Additional file 1 of A novel C-terminal degron identified in bacterial aldehyde decarbonylases using directed evolution
Bibliographic record
Abstract
Additional file 1: Figure S1. Whole cell lysis activity analysis of different mutants. M2 give the highest activity, which has a premature stop codon in the C-terminal region. WT wild type ADpm, M1–M9 different mutants. Figure S2. Comparison of ADpm and ADpm-9. a Specific activity of ADpm and ADpm-9. b Relative protein thermal stability estimated using SYPRO Orange dye. c Investigation of oligomeric state of ADpm and ADpm-9 using size exclusion chromatography. Figure S3. Comparison of C-terminal of ADpm and C-motif 1 [35] of protease trapped proteins. Figure S4. Modelling results of degron subtraction in three representative ADs from P. marinus (ADpm), N. punctiforme (ADnp) and S. elongates (ADse). a Thermostability and hexanal docking analysis of three ADs and their C-terminal truncations. (b–d) Examples of docking analysis in ADpm and ADpm-9. b ADpm, c ADpm-9, d Superimposed structures. Note, residues shown in red indicate the interact amino acids keep consistent in the truncated and wild-type ones. Figure S5. Effect of C-terminal His-tag on GFP degradation. C-terminal 6His-tag was added to GFP with conserved degron. Figure S6. Effects of AD degron elimination on fermentation. Headspace analysis of ADse (Red) and ADse-10 (Blue). U1–U7, unidentified peaks. Figure S7. Effects of AD degron elimination on cell growth. (a–d) Growth curves of ADse (black) and ADse-10 (red) in M9 medium containing different concentrations (0.5, 1, 2 and 10 g/L) of glucose. Table S1. Statistical analysis of amino acid usage frequency (%) at C-terminus in 371 bacterial ADs.
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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 | 0.002 | 0.012 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.003 | 0.001 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.843 | 0.192 |
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".