Table 1. Workflow summarizing the steps followed in the identification of HGT genes in mycobacteria.

1.	The proteomes of 15 Mycobacterium spp., D. discoideum and 34 amoeba-resistant bacteria (Table S1) were downloaded from the National Center for Biotechnology Information (NCBI).
2.	Search for homologous genes of mycobacterial open reading frames (ORFs) in the genomes of D. discoideum and 34 amoeba-resistant bacteria using the BLASTp program from NCBI (E-value<1.10–4, similarity >30% and coverage >80%).
3.	Search for the homologous sequences of the mycobacterial ORFs found in step 2 in the NR database using BLASTp (E-value<1.10–4, similarity >30% and coverage >80%).
4.	Selection of ORFs from mycobacteria found in step 3 presenting significant homology with D. discoideum and 34 amoeba-resistant bacteria in the first 100 hits.
5.	Infer phylogenetic relationships between the protein sequences found in steps 4 using MUSCLE for alignment and two construction methods (Maximum Likelihood within the PHYML program and M. Bayes).
6.	Analysis of the trees generated in step 5, looking for possible HGT between Mycobacterium spp. and amoebae and/or amoeba-resistant bacteria.

More details can be found in the materials and methods.