SysBioChalmers · edkerk · Jul 11, 2026 · Jul 11, 2026
diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
@@ -2272,3 +2272,6 @@ MAM00208c	MAM00208		C16832							M00208	MNXM21289	m00208c	m00208c
 MAM00209c	MAM00209		C16237							M00209	MNXM96070	m00209c	m00209c
 MAM00210c	MAM00210		C16236							M00210	MNXM4090	m00210c	m00210c
 MAM01622x	MAM01622	b2coa	C00877		CHEBI:15473	5280381			HC00572	b2coa	MNXM214	m01622p	m01622p
+
+MAM00348c	MAM00348	13_cis_oretn								13_cis_oretn	MNXM146866	m00348c	m00348c
+MAM00348n	MAM00348	13_cis_oretn								13_cis_oretn	MNXM146866		m00348n
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -401,3 +401,6 @@ 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
+
+MAR08704		RAI4				RAI4	MNXR103425	HMR_8704	RCR13922		0			HMR_8704
+MAR01564		ORETNtn2				ORETNtn2	MNXR102215				0			ORETNtn2
diff --git a/data/testResults/README.md b/data/testResults/README.md
@@ -4,7 +4,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/
 
 The test results shown here were obtained by the GitHub Actions run in:
 
-- **PR #1035** (QC)
+- **PR #1044** (QC)
 - **PR #973** (gene essentiality)
 
 The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request.

diff --git a/data/testResults/macaw_results.csv b/data/testResults/macaw_results.csv
@@ -4627,9 +4627,8 @@ MAR08698,2 MAM02039c + MAM02555c + MAM02833c <=> MAM02040c + MAM02554c + MAM0283
 MAR08699,MAM00349c + MAM02040c + MAM02554c <=> MAM00350c + 2 MAM02039c + MAM02555c,ok,ok,ok,ok,N/A
 MAR08700,MAM02039c + MAM02555c + MAM02630c + MAM02833c --> MAM01006c + MAM02040c + MAM02554c,ok,ok,ok,ok,N/A
 MAR08702,MAM01230c <=> MAM02832c,ok,ok,ok,ok,N/A
-MAR08703,MAM02630c + 2 MAM02833c --> 2 MAM01026c,MAM01026c,ok,ok,ok,N/A
-MAR08704,MAM00348c <=> MAM01026c,MAM00348c;MAM01026c,ok,ok,ok,N/A
-MAR08706,2 MAM00350c + MAM02630c --> 2 MAM00348c,MAM00348c,ok,ok,ok,N/A
+MAR08703,MAM02630c + 2 MAM02833c --> 2 MAM00993c,ok,ok,ok,ok,N/A
+MAR08706,2 MAM00350c + MAM02630c --> 2 MAM01026c,MAM01026c,ok,ok,ok,N/A
 MAR08709,MAM00290c + MAM02039c + MAM02555c <=> MAM00291c + MAM02554c,ok,ok,ok,ok,N/A
 MAR08710,MAM00349c + MAM02039c + MAM02553c <=> MAM00351c + MAM02552c,only when going forwards,ok,ok,ok,N/A
 MAR08711,MAM00291c <=> MAM02834c,ok,ok,ok,ok,N/A
@@ -8290,7 +8289,6 @@ MAR01560,MAM02040e + MAM03622e --> MAM01965e + MAM03623e,ok,ok,ok,ok,N/A
 MAR01561,MAM02644c <=> MAM02644x,ok,ok,ok,ok,N/A
 MAR01562,MAM02647c <=> MAM02647x,ok,ok,ok,ok,N/A
 MAR01563,MAM01026c <=> MAM01026n,MAM01026c;MAM01026n,ok,ok,ok,N/A
-MAR01564,MAM00348c <=> MAM00348n,MAM00348c;MAM00348n,ok,ok,ok,N/A
 MAR01566,MAM02661x --> MAM02661c,ok,ok,ok,ok,N/A
 MAR01567,MAM01093m + MAM02039m + MAM02555m + MAM02630m --> MAM00756m + 2 MAM02040m + MAM02554m,ok,ok,ok,ok,N/A
 MAR01569,MAM00610r + MAM02039r + MAM02555r + MAM02630r --> MAM01446r + MAM02040r + MAM02554r,ok,ok,ok,ok,N/A

diff --git a/data/testResults/qc_summary.md b/data/testResults/qc_summary.md
@@ -2,8 +2,8 @@
 
 ```
 Starting dead-end test...
- - Found 1384 dead-end metabolites.
- - Found 1141 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
+ - Found 1382 dead-end metabolites.
+ - Found 1138 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
  - Found 1369 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
 Starting duplicate test...
  - Skipping redox duplicates because no redox_pairs and/or proton_ids were provided.

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -4535,13 +4535,6 @@
       - formula: "C28H39O4"
       - charge: -1
       - metFrom: "HMRdatabase"
-    - !!omap
-      - id: "MAM00348c"
-      - name: "13-cis-oxo-retinoate"
-      - compartment: "c"
-      - formula: "C20H27O3"
-      - charge: -1
-      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM00349c"
       - name: "13-cis-retinal"
@@ -11333,14 +11326,14 @@
       - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM01026c"
-      - name: "4-oxo-13-cis-retinoate"
+      - name: "4-hydroxy-13-cis-retinoate"
       - compartment: "c"
       - formula: "C20H27O3"
       - charge: -1
       - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM01026r"
-      - name: "4-oxo-13-cis-retinoate"
+      - name: "4-hydroxy-13-cis-retinoate"
       - compartment: "r"
       - formula: "C20H27O3"
       - charge: -1
@@ -39428,13 +39421,6 @@
       - charge: 0
       - inchis: "InChI=1S/C27H42O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h7,9-10,19,21,23-25,28H,6,8,11-17H2,1-5H3/t19-,21+,23-,24+,25+,26+,27-/m1/s1"
       - metFrom: "Recon3D"
-    - !!omap
-      - id: "MAM00348n"
-      - name: "13-cis-oxo-retinoate"
-      - compartment: "n"
-      - formula: "C20H27O3"
-      - charge: -1
-      - metFrom: "Recon3D"
     - !!omap
       - id: "MAM00350n"
       - name: "13-cis-retinoate"
@@ -39458,7 +39444,7 @@
       - metFrom: "Recon3D"
     - !!omap
       - id: "MAM01026n"
-      - name: "4-oxo-13-cis-retinoate"
+      - name: "4-hydroxy-13-cis-retinoate"
       - compartment: "n"
       - formula: "C20H27O3"
       - charge: -1
@@ -134283,29 +134269,19 @@
     - !!omap
       - id: "MAR08703"
       - metabolites: !!omap
-          - MAM01026c: 2
+          - MAM00993c: 2
           - MAM02630c: -1
           - MAM02833c: -2
       - lower_bound: 0
       - upper_bound: 1000
       - rxnFrom: "HMRdatabase"
       - subsystem: "Retinol metabolism"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR08704"
-      - metabolites: !!omap
-          - MAM00348c: -1
-          - MAM01026c: 1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - rxnFrom: "HMRdatabase"
-      - subsystem: "Retinol metabolism"
-      - confidence_score: 0
     - !!omap
       - id: "MAR08706"
       - metabolites: !!omap
-          - MAM00348c: 2
           - MAM00350c: -2
+          - MAM01026c: 2
           - MAM02630c: -1
       - lower_bound: 0
       - upper_bound: 1000
@@ -183606,18 +183582,6 @@
       - references: "PMID:1503811"
       - subsystem: "Transport reactions"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR01564"
-      - name: "13-Cis-4-Oxo-Retinoic Acid Transport, Nuclear"
-      - metabolites: !!omap
-          - MAM00348c: -1
-          - MAM00348n: 1
-      - lower_bound: -1000
-      - upper_bound: 1000
-      - rxnFrom: "Recon3D"
-      - references: "PMID:1503811"
-      - subsystem: "Transport reactions"
-      - confidence_score: 0
     - !!omap
       - id: "MAR01566"
       - name: "Oxalate Transport Out of Peroxisome"

diff --git a/model/metabolites.tsv b/model/metabolites.tsv
@@ -639,7 +639,6 @@ MAM00346r	MAM00346					53481463		CE4898		CE4898	MNXM164055	m00346r	m00346r
 MAM00347c	MAM00347					53481464		CE7072		CE7072	MNXM164056	m00347c	m00347c
 MAM00347m	MAM00347					53481464		CE7072		CE7072	MNXM164056	m00347m	m00347m
 MAM00347r	MAM00347					53481464		CE7072		CE7072	MNXM164056	m00347r	m00347r
-MAM00348c	MAM00348	13_cis_oretn								13_cis_oretn	MNXM146866	m00348c	m00348c
 MAM00349c	MAM00349	retinal_cis_13		HMDB0006220	CHEBI:45487	6436079	LMPR01090018			retinal_cis_13	MNXM425;MNXM6641	m00349c	m00349c
 MAM00349r	MAM00349	retinal_cis_13		HMDB0006220	CHEBI:45487	6436079	LMPR01090018			retinal_cis_13	MNXM425;MNXM6641	m00349r	m00349r
 MAM00350c	MAM00350	13_cis_retn	D00348	HMDB0006219	CHEBI:6067	5282379	LMPR01090021			13_cis_retn	MNXM521;MNXM58377	m00350c	m00350c
@@ -1601,8 +1600,8 @@ MAM01023r	MAM01023							CE5592		CE5592	MNXM164317	m01023r	m01023r
 MAM01024c	MAM01024					14015984		CE5593		CE5593	MNXM37693	m01024c	m01024c
 MAM01024r	MAM01024					14015984		CE5593		CE5593	MNXM37693	m01024r	m01024r
 MAM01025c	MAM01025		C19567							M01025	MNXM10233	m01025c	m01025c
-MAM01026c	MAM01026	oretn				104857		CE5654		CE5654;oretn	MNXM37697;MNXM6902	m01026c	m01026c
-MAM01026r	MAM01026	oretn				104857		CE5654		CE5654;oretn	MNXM37697;MNXM6902	m01026r	m01026r
+MAM01026c	MAM01026	oretn				104857		CE5654		CE5654;oretn		m01026c	m01026c;MAM00348
+MAM01026r	MAM01026	oretn				104857		CE5654		CE5654;oretn		m01026r	m01026r;MAM00348
 MAM01027c	MAM01027				CHEBI:58972	216297		CE2577		CE2577	MNXM7935	m01027c	m01027c
 MAM01028c	MAM01028							CE5652		CE5652		m01028c	m01028c
 MAM01028r	MAM01028							CE5652		CE5652		m01028r	m01028r
@@ -5576,11 +5575,10 @@ MAM01066r	MAM01066	chlstol	C05439		CHEBI:16290				HC01452	chlstol	MNXM162749;MNX
 MAM02343r	MAM02343	lthstrl	C01189	HMDB0001170	CHEBI:17168	65728	LMST01010089		HC00706	lthstrl	MNXM162760;MNXM810		m02343r
 MAM01675r	MAM01675	dsmsterol	C01802	HMDB0002719	CHEBI:17737	439577	LMST01010016		HC00847	dsmsterol	MNXM162959;MNXM695		m01675r
 MAM01189r	MAM01189	ddsmsterol	C05107	HMDB0003896	CHEBI:27910	440558	LMST01010121	CE2321	HC01373	ddsmsterol	MNXM162832;MNXM941		m01189r
-MAM00348n	MAM00348	13_cis_oretn								13_cis_oretn	MNXM146866		m00348n
 MAM00350n	MAM00350	13_cis_retn	D00348	HMDB0006219	CHEBI:6067	5282379	LMPR01090021			13_cis_retn	MNXM521;MNXM58377		m00350n
 MAM01006n	MAM01006	hretn	C16677	HMDB0006254	CHEBI:63795	6438629				hretn	MNXM8133		m01006n
 MAM03758c	MAM03758	melanin								melanin	MNXM92454		melanin_c
-MAM01026n	MAM01026	oretn				104857		CE5654		CE5654;oretn	MNXM37697;MNXM6902		m01026n
+MAM01026n	MAM01026	oretn				104857		CE5654		CE5654;oretn			m01026n;MAM00348
 MAM03395l	MAM03395	Ser_Thr								Ser_Thr	MNXM147296		Ser_Thr_l
 MAM01706x	MAM01706	dmpp	C00235	HMDB0001120	CHEBI:16057	647	LMPR01010001		HC00213	dmpp	MNXM132		m01706p
 MAM01953x	MAM01953	grdp	C00341		CHEBI:17211	445995			HC00288	grdp	MNXM100		m01953p

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -4627,7 +4627,6 @@ MAR08699		RADH4				RADH4	MNXR103415	HMR_8699	RCR13920		0			HMR_8699
 MAR08700	R08392	RAHY				RAHY	MNXR103421	HMR_8700	RCR13921		0			HMR_8700
 MAR08702		RAI2				RAI2	MNXR103423	HMR_8702	RCR10991		0			HMR_8702
 MAR08703		ORETNF				ORETNF	MNXR102210	HMR_8703	RCR10992		0			HMR_8703
-MAR08704		RAI4				RAI4	MNXR103425	HMR_8704	RCR13922		0			HMR_8704
 MAR08706		ORETNF2				ORETNF2	MNXR102211	HMR_8706	RCR13923		0			HMR_8706
 MAR08709	R08380	RDH3a				RDH3a	MNXR96890	HMR_8709	RCR13924		0	RHEA:54915	RHEA:54912	HMR_8709
 MAR08710		RDH4				RDH4	MNXR103443	HMR_8710	RCR13925		0	RHEA:42059	RHEA:42056	HMR_8710
@@ -8289,7 +8288,6 @@ MAR01560		O16G1e				O16G1e	MNXR102083				0			O16G1e
 MAR01561		OCCOAtx				OCCOAtx	MNXR102138				0			OCCOAtx
 MAR01562		ODECOAtx				ODECOAtx	MNXR102156				0			ODECOAtx
 MAR01563		ORETNtn				ORETNtn	MNXR102214				0			ORETNtn
-MAR01564		ORETNtn2				ORETNtn2	MNXR102215				0			ORETNtn2
 MAR01566		OXAtp				OXAtp	MNXR102238				0			OXAtp
 MAR01567		P45027A15m				P45027A15m	MNXR102269				0			P45027A15m
 MAR01569		P45039A1r				P45039A1r	MNXR102283				0			P45039A1r