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fix: reformulate SAM synthesis GPR and remove non-catalytic MAT2B #1030

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a66f3e6
fix: correct SAM synthesis GPR and remove non-catalytic MAT2B (#1013)
edkerk Jul 11, 2026
2ffaa2c
Merge develop into fix/sam-synthesis-gpr
edkerk Jul 18, 2026
5e11c17
chore: update model QC results [skip ci]
edkerk Jul 18, 2026
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10 changes: 5 additions & 5 deletions data/testResults/README.md
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Expand Up @@ -21,11 +21,11 @@ own files. The pull request in each row is the one whose run last wrote those fi

| Result file(s) | Produced by | Last updated by |
| --- | --- | --- |
| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1061** (model QC checks) |
| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1061** (model QC checks) |
| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1061** (model QC checks) |
| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1061** (MACAW and balance) |
| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1061** (MEMOTE) |
| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1030** (model QC checks) |
| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1030** (model QC checks) |
| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1030** (model QC checks) |
| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1030** (MACAW and balance) |
| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1030** (MEMOTE) |
| `gene-essential.csv`, `gene-essential_summary.md` | `geneEssentiality.py` via `/run gene-essentiality` | **PR #1027** (gene essentiality) |

## 2. What each check means
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72 changes: 36 additions & 36 deletions data/testResults/model_qc_summary.md
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## Model quality report

:warning: **6 pre-existing finding(s), no regressions vs `main`.** Non-blocking.
:warning: **6 pre-existing finding(s), no regressions vs `develop`.** Non-blocking.

_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md)._
_Each check name links to its explanation in the [testResults README](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md)._

### Model checks
_Duplicate keys (model unloadable) and no growth block the merge; every other row is a non-blocking report._

| Check | Result | Δ vs `main` | |
| Check | Result | Δ vs `develop` | |
| --- | ---: | ---: | :---: |
| [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#duplicate-omap-keys) | 0 | new | :white_check_mark: |
| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#growth-biomass-producible) | 125 | new | :white_check_mark: |
| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-with-no-metabolites) | 0 | new | :white_check_mark: |
| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | new | :white_check_mark: |
| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | new | :white_check_mark: |
| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#metabolites-missing-formula) | 0 | new | :white_check_mark: |
| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#metabolites-missing-charge) | 0 | new | :white_check_mark: |
| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | new | :white_check_mark: |
| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | new | :white_check_mark: |
| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#unused-metabolites) | 0 | new | :white_check_mark: |
| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#unused-genes) | 0 | new | :white_check_mark: |
| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#malformed-cross-references) | 0 | new | :white_check_mark: |
| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/qc_annotation_issues.csv) | new | :warning: |
| [Duplicate `!!omap` keys](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#duplicate-omap-keys) | 0 | 0 | :white_check_mark: |
| [Growth (biomass producible)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#growth-biomass-producible) | 125 | 0 | :white_check_mark: |
| [Reactions with no metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#reactions-with-no-metabolites) | 0 | 0 | :white_check_mark: |
| [Model / annotation-table inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#model--annotation-table-inconsistencies) | 0 | 0 | :white_check_mark: |
| [Removed reactions or metabolites not deprecated](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#removed-reactions-or-metabolites-not-deprecated) | 0 | 0 | :white_check_mark: |
| [Metabolites missing formula](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#metabolites-missing-formula) | 0 | 0 | :white_check_mark: |
| [Metabolites missing charge](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#metabolites-missing-charge) | 0 | 0 | :white_check_mark: |
| [Reaction bound / GPR issues](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#reaction-bound--gpr-issues) | 0 | 0 | :white_check_mark: |
| [Exact-duplicate reaction groups](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#exact-duplicate-reaction-groups) | 0 | 0 | :white_check_mark: |
| [Unused metabolites](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#unused-metabolites) | 0 | 0 | :white_check_mark: |
| [Unused genes](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#unused-genes) | 0 | 0 | :white_check_mark: |
| [Malformed cross-references](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#malformed-cross-references) | 0 | 0 | :white_check_mark: |
| [Cross-refs inconsistent across compartments](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#cross-refs-inconsistent-across-compartments) | [3](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/qc_annotation_issues.csv) | 0 | :warning: |

