, !These!elements!may!lack!a!few!components!of!an!active! conjugation!system,!but!still!be!regarded!as!valid!systems!by!CONJscan!because!they!fit!the! minimal!conditions!of!the!model.!Degenerate!elements!may!also!complicate!the! identification!of!the!ICEs!because!the!gene!families!of!the!element!are!present!at!different! 420! frequencies!in!the!pan:genome.!It!is!difficult!to!distinguish!mildly!degenerate!elements!from! atypical!functional!ones!, Mobile!genetic!elements!may!endure!inactivating!mutations!:!including!large!deletions:!that! result!in!degenerate!elements
, Intermingled!components!of!conjugative!elements!can!occur!in!a!number!of!cases
, !leading!to!a!series!of! 425! components!from!different!MPFs!and!thus!to!an!apparent!intermingled!set!of!conjugative! elements.!Some!cases!of!true!intermingled!elements!occur!when!an!element!integrates! inside!another!element.!These!cases!may!be!hard!to!disentangle!without!experimental! evidence, MPF!types!are!close!and!their!protein!profiles!cross:match
, !If!the!MGE!of!interest! has!many!such!elements!after!annotation!with!standard!tools!(generic!tools!like!Prokka)! then!specific!curation!may!be!necessary,!e.g.,!by!using!broader!databases!of!protein!profiles! like!EggNOG!or!using!iterative!searches!with!PSI:BLAST!or!jackhmmer!(Table!2).!It!is!not! unusual!that!several!genes!remain!of!unknown!function!after!all!these!analyses, Many!genes!in!mobile!genetic!elements!have!their!function!unknown
, This!work!was!supported!by!the!ANR!MAGISBAC!project,!the!CNRS!and!the!Institut!Pasteur
, We!thank!the!collaborators!who!have!worked!with!us!on!this!topic!in!the!last!decade
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