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Remove Duplicate V-Type ATPase Reaction #829

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merged 8 commits into from
Oct 17, 2024
Merged

Remove Duplicate V-Type ATPase Reaction #829

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b5de64c
fix: removed MAR07799 for being a less-accurate version of MAR00080
Devlin-Moyer Jun 19, 2024
0e3d886
fix: added ATP6AP1 to GPR of MAR00080 so it was still associated with…
Devlin-Moyer Jun 19, 2024
52362c9
feat: adds new reference for MAR00080
Devlin-Moyer Jun 19, 2024
f20c753
Merge branch 'develop' into fix/v_type_atpases
edkerk Jun 24, 2024
d5a90b2
Merge remote-tracking branch 'origin/develop' into fix/v_type_atpases
edkerk Sep 30, 2024
6e76c48
chore: add macaw test result
edkerk Sep 30, 2024
e15df44
fix: stoichiometry of V-ATPase
edkerk Oct 3, 2024
3c8bdfd
chore: add macaw test result
edkerk Oct 3, 2024
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1 change: 1 addition & 0 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -299,3 +299,4 @@ rxns rxnKEGGID rxnBiGGID rxnEHMNID rxnHepatoNET1ID rxnREACTOMEID rxnRecon3DID rx
"MAR04205" "" "" "RT0084" "" "" "HMR_4205" "" "HMR_4205" "RCR20258" "" 0 "" "" "HMR_4205"
"MAR08745" "" "THMMPtm" "" "" "" "" "MNXR104822" "HMR_8745" "RCR20669" "" 0 "" "" "HMR_8745"
"MAR08747" "" "THMPPtm" "" "" "" "" "MNXR104824" "HMR_8747" "RCR20670" "" 0 "" "" "HMR_8747"
"MAR07799" "" "ATPasel" "" "" "" "" "MNXR96136" "HMR_7799" "RCR20334" "" 0 "" "" "HMR_7799"
2 changes: 1 addition & 1 deletion data/macawResults/README.md
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Expand Up @@ -2,7 +2,7 @@

The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests.

The test results shown here were obtained by the GitHub Actions run in **PR #840**, and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
The test results shown here were obtained by the GitHub Actions run in **PR #829**, and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.

### `dead_end_test`
Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in.
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