### MACAW and mass/charge balance

| Check | Result | Δ vs `main` | |
| Check | Result | Δ vs `develop` | |
| --- | ---: | ---: | :---: |
| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/macaw_results.csv) | -703 | :warning: |
| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/macaw_results.csv) | -2 | :warning: |
| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/balance_results.csv) | new | :warning: |
| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/balance_results.csv) | new | :warning: |
| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/qc_structure_consistency.csv) | new | :warning: |
| [Reactions flagged by MACAW dead-end test](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#reactions-flagged-by-macaw-dead-end-test) | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/macaw_results.csv) | 0 | :warning: |
| [Reactions flagged as MACAW duplicates](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#reactions-flagged-as-macaw-duplicates) | [377](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/macaw_results.csv) | 0 | :warning: |
| [Mass-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#mass-imbalanced-reactions) | [87](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/balance_results.csv) | 0 | :warning: |
| [Charge-imbalanced reactions](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#charge-imbalanced-reactions) | [234](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/balance_results.csv) | 0 | :warning: |
| [Structure vs formula/charge inconsistencies](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#structure-vs-formulacharge-inconsistencies) | [397](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/qc_structure_consistency.csv) | 0 | :warning: |

### Model file and metabolic tasks

| Check | Result | |
| --- | ---: | :---: |
| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: |
| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: |
| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: |
| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: |
| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: |
| [YAML round-trip (cobrapy)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#yaml-round-trip-cobrapy) | pass | :white_check_mark: |
| [YAML round-trip (RAVEN)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#yaml-round-trip-raven) | pass | :white_check_mark: |
| [YAML lint](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#yaml-lint) | pass | :white_check_mark: |
| [Essential metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#essential-metabolic-tasks) | 57 passed | :white_check_mark: |
| [Verification metabolic tasks](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#verification-metabolic-tasks) | 21 passed | :white_check_mark: |

### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#memote)
### [MEMOTE](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#memote)

**Total score: 63.2%** (core subset)  
**Total score: 63.2%** (core subset)   0

| Section | Score | Δ vs base |
| --- | ---: | ---: |
| consistency | 42.4% | |
| annotation_met | 73.0% | |
| annotation_rxn | 72.7% | |
| annotation_gene | 46.7% | |
| annotation_sbo | 81.7% | |
| consistency | 42.4% | 0 |
| annotation_met | 73.0% | 0 |
| annotation_rxn | 72.7% | 0 |
| annotation_gene | 46.7% | 0 |
| annotation_sbo | 81.7% | 0 |

<details><summary>Per-test scores</summary>

Expand Down Expand Up @@ -89,11 +89,11 @@ _Duplicate keys (model unloadable) and no growth block the merge; every other ro

</details>

**Full suite: 64.2%** &nbsp; &middot; _from the last_ `/run memote`.
**Full suite: 64.2%** &nbsp; 0 &middot; _from the last_ `/run memote`.

_The score above is the fast core subset. Comment_ `/run memote` _to run the full suite on this pull request; the score updates here when it finishes._

### [Gene essentiality (Hart 2015)](https://github.com/SysBioChalmers/Human-GEM/blob/develop/data/testResults/README.md#gene-essentiality-hart-2015)
### [Gene essentiality (Hart 2015)](https://github.com/SysBioChalmers/Human-GEM/blob/fix/sam-synthesis-gpr/data/testResults/README.md#gene-essentiality-hart-2015)

_Not run automatically (it takes hours). Comment_ `/run gene-essentiality` _to run it on this pull request; the result posts as its own comment._

