From fc0ae2d825491a7a01d46973620a141556ae1419 Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Sat, 11 Jul 2026 14:57:27 +0200 Subject: [PATCH] fix: remove charge-imbalanced duplicate lipoxygenase reactions (#348) Five arachidonate/DHA peroxidation reactions are 1:1 duplicates of balanced multi-stoichiometry reactions that produce the same hydroperoxide (same substrate and product, no GPR), but with charge-imbalanced stoichiometry. Remove the imbalanced 1:1 versions and keep the balanced counterparts: removed kept product MAR01364 MAR03880 12-peroxy-eicosatetraenoate MAR01355 MAR03882 8-peroxy-eicosatetraenoate MAR01358 MAR03878 9-peroxy-eicosatetraenoate MAR01361 MAR03884 11-peroxy-eicosatetraenoate MAR01405 MAR03261 10-peroxy-docosahexaenoate Each product is still produced by its balanced counterpart, so the model stays balanced. Removed reactions moved to deprecatedReactions.tsv. The deeper cause (hydroperoxide and hydroxy fatty-acid metabolites that are one H short, affecting ~105 reactions) is tracked in a separate issue. --- .../deprecatedReactions.tsv | 5 ++ model/Human-GEM.yml | 65 ------------------- model/reactions.tsv | 5 -- 3 files changed, 5 insertions(+), 70 deletions(-) diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv index b48534b3..fabcd8e1 100644 --- a/data/deprecatedIdentifiers/deprecatedReactions.tsv +++ b/data/deprecatedIdentifiers/deprecatedReactions.tsv @@ -401,3 +401,8 @@ MAR07851 DNDPt62m DNDPt62m MNXR97327 HMR_7851 RCR20193 0 HMR_7851 MAR07852 DNDPt63m DNDPt63m MNXR97676 HMR_7852 RCR20146 0 HMR_7852 MAR07853 DNDPt6m DNDPt6m MNXR97677 HMR_7853 RCR20194 0 HMR_7853 MAR07854 DNDPt7m DNDPt7m MNXR97175 HMR_7854 RCR20122 0 HMR_7854 +MAR01364 RE3452C HMR_1364 RCR13344 0 HMR_1364 +MAR01355 RE3455C HMR_1355 RCR13335 0 HMR_1355 +MAR01358 RE3449C HMR_1358 RCR13338 0 HMR_1358 +MAR01361 RE3458C HMR_1361 RCR13341 0 HMR_1361 +MAR01405 RE2852C HMR_1405 HMR_1405 RCR13691 0 HMR_1405 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 681c03b0..29a1a670 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -119725,19 +119725,6 @@ - references: "PMID:11641243" - subsystem: "Prostaglandin biosynthesis" - confidence_score: 0 - - !!omap - - id: "MAR01355" - - metabolites: !!omap - - MAM01214c: 1 - - MAM01362c: -1 - - MAM02039c: 1 - - MAM02630c: -1 - - lower_bound: 0 - - upper_bound: 1000 - - rxnFrom: "HMRdatabase" - - references: "PMID:2123555" - - subsystem: "Prostaglandin biosynthesis" - - confidence_score: 0 - !!omap - id: "MAR01356" - metabolites: !!omap @@ -119766,19 +119753,6 @@ - references: "PMID:2123555" - subsystem: "Prostaglandin biosynthesis" - confidence_score: 0 - - !!omap - - id: "MAR01358" - - metabolites: !!omap - - MAM01246c: 1 - - MAM01362c: -1 - - MAM02039c: 1 - - MAM02631c: -1 - - lower_bound: 0 - - upper_bound: 1000 - - rxnFrom: "HMRdatabase" - - references: "PMID:2123555" - - subsystem: "Prostaglandin biosynthesis" - - confidence_score: 0 - !!omap - id: "MAR01359" - metabolites: !!omap @@ -119807,19 +119781,6 @@ - references: "PMID:2123555" - subsystem: "Prostaglandin biosynthesis" - confidence_score: 0 - - !!omap - - id: "MAR01361" - - metabolites: !!omap - - MAM00302c: 1 - - MAM01362c: -1 - - MAM02039c: 1 - - MAM02631c: -1 - - lower_bound: 0 - - upper_bound: 1000 - - rxnFrom: "HMRdatabase" - - references: "PMID:2123555" - - subsystem: "Prostaglandin biosynthesis" - - confidence_score: 0 - !!omap - id: "MAR01362" - metabolites: !!omap @@ -119847,19 +119808,6 @@ - references: "PMID:2123555" - subsystem: "Prostaglandin biosynthesis" - confidence_score: 0 - - !!omap - - id: "MAR01364" - - metabolites: !!omap - - MAM00335c: 1 - - MAM01362c: -1 - - MAM02039c: 1 - - MAM02631c: -1 - - lower_bound: 0 - - upper_bound: 1000 - - rxnFrom: "HMRdatabase" - - references: "PMID:2123555" - - subsystem: "Prostaglandin biosynthesis" - - confidence_score: 0 - !!omap - id: "MAR01365" - metabolites: !!omap @@ -127689,19 +127637,6 @@ - references: "PMID:10694406" - subsystem: "Isolated" - confidence_score: 0 - - !!omap - - id: "MAR01405" - - metabolites: !!omap - - MAM00275c: 1 - - MAM01689c: -1 - - MAM02039c: 1 - - MAM02631c: -1 - - lower_bound: 0 - - upper_bound: 1000 - - rxnFrom: "HMRdatabase" - - references: "PMID:10694406" - - subsystem: "Isolated" - - confidence_score: 0 - !!omap - id: "MAR01406" - metabolites: !!omap diff --git a/model/reactions.tsv b/model/reactions.tsv index e5b1099e..65dd66c9 100644 --- a/model/reactions.tsv +++ b/model/reactions.tsv @@ -3681,16 +3681,12 @@ MAR01346 R09536 RE1978C RE1978C MNXR103590 HMR_1346 RCR14606 0 RHEA:26136 H MAR01347 RE2563C RE2563C MNXR103699 HMR_1347 RCR10893 0 HMR_1347 MAR01350 RE2050C RE2050C MNXR103599 HMR_1350 RCR13334 0 HMR_1350 MAR01352 RE2051C RE2051C MNXR103600 HMR_1352 RCR14607 0 HMR_1352 -MAR01355 RE3455C HMR_1355 RCR13335 0 HMR_1355 MAR01356 RE3457C RE3457C HMR_1356 RCR13336 0 HMR_1356 MAR01357 RE3456C RE3456C HMR_1357 RCR13337 0 HMR_1357 -MAR01358 RE3449C HMR_1358 RCR13338 0 HMR_1358 MAR01359 RE3451C RE3451C HMR_1359 RCR13339 0 HMR_1359 MAR01360 RE3450C RE3450C HMR_1360 RCR13340 0 HMR_1360 -MAR01361 RE3458C HMR_1361 RCR13341 0 HMR_1361 MAR01362 RE3460C RE3460C HMR_1362 RCR13342 0 HMR_1362 MAR01363 RE3459C RE3459C HMR_1363 RCR13343 0 HMR_1363 -MAR01364 RE3452C HMR_1364 RCR13344 0 HMR_1364 MAR01365 RE3454C RE3454C HMR_1365 RCR13345 0 HMR_1365 MAR01366 RE3453C RE3453C HMR_1366 RCR13346 0 HMR_1366 MAR01367 RE3533C RE3533C MNXR103951 HMR_1367 RCR13347 0 HMR_1367 @@ -4196,7 +4192,6 @@ MAR01896 BILDGLCURte r0814 BILDGLCURte MNXR96252 HMR_1896 RCR40175 3.A.1.208. MAR01897 HMR_1897 HMR_1897 RCR40343 3.A.1.208.2;3.A.1.208.9;3.A.1.208.7 0 HMR_1897 MAR01403 RE2849C HMR_1403;RE2849C MNXR103728 HMR_1403 RCR13690 0 HMR_1403 MAR01404 RE2854C HMR_1404;RE2854C MNXR103732 HMR_1404 RCR14647 0 HMR_1404 -MAR01405 RE2852C HMR_1405 HMR_1405 RCR13691 0 HMR_1405 MAR01406 RE2848C HMR_1406;RE2848C MNXR103727 HMR_1406 RCR13692 0 HMR_1406 MAR01407 RE2850C HMR_1407;RE2850C MNXR103729 HMR_1407 RCR13693 0 HMR_1407 MAR01408 RE2853C HMR_1408;RE2853C MNXR103731 HMR_1408 RCR13694 0 HMR_1408