Additional file 6 of Kinetic characterization of annotated glycolytic enzymes present in cellulose-fermenting Clostridium thermocellum suggests different metabolic roles
Bibliographic record
Abstract
Additional file 6: PfkA, PfkB and Aldoa kinetic data used to generate kinetic parameters in this study. Table S4. Velocities produced by PfkA while varying the concentration of either ATP or GTP to determine the Km of the phosphate donors while F6P was held at a concentration of 2 mM. Values generated kinetic parameters in Table 1. Table S5. Velocities produced by PfkA while varying the concentration of F6P to determine the Km of the sugar phosphate while phosphate donor (ATP/GTP) concentration was held constant at 2 mM. Values generated kinetic parameters in Table 1. Table S6. Velocities produced by PfkA with respective phosphate donors (ATP or GTP) for each trial without any effector, with the addition of NH4Cl(*) appearing to be required for maximal activity and subsequent combination NH4Cl(*) and other potential activating or inhibiting compound. These values were used to produce Fig. 4A–C. The effect of each effector was compared to the reaction with only NH4Cl(*), GTP/ATP and F6P which is considered 100% relative activity. Final concentration of each effector was 2 mM, F6P 2 mM and GTP/ATP 2 mM. Table S7. Inhibition assay for PfkA activity with varying concentrations of PPi was done separately with another protein preparation. Note that PfkA once purified is not very stable and has the tendency to precipitate. The concentration of Mg2+ in the assay was reduced 50% to 2.5 mM to avoid precipitation with PPi. The reduction in Mg2+ along with potential precipitation of PfkA could explain the difference in velocities between Table S5 and Table S6. These values were used to produce Fig. 4D Table S8. Velocities produced by PfkB while varying the concentration of fructose to determine the Km of the sugar while phosphate donor (ATP/GTP) concentration was held constant at 2 mM. Values generated kinetic parameters in Table 3. Table S9. Velocities produced by PfkB while varying the concentration of either ATP or GTP to determine the Km of the phosphate donors while fructose concentration was held at 2 mM. Values generated kinetic parameters in Table 3. Table S10. Velocities produced by Aldoa while varying the concentration of FBP to determine the Km of the sugar phosphate. Table S11. Velocities produced by Aldoa without any potential activating ions, with the addition of either a monovalent or divalent ion and a combination of both. The values were used to produce Fig. 11.
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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 | 0.019 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.003 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.003 | 0.003 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.001 |
| Insufficient payload (model declined to judge) | 0.782 | 0.177 |
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".