This pipeline from the Sanger is a great start

https://sanger-pathogens.github.io/Roary/

I would also like to do a comparative genome analysis, please recommend me some tools to do so, with a focus on enzyme-coding genes

Thanks

You can also try to use progressiveMauve (http://darlinglab.org/mauve/user-guide/progressivemauve.html). As an input you'll need the *gbk files, and after perform the genomic alignment it's possible export positional orthologous genes (*ort file) from collinear blocks. The complementary list (the genes not included in ort files) will correspond with the accesory genome, and the sum of both lists will be the pangenome.