Table 1.
General features of the predicted genes (ORFs) of TPV1 virus.
| Predicted gene | Predicted protein size (aa) | Closest homologue: e-value, % identity, taxonomy | Homologues: taxonomic range | Conserved motifs/domains and predicted function(s) | Comments |
|---|---|---|---|---|---|
| TPV1-1 | 200 | TK_1361. 2e-45; 44% TKV4 (T. kodakaraensis) |
TKV4 (T. kodakaraensis) only | None | N-terminal part of the MCM2-like helicase in TKV4 but a separate protein in TPV1 |
| TPV1-2 | 561 | TK_1361. 7e-88; 36% TKV4 (T. kodakaraensis) |
All archaea and eukaryotes | All conserved motifs of the MCM family within the AAA+ ATPase superfamily. MCM2-like helicase involved in DNA replication initiation (licensing factor). | C-terminal part of the MCM2-like helicase in TKV4 but a separate protein in TPV1; contains all elements required for licensing factor activity |
| TPV1-3 | 136 | None | None | MutL-transducer domain (e-value 1.7e-03, RPS-BLAST); possible involvement in replication, interaction with TPV1-2. | In DNA gyrase, involved in transduction of structural change from ATP-binding site to breakage-rejoining Toprim domain |
| TPV1-4 | 83 | None | None | None | |
| TPV1-5 | 133 | TGAM_0671. 1e-47; 61% TGV1 (T. gammatolerans) |
T. gammatolerans provirus and T. barophilus plasmid | None | |
| TPV1-6 | 174 | TGAM_0672. 8e-119; 94% TGV1 (T. gammatolerans) |
Most archaea, some bacteria, some archaeal and bacterial viruses | Archaeal-type Holliday junction resolvase, all catalytic motifs conserved | Member of a distinct family of Holliday junction conserved in Thermococcales and Archaeoglobales |
| TPV1-7 | 187 | None | None | None | |
| TPV1-8 | 117 | TK0576/TK0420. 1e-54; 81% TKV3/TKV2 (T. kodakaraensis) |
Many archaea and bacteria | Winged helix–turn–helix domain; transcription regulator of the IclR family | |
| TPV1-9 | 71 | None | None | Predicted integral membrane protein | |
| TPV1-10 | 318 | TK0381. 9e-66; 45% TKV2 (T. kodakaraensis) |
Many archaeal viruses and proviruses integrated in archaeal genomes | SSV1-type integrase | |
| TPV1-11 (−) | 87 | None | None | None | |
| TPV1-12 | 119 | None | None | Predicted integral membrane protein | |
| TPV1-13 | 136 | None | None | Predicted integral membrane protein | |
| TPV1-14 (−) | 62 | None | None | None | |
| TPV1-15 | 112 | None | None | Predicted integral membrane protein | |
| TPV1-16 | 89 | None | None | Predicted integral membrane protein | |
| TPV1-17 | 152 | None | None | None | |
| TPV1-18 | 285 | None | None | Predicted integral membrane protein | |
| TPV1-19 | 147 | None | None | None | |
| TPV1-20 | 258 | MA2591. 0.026; 26% Methanosarcina acetivorans |
Distant homologues in all Archaea, bacteria and eukaryotes, some archaeal viruses | A distinct AAA+ superfamily ATPase; all motifs characteristic of active ATPases conserved | AAA+ ATPases with low sequence similarity but similar size and arrangement of conserved motifs found in several crenarchaeal viruses (Fig. S10) |
| TPV1-21 | 884 | None | None | Predicted non-globular protein | Large non-globular proteins are common among bacteriophage tail subunits |
| TPV1-22 | 623 | PAV1_ORF676. 7e-15; 23% PAV1 |
Distant homologues in many Archaea, bacteria and eukaryotes | Concanavalin A-lectin/glucanase domain (jelly roll fold); two predicted transmembrane helices | Potential role in adsorption |
| TPV1-23 | 688 | PAV1_ORF678. 3e-91; 36% | Distant homologues in many Archaea, bacteria and eukaryotes | Concanavalin A-lectin/glucanase domain (jelly roll fold); three predicted transmembrane helices | Potential role in adsorption |
| TPV1-24 | 183 | None | None | None | |
| TPV1-25 | 182 | PNA2_1322. 0.002; 34% Pyrococcus sp (predicted provirus) |
TKV3 (TK_0597) and other putative proviruses in Thermococcales | None | |
| TPV1-26 (−) | 234 | PNA2_0680. 7e-30; 37% Pyrococcus sp. |
Distant homologues in most archaea and bacteria | A distinct subfamily of RecB family nucleases; restriction-like endonuclease superfamily motifs | |
| TPV1-27 (−) | 83 | Arcve_1816. 6e-18; 71% Archaeoglobus veneficus |
Archaeoglobus veneficus, A. fulgidus, Pyrococcus sp.; more distant homologues in all eukaryotes | C2H2 Zn finger | |
| TPV1-28 | 106 | PNA2_0681. 6e-12; 33% Pyrococcus sp. |
Most Archaea (including TKV2/3), many bacteria | Helix–turn–helix domain; transcription regulator of the SpoVT/AbrB family |