Sequencing and modular analysis of the hybrid non-ribosomal peptide synthase – polyketide synthase gene cluster from the marine sponge <i>Hymeniacidon perleve</i>-associated bacterium <i>Pseudoalteromonas</i> sp. strain NJ631
Bibliographic record
Abstract
In the present study, we sought to confirm a putative non-ribosomal peptide synthase (NRPS) - polyketide synthase (PKS) gene cluster in marine sponge-associated bacterium with cytotoxic activity and elucidate the gene's structural information. The genomic library of the marine sponge Hymeniacidon perleve-associated bacterium Pseudoalteromonas sp. strain NJ631 was constructed using a pCC1FOS fosmid. Positive clones that covered the whole gene cluster region of hybrid NRPS-PKS were selected for shotgun sequencing. The results obtained from BlastX and open reading frame (ORF) analysis indicated that there are 3 big ORFs, NJA1, NJA2, and NJA3, that encoded proteins with similarities to amino acid adenylation, beta-ketoacyl synthase, and non-ribosomal peptide synthase, respectively, from different organisms. The results gave us a clue that there could be PKS or NRPS modules in the 3 ORFs. Further analysis demonstrated 3 ORFs encoding 2 NRPS modules, 1 PKS module, and 3 NRPS modules. Using the specificity-conferring selection rule, the substrate specificity of 4 adenylation (A) domains (A2, A3, A4, and A5) were successfully predicted, and the amino acids of the substrate specificity were glutamic acid - glutamine, serine, D-serine, and Aeo (2-amino-9,10-epoxy-8-oxodecanoic acid), respectively.
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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 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
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".