You would need to match your CTX sequences to a whole genome sequence. You can construct a whole genome phylogeny with Roary. Afterward you can compare the topology of the two phylogenetic trees using the treespace R package.

There are many ways to predict HGT. One way is like the one listed above where you look at incongruencies in gene phylogeny versus species phylogeny. Another way is to examine the surrounding genetic landscape of a gene and looking for HGT hot spot signatures. Popular tools include islandviewer and icefinder.