SysBioChalmers · edkerk · Jul 11, 2026 · Jul 11, 2026
diff --git a/data/deprecatedIdentifiers/deprecatedMetabolites.tsv b/data/deprecatedIdentifiers/deprecatedMetabolites.tsv
@@ -2272,3 +2272,4 @@ 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
+MAM02768c	MAM02768	pcollglys	C16740						HC00904	pcollglys	MNXM149166	m02768c	m02768c
diff --git a/data/deprecatedIdentifiers/deprecatedReactions.tsv b/data/deprecatedIdentifiers/deprecatedReactions.tsv
@@ -401,3 +401,4 @@ 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
+MAR09553		PCLYSOX				PCLYSOX	MNXR102412	HMR_9553	RCR14815		0			HMR_9553
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 #1043** (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
@@ -727,9 +727,9 @@ MAR06979,MAM01306c + MAM02517c + MAM02630c --> MAM00789c + MAM01596c + MAM02943c
 MAR06980,MAM00789c + MAM02039c --> MAM01034c + MAM01986c,ok,ok,ok,ok,N/A
 MAR06981,MAM01034c + MAM02040c + MAM02552c --> MAM01922c + 2 MAM02039c + MAM02553c,ok,ok,ok,ok,N/A
 MAR06982,MAM01306c + MAM01922c + MAM02630c --> MAM01596c + MAM02348c + MAM02943c,ok,ok,ok,ok,N/A
-MAR06983,MAM00204c + MAM01306c + MAM02630c --> MAM01596c + MAM02767c + MAM02943c,MAM02767c,ok,ok,ok,N/A
-MAR06984,MAM02767c + MAM03107c --> MAM01036c + MAM02039c + MAM03106c,MAM01036c;MAM02767c,ok,ok,ok,N/A
-MAR06985,MAM01036c + MAM03108c --> MAM00232c + MAM02039c + MAM03106c,MAM00232c;MAM01036c,ok,ok,ok,N/A
+MAR06983,MAM00204c + MAM01306c + MAM02630c --> MAM01596c + MAM02767c + MAM02943c,ok,ok,ok,ok,N/A
+MAR06984,MAM02767c + MAM03107c --> MAM01036c + MAM02039c + MAM03106c,ok,ok,ok,ok,N/A
+MAR06985,MAM01036c + MAM03108c --> MAM00232c + MAM02039c + MAM03106c,ok,ok,ok,ok,N/A
 MAR08017,MAM01802x + MAM02040x + MAM02426x --> MAM01157x + MAM01803x + MAM02039x + MAM02578x,ok,ok,ok,ok,N/A
 MAR08018,MAM01157x --> MAM01663x + MAM02040x,ok,ok,ok,ok,N/A
 MAR08019,MAM01663x + MAM02039x + MAM02553x --> MAM02413x + MAM02552x,ok,ok,ok,ok,N/A
@@ -4989,7 +4989,6 @@ MAR09549,MAM02039c + MAM02700c + MAM02871c <=> MAM02699c + MAM02877c,MAM02699c;M
 MAR09550,2 MAM00188c + MAM02555c + 2 MAM02877c <=> 2 MAM00189c + MAM02039c + MAM02554c + 2 MAM02871c,MAM00188c;MAM00189c,ok,ok,ok,N/A
 MAR09551,MAM01838c + MAM02040c --> MAM01833c + MAM02039c + MAM02472c,MAM01838c;MAM02472c,ok,ok,ok,N/A
 MAR09552,MAM01710c + MAM02040c --> MAM02039c + MAM02493c + MAM02751c,MAM01710c;MAM02493c,ok,ok,ok,N/A
-MAR09553,MAM01306c + MAM02630c + MAM02768c --> MAM01596c + MAM02767c + MAM02943c,MAM02767c;MAM02768c,ok,ok,ok,N/A
 MAR09801,MAM02034c + MAM02381c <=> MAM01948c + MAM03167c,only when going backwards,ok,ok,ok,N/A
 MAR09807,MAM02040c + MAM03167c --> MAM00631c + MAM02039c + MAM02578c + MAM02751c,ok,ok,ok,ok,N/A
 MAR09554,MAM00683c + 2 MAM02040c --> MAM00774c + 2 MAM02039c + 2 MAM10005c,MAM00683c;MAM00774c,ok,ok,ok,N/A
@@ -12876,3 +12875,5 @@ MAR20188,MAM01098m <=> MAM01098c,MAM01098c;MAM01098m,ok,ok,ok,N/A
 MAR20189,MAM01329c + 2 MAM01824m + 5 MAM02039m --> MAM01328c + 2 MAM01826m + 4 MAM02039i,MAM01328c;MAM01329c,ok,ok,ok,N/A
 MAR20190,MAM01329c + MAM02039c + MAM02553c --> MAM01328c + MAM02552c,MAM01328c;MAM01329c,ok,ok,ok,N/A
 MAR20191,MAM01371m + MAM01974m + MAM02578m --> MAM01285m + MAM01975m + MAM02751m,ok,ok,ok,ok,N/A
+MAR20192,MAM00232c --> MAM00232e,ok,ok,ok,ok,N/A
+MAR20193,MAM00232e <=> ,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 1380 dead-end metabolites.
+ - Found 1137 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
@@ -3064,6 +3064,13 @@
       - formula: "C19H34N3O13R2"
       - charge: 1
       - metFrom: "HMRdatabase"
+    - !!omap
+      - id: "MAM00232e"
+      - name: "1,2-D-glucosyl-5-D-(galactosyloxy)-L-lysine-procollagen"
+      - compartment: "e"
+      - formula: "C19H34N3O13R2"
+      - charge: 1
+      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM00233c"
       - name: "1,2-diacylglycerol-bile-PC pool"
@@ -33612,13 +33619,6 @@
       - formula: "C7H14N3O3R2"
       - charge: 1
       - metFrom: "HMRdatabase"
-    - !!omap
-      - id: "MAM02768c"
-      - name: "procollagen-L-lysine"
-      - compartment: "c"
-      - formula: "C7H14N3O2R2"
-      - charge: 1
-      - metFrom: "HMRdatabase"
     - !!omap
       - id: "MAM02769c"
       - name: "progesterone"
@@ -140067,22 +140067,6 @@
       - eccodes: "3.6.1.52"
       - subsystem: "Isolated"
       - confidence_score: 0
-    - !!omap
-      - id: "MAR09553"
-      - metabolites: !!omap
-          - MAM01306c: -1
-          - MAM01596c: 1
-          - MAM02630c: -1
-          - MAM02767c: 1
-          - MAM02768c: -1
-          - MAM02943c: 1
-      - lower_bound: 0
-      - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000083444 or ENSG00000106397 or ENSG00000152952"
-      - rxnFrom: "HMRdatabase"
-      - eccodes: "1.14.11.4"
-      - subsystem: "Isolated"
-      - confidence_score: 0
     - !!omap
       - id: "MAR09801"
       - name: "GTP:5-hydroxy-L-lysine O-phosphotransