TABLE 2.
Genes positively associated to cluster B (Benjamini–Hochberg p < 0.05 and OR > 1).
| Putative functions | Gene annotation | Functional annotation | Frequency in cluster B % | Frequency in cluster A/C % |
| Formate detoxification | group_862 group_863 | Putative formate dehydrogenase Putative formate dehydrogenase |
91 22 |
0 0 |
| Formaldehyde assimilation/detoxification | hxlR_1 | HTH-type transcriptional activator HxlR | 22 | 0 |
| Copper resistance | cueR∗ | HTH-type transcriptional regulator | 22 | 0 |
| Oxidative stress response | group_3122 (crtO)∗∗(?) | Glycosyl-4,4′-diaponeurosporenoate acyltransferase | 22 | 0 |
| crtP∗∗ | Diapolycopene oxygenase | 22 | 0 | |
| crtQ∗∗ | 4,4′-diaponeurosporenoate glycosyltransferase | 22 | 0 | |
| crtM∗∗ | Dehydrosqualene synthase | 22 | 0 | |
| crtN∗∗ | Dehydrosqualene desaturase | 22 | 0 | |
| Host-interaction and Virulence | esaA∗ | ESAT-6 secretion accessory factor | 65 | 0 |
| esaB∗ | ESAT-6 secretion accessory factor | 65 | 0 | |
| essC∗∗ | ESAT-6 secretion machinery protein | 65 | 0 | |
| esxA∗ | ESAT-6 secretion system extracellular protein A | 65 | 0 | |
| essB∗∗ group_2414∗∗ | ESAT-6 secretion machinery protein ESAT-6 secretion machinery protein |
39 30 |
0 0 |
|
|
yezG_1 yezG_2 yezG_3 yezG_5 |
Putative antitoxin Putative antitoxin Putative antitoxin Putative antitoxin |
52 48 43 26 |
0 0 0 2 |
|
| Carbohydrate metabolism | treA∗ | Trehalose-6-phosphate hydrolase | 26 | 0 |
| mtlR∗ | Transcriptional regulator MtlR | 22 | 0 | |
| mtlA∗ | PTS system mannitol-specific EIICB component | 22 | 0 | |
| Lipid metabolism | group_3907∗ | NADP-dependent 7-alpha-hydroxysteroid dehydrogenase | 48 | 0 |
| Benzoate degradation | ligI∗ | 2-pyrone-4,6-dicarbaxylate hydrolase | 26 | 0 |
| Transport systems | group_1444 | ABC transporter ATP-binding protein NatA | 43 | 0 |
| Cell wall biosynthesis | dacA | D-alanyl-D-alanine carboxypeptidase DacA | 39 | 2 |
| yodJ∗∗∗ | Putative carboxypeptidase YodJ | 35 | 2 | |
| Transposable elements | bin3_3 | Tn552 DNA-invertase | 43 | 0 |
| int-tn | Tn916 transposase Int-Tn | 87 | 34 |
∗Only one gene/allele for that function and function is exclusive in cluster; ∗∗More than one gene/allele for that function but function is exclusive in cluster; ∗∗∗Only one gene/allele for that function and is enriched in the cluster but the function is not exclusive in cluster.