Table 3.
Prediction of impact of non-synonymous (fixed or under selection cf. Table 1) amino acid substitutions between B. calyciflorus s.s. and B. fernandoi in comparison to B. rubens, B. angularis and B. diversicornis.
| Site (aa) | Code | Bc–Bf–Br–Ba–Bd | Ancestral | Score | Sensitivity | Specificity | Prediction |
|---|---|---|---|---|---|---|---|
| 10* | H10V/I | H–V/I–H–R–-R | H | 0.002 | 0.99 | 0.30 | Benign |
| H10V/I | H–V/I–H–R–R | H | 0.004 | 0.97 | 0.59 | Benign | |
| 27 | E27G | E–G–E–E–E | E | 0.000 | 1.00 | 0.00 | Benign |
| 30 | F30- | F–F–F–F | F | – | – | – | – |
| 31 | S31- | S–S–S–S | S | – | – | – | – |
| 38* | E/K38E/K | E/K–E/K–E–E–E | E | 0.231 | 0.91 | 0.88 | Benign |
| 63 | L63M | L–M–L–M–L | L | 0.953 | 0.97 | 0.93 | Possibly damaging |
| 66 | T66S/F | T–F–T–F–T | T | 0.143 | 0.92 | 0.86 | Benign |
| T66S/F | T–F–T–F–T | T | 0.997 | 0.41 | 0.98 | Possibly damaging | |
| 127 | T127A | T–A–T–T–T | T | 0.019 | 0.95 | 0.80 | Benign |
| 175 | F175V | F–V–V–F–V | V | 0.001 | 0.99 | 0.15 | Benign |
| 177 | Y177N | Y–N–Y–Y–Y | Y | 0.000 | 1.00 | 0.00 | Benign |
| 226 | R226K | R–K–R–K–R | R | 0.000 | 1.00 | 0.00 | Benign |
| 242 | H242L | H–L–I–H–H | H | 0.000 | 1.00 | 0.00 | Benign |
| 249* | P/S249P | P/S–P–P–Q–Q | E | 0.116 | 0.93 | 0.86 | Benign |
| 256* | L/F/N256L | L/F/N–L–L–L–L | L | 0.024 | 0.95 | 0.81 | Benign |
| L/F/N256L | L/F/N–L–L–L–L | L | 0.094 | 0.93 | 0.85 | Benign | |
| 285 | D285E | D–E–D–E–D | E | 0.000 | 1.00 | 0.00 | Benign |
| 286* | I/K286I | I/K–I–I–I–I | I | 0.914 | 0.81 | 0.94 | Possibly damaging |
| 292* | T/I292R | T/I–R–A–S–V | ? | 0.001 | 0.99 | 0.15 | Possibly damaging |
| T/I292R | T/I–R–A–S–V | ? | 0.000 | 1.00 | 0.00 | Benign |
Predictions were made using Polyphen2. The code provides details on the amino acid substitution and the position. Bc–Bf–Br–Ba–Bd provides the information of the respective amino acid of B. calyciflorus s.s. (Bc), B. fernandoi (Bf), B. rubens (Br), B. angularis (Ba) and B. diversicornis (Bd). Ancestral amino acid was inferred using the most parsimonious (i.e., fewest substitutions) scenario, taking the species' phylogeny into account. In case of multiple amino acids (aa) per species, compared aa are bold in the row Code. Asteriks indicate sites under selection inferred by codeML. Note that Polyphen2 does not consider the possibility of a positive effect of an aa substitution, such that it ranks any predicted change in protein function as "damaging".