Table 1.

List of positively selected amino acids specific to each of the subspecies.

Protein	Position	Original amino acid	Substituted amino acid	BEB probability (%)	Subspecies
Name: 30S ribosomal protein S3 Function: binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Subcellular localization: cytoplasmic	217 220 222 223	S A P A	A E G R	75 96 98 99	M. abscessus M. abscessus M. abscessus M. abscessus
Name: pyridoxine 5-phosphate oxidase Function: catalyzes the oxidation of either pyridoxine 5′-phosphate (PNP) or pyridoxamine 5′-phosphate (PMP) into pyridoxal 5′-phosphate (PLP) Subcellular localization: cytoplasmic	86 142 172 199 200 201 202 203 204	A A E E N L S L P	T G D G P V T A L	82 88 84 85 99 87 88 99 85	M. abscessus M. abscessus M. abscessus M. abscessus M. abscessus M. abscessus M. abscessus M. abscessus M. abscessus
Name: MAB_2825 hypothetical protein Function: uncharacterized Subcellular localization: membrane	60 109 410 412	K I G P	R V K A	70 71 92 72	M. massiliense M. massiliense M. massiliense M. massiliense
Name: 30S ribosomal protein S3 Function: binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. Subcellular localization: cytoplasmic	259 260 261 262 263 265 268 269 270 271	P A S D G S S A E T	G G N T S E A E T S	99 84 100 99 99 100 79 81 99 77	M. massiliense M. massiliense M. massiliense M. massiliense M. massiliense M. massiliense M. massiliense M. massiliense M. massiliense M. massiliense
Name: thymidylate kinase Tmk Function: phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis Subcellular localization: cytoplasmic	20 21 23 24 26 27	E K I A G N	R A T R S I	100 98 74 98 99 63	M. massiliense M. massiliense M. massiliense M. massiliense M. massiliense M. massiliense
Name: isochorismatase hydrolase Function: involved in isochorismatase metabolism Subcellular localization: cytoplasmic	209 211	T A	S E	84 98	M. massiliense M. massiliense
Name: beta-lactamase -like protein Function: unknown. Hypothetically involved in drugs resistant Subcellular localization: cytoplasmic	242 243	N T	S K	52 84	M. massiliense M. massiliense
Name: MAB_1249 hypothetical protein Function: uncharacterized Subcellular localization: cytoplasmic	31 172	G Y	S S	66 64	M. bolletii M. bolletii
Name: cytochrome P450 Function: oxidoreductase activity Subcellular localization: cytoplasmic	56 93 275 351	K M E A	R L A G	57 60 73 67	M. bolletii M. bolletii M. bolletii M. bolletii
Name: MAB_2993C hypothetical protein Function: amino acid transmembrane transporter activity Subcellular localization: membrane	301	R	T	68	M. bolletii
Name: fructose-bisphosphate aldolase Function: glycolytic process Subcellular localization: cytoplasmic	150 154 157 160	A S V K	Q A L H	99 97 56 96	M. bolletii M. bolletii M. bolletii M. bolletii

BEB, Bayes Empirical Bayes.