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7 changes: 2 additions & 5 deletions model/Human-GEM.yml
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- MAM02877c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000038274 or ENSG00000151224 or ENSG00000168906"
- gene_reaction_rule: "ENSG00000151224 or ENSG00000168906"
- rxnFrom: "HMRdatabase"
- eccodes: "2.5.1.6"
- references: "PMID:7213623"
Expand Down Expand Up @@ -77128,7 +77128,7 @@
- MAM02891c: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000038274 or ENSG00000151224 or ENSG00000168906"
- gene_reaction_rule: "ENSG00000151224 or ENSG00000168906"
- rxnFrom: "HMRdatabase"
- eccodes: "2.5.1.6"
- subsystem: "Metabolism of other amino acids"
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- !!omap
- id: "ENSG00000038210"
- name: "PI4K2B"
- !!omap
- id: "ENSG00000038274"
- name: "MAT2B"
- !!omap
- id: "ENSG00000039123"
- name: "MTREX"
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1 change: 0 additions & 1 deletion model/genes.tsv
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"ENSG00000037897" "ENST00000324871;ENST00000257848;ENST00000547653;ENST00000548504;ENST00000551117;ENST00000553125;ENST00000548681;ENST00000549773" "ENSP00000314441;ENSP00000257848;ENSP00000447838;ENSP00000449397;ENSP00000447988;ENSP00000448342" "Q9UBP6" "METTL1" "4234" "methyltransferase like 1" "C12orf1;TRM8;TRMT8" "Nucleus" "SwissProt;CellAtlas"
"ENSG00000038002" "ENST00000264595;ENST00000502310;ENST00000506853;ENST00000510635;ENST00000510955;ENST00000511231" "ENSP00000264595;ENSP00000423798;ENSP00000421471" "P20933" "AGA" "175" "aspartylglucosaminidase" "ASRG" "Lysosome" "SwissProt"
"ENSG00000038210" "ENST00000512921;ENST00000264864" "ENSP00000423373;ENSP00000264864" "Q8TCG2" "PI4K2B" "55300" "phosphatidylinositol 4-kinase type 2 beta" "FLJ11105;PI4KIIB;PIK42B" "Endoplasmic reticulum;Golgi apparatus;Cytosol" "SwissProt;CellAtlas"
"ENSG00000038274" "ENST00000280969;ENST00000519719;ENST00000321757;ENST00000421814;ENST00000518095;ENST00000523606;ENST00000520449;ENST00000521838" "ENSP00000280969;ENSP00000325425;ENSP00000397371;ENSP00000428046;ENSP00000431071" "Q9NZL9" "MAT2B" "27430" "methionine adenosyltransferase 2B" "MATIIbeta;SDR23E1" "Cytosol" "DeepLoc2"
"ENSG00000039123" "ENST00000230640;ENST00000504388;ENST00000506750;ENST00000503165;ENST00000504997;ENST00000505565;ENST00000502953;ENST00000518955;ENST00000508716" "ENSP00000230640;ENSP00000425042;ENSP00000422125;ENSP00000426641" "P42285" "MTREX" "23517" "Mtr4 exosome RNA helicase" "Dob1;fSAP118;KIAA0052;Mtr4;SKIV2L2" "Nucleus" "SwissProt;CellAtlas"
"ENSG00000039650" "ENST00000596624;ENST00000636840;ENST00000595081;ENST00000601816;ENST00000594661;ENST00000627232;ENST00000593946;ENST00000600910;ENST00000322344;ENST00000599454;ENST00000631020;ENST00000596014;ENST00000600573;ENST00000597965;ENST00000640501;ENST00000625216;ENST00000593706;ENST00000627317;ENST00000629179;ENST00000637325;ENST00000636214;ENST00000599543;ENST00000596726;ENST00000625299;ENST00000598020;ENST00000637897;ENST00000626274;ENST00000629088;ENST00000595792;ENST00000636994;ENST00000638016" "ENSP00000490737;ENSP00000486037;ENSP00000468896;ENSP00000473137;ENSP00000323511;ENSP00000486707;ENSP00000472300;ENSP00000469826;ENSP00000471097;ENSP00000491347;ENSP00000486898;ENSP00000486500;ENSP00000489983;ENSP00000469848;ENSP00000470887;ENSP00000470346;ENSP00000490539;ENSP00000490791;ENSP00000489771" "Q96T60" "PNKP" "11284" "polynucleotide kinase 3'-phosphatase" "PNK" "Nucleus" "SwissProt;CellAtlas"
"ENSG00000040933" "ENST00000409016;ENST00000409851;ENST00000409463;ENST00000409540;ENST00000463367;ENST00000523221;ENST00000468638;ENST00000467042;ENST00000498026;ENST00000074304" "ENSP00000386704;ENSP00000386777;ENSP00000386329;ENSP00000387294;ENSP00000427722;ENSP00000074304" "Q96PE3" "INPP4A" "3631" "inositol polyphosphate-4-phosphatase type I A" "INPP4" "Nucleus;Cytosol" "SwissProt;CellAtlas"
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