Table 1. List of the aerobic traits considered for the analysis in Fig. 2.
AOX, alternative oxidase.
| Protein and defining trait | Premium for synteny* | Penalty for absence | Considered earlier |
|---|---|---|---|
| Cyt C cytochrome c | No, this work | ||
| COX1 COX – complex IV | +2 with COX2 | −1 | Yes |
| COX2 COX – complex IV | −1 | Yes | |
| COX3 COX – complex IV | +2 with COX11 | Yes | |
| Cox11 COX assembly | Yes | ||
| Cox15 type2, heme A synthesis | Yes | ||
| SURF1 COX assembly | Yes | ||
| SCO COX assembly | Numeral as its multiple genes† | Yes | |
| Zf-CHCC precursor subunit Vb | No, this work | ||
| M16B precursor of MPP | +2 with ISP | 0 if not close to COX | No, this work |
| Cbp3 bc1 assembly | No, this work | ||
| ISP bc1 – complex III | Yes | ||
| CytB bc1 – complex III | Yes | ||
| CytC1 bc1 – complex III | Yes | ||
| CcmF cyt C biosynthesis | +1 with two other Ccm genes | Yes | |
| CcmE cyt C biosynthesis | No, this work | ||
| CcmA cyt C biosynthesis | No, this work | ||
| AOX alternative oxidase | Numeral as its multiple genes† | Yes | |
| M16A fused zinc peptidases | Capped numeral for multiple genes‡ | No, this work | |
| Cys near C terminus COX1 | No, this work |
*Numerical premium given to collinear synteny, as described in the Materials and Methods.
†A few alphaproteobacterial genomes have multiple genes for SCO proteins, while some eukaryotes have multiple AOX genes.
‡Several eukaryotes have up to eight M16 (A, B, and C subfamily) peptidases, but their maximal numeral was capped at five as described in Materials and Methods.