Table 2.
PV_PfamA domain occurrence in biosphere.
| Papillomaviridae 1,5 | PDB PfamA_28 2 | PfamA Domain Length 3 | PDB PfamA_31 2 | Best Coverage of PfamA by PDB (% aa) | Eukaryota (Proteomes) 1 | Bacteria (Proteomes) 1 | Archaea (Proteomes) 1 | Viruses 1,4 | Eukaryota (Full up) 1 | Bacteria (Full up) 1 | Archaea (Full up) 1 | Viruses (Full up) 1,4,6 | HMMER E 1 | HMMER B 1 | HMMER A 1 | HMMER V 1,6 | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| PF00500 | Late_protein_L1 | 76 | 10 | 498 | 18 | 0.96 | - | - | - | - | - | - | - | - | - | - | - | - |
| PF00508 | PPV_E2_N | 76 | 8 | 200 | 8 | 0.98 | - | - | - | - | - | - | - | - | - | - | - | - |
| PF00511 | PPV_E2_C | 76 | 16 | 80 | 16 | 0.96 | - | - | - | - | - | - | - | - | - | - | - | - |
| PF00513 | Late_protein_L2 | 76 | 0 | 525 | 0 | - | - | - | - | - | - | - | - | - | - | - | - | |
| PF00518 | E6 | 71 | 7 | 110 | 8 | 0.99 | - | - | - | - | - | - | - | - | - | - | - | - |
| PF00519 | PPV_E1_C | 74 | 7 | 432 | 8 | 0.96 | - | 1 | - | - | - | 20 | - | 1 | - | 1 | - | 1 |
| PF00524 | PPV_E1_N | 72 | 0 | 121 | 0 | 2 | - | - | - | 4 | - | - | - | - | - | - | - | |
| PF00527 | E7 | 71 | 3 | 93 | 4 | 0.50 | - | - | - | - | - | - | - | - | - | - | - | - |
| PF02711 | Pap_E4 | 25 | 0 | 95 | 0 | - | - | - | - | - | - | - | - | - | - | - | - | |
| PF03025 | Papilloma_E5 | 9 | 0 | 72 | 0 | - | - | - | - | - | - | - | - | - | - | - | - | |
| PF05776 | Papilloma_E5A | 5 | 0 | 91 | 0 | - | - | - | - | - | - | - | - | - | - | - | - | |
| PF08135 | EPV_E5 | 3 | 0 | 43 | 0 | - | - | - | - | - | - | - | - | - | - | - | - |
“-” No true positive hits were found. 1 Number of distinct proteomes/species in database with given taxonomic restrictions coding respective domain. 2 Number of Protein Data Bank (PDB) entries for respective PfamA domain. 3 Model length. 4 Excluding papillomaviruses. 5 76 PV proteomes in this database. 6 Excluding Polyomaviridae and Parvoviridae.