Table 2. FATCAT25 Structural Alignment Statistics for Proteins of Formerly Unknown Function in JCVI-syn3A Cell Growth, Maintenance, and Divisiona.
| gene | exp. struct. PDB ID | p-value | RMSD, Å (% aligned) |
|---|---|---|---|
| ezrA/0239 | 4UXV65 | 3.01 × 10–10 | 4.64 (84%) |
| gpsB/0353 | 4UG358 | 2.72 × 10–6 | 1.10 (100%) |
| secD/0412 | 5XAM102 | 9.20 × 10–4 | 6.10 (41%) |
| secF/0412 | 5MG3103 | 6.49 × 10–5 | 3.05 (53%) |
| yloU/0421 | B. subtilis (AF2)104 | 1.11 × 10–11 | 2.29 (99%) |
| ylxM/0430 | 1S7O82 | 3.21 × 10–10 | 1.99 (99%) |
| yqgP-gplG/0516 | B. subtilis (AF2)87 and 2NR989 | 7.19 × 10–9 | 3.07 (82%) |
| yqkD/0520 | B. subtilis (AF2)68 | 0.00 × 10–0 | 3.00 (96%) |
| ylbN/0527 | B. subtilis (AF2)76 | 3.03 × 10–7 | 2.45 (84%) |
| lemA-gacS/0604 | 2ETD61 | 6.78 × 10–5 | 1.67 (68%) |
| atpI/0797 | B. subtilis (AF2)98 and 6FKI101 | 1.81 × 10–11 | 1.22 (92%) |
| gabP/0878 | B. subtilis (AF2105) | 4.47 × 10–11 | 3.23 (87%) |
| yidC/0908 | M. pneumoniae (AF2106) | 0.00 × 10–0 | 2.33 (92%) |
a
Alignment values generated from experimentally solved crystal structures or with AlphaFold2 (AF2) structures where this abbreviation is indicated, aligned with predicted AlphaFold2 structures for JCVI-syn3A genes. A p-value of less than 5.0 × 10–2 demonstrates significant structural similarity. A value of 0.00 indicates a p-value of less than 1.0 × 10–20. The percent aligned relates to the percentage of residues in the protein of shorter length that are well-aligned to the larger structure by FATCAT, with the associated RMSD. Equations generating these statistical values are given in the Formulas section.