGE category assignment might overlook them; (iii) beyond the recombinase marker gene, phage structural genes for phages and conjugation machinery genes for conjugative elements other gene features may not be annotated and or well-defined for all the predicted MGEs.

proMGE can annotate MGEs in user submitted protein sequences through the Annotate page. Sequences are annotated using a collection of 68 recombinase subfamily specific profile Hidden Markov Models (HMM) (Letunic et al., 2020). The association of these HMMs to specific MGE types as shown in the table below allows inference of 6 different MGE categories as per rules described in the figure.