In Silico Prophage Analysis of Halobacterium salinarum ATCC 33170
Bibliographic record
Abstract
The extremophile Halobacterium salinarum is an aerobic archaeon that has adapted to thrive in high-salt environments such as salted fish, hypersaline lakes, and salterns. Halophiles have garnered significant interest due to their unique interactions with bacteriophages known as haloarchaeophages. Studies have identified and characterized prophages in halophilic archaea, such as Haloferax volcanii, Haloquadratum walsbyi, and Haloarcula marismortui. Still, an investigation has yet to be conducted into the presence of prophage elements on Halobacterium salinarum ATCC 33170. This is of particular interest to us as we are using this strain as a source of archaeol, as one of the components of our sulfated lactosyl archaeol (SLA) archaeosome adjuvant. Genomic contigs of strain 33170 were bioinformatically assessed for prophage-like features using BLAST, PHASTER, InterProScan, and PHYRE2. A 7 kb region encoding six genes was identified as an incomplete prophage, and the proteins were further analyzed, revealing high homology to proteins encoded by bacteria, archaea, and an IS200 transposon. Restricting the BLASTp database to viruses resulted in hits to both myo- and siphoviral proteins, which would be unusual for an intact prophage. Additionally, no known phage structural proteins were identified in the search, suggesting a low chance that H. salinarum ATCC 33170 harbors a latent prophage.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".