Table 3.
Structural prediction and annotation using PHYRE2, SWISS-MODEL and IntFOLD3 of the top 17 unknown and highly differentially-expressed genes.
| Gene symbol | PHYRE-2 RMSD (Å) (% Coverage) |
SWISS-MODEL RMSD (Å) (% Coverage) |
INTFOLD3 RMSD (Å) (% Coverage) |
Annotation based on the template function |
|---|---|---|---|---|
| B0507.8 | 0 (26) | 1 (25) | 1 (98) | Transportin 3 – Protein import to nucleus (α -helix) |
| F26F2.4 isoform a | 1 (66) | 1 (32) | 1 (82) | Synaptonemal complex 1 (α-helix) |
| F26F2.4 isoform b | 1 (55) | N.T. | 5 (90) | Similar to F26F2.4 isoform a |
| F26F2.5 | 1 (14) | 1 (32) | 4 (96) | Zinc finger domain (α-helix) |
| B0507.10 | 0 (26) | 0 (32) | 1(80) | Spectrin (α-helix bundle) |
| CELE_T26F2.3 | 1 (99) | 1 (96) | 1 (97) | Dom3z protein Exoribonuclease (α/β- protein) |
| CELE_C43D7.4 | 1 (21) | 0 (25) | 1 (90) | No consensus fold across methods |
| CELE_C17H1.6 | 1 (36) | 0 (31) | 1 (87) | Reticulocyte binding protein 5 signaling (α-helix bundle) |
| CELE_C17H1.7 | 0 (26) | 1 (73) | 1 (55) | Helical repeat domain (α-helix) |
| CELE_Y75B8A.39 | 0 (22) | 0 (23) | 1 (100) | De novo three helix bundle |
| F26F2.2 | 0 (17) | 1 (46) | 5 (87) | Adhesin coiled-coil (α-helix) |
| CELE_C43D7.7 | 0 (17) | 0 (59) | 1 (93) | Virb DNA binding domain (Helix-Turn-Helix) |
| F26F2.3 | 0 (18) | 0 (15) | 1 (95) | alpha/alpha toroid |
| F26F2.1 | 0 (1) | 0 (6) | N.T. (0) | No consensus fold across methods |
| C49C8.2 | 0 (5) | 0 (35) | 1 (90) | Apolipophorin-iii lipid transport (5 helix bundle) |
| CELE_B0284.4 | 0 (31) | 1 (28) | 1 (90) | Ezra cytoplasmic domain (3 helix bundle repeat) |
| F42C5.3 isoform a | 0 (35) | 0 (17) | 1 (91) | Reticulocyte binding protein 5 signaling (α-helix bundle) |
| F42C5.3 isoform b | 0 (4) | 0 (22) | 1 (86) | Hof1p f-bar domain protein binding (coiled-coil) |
| sdz-6 | 0 (14) | 0 (26) | 1 (82) | Ectodomain of protein eff-1 (α-helix) |
The root mean squared deviation (RMSD) between the best template and model were computed as well as the percent coverage (In brackets) of the C. elegans protein sequence by the model. (N.T.: No Template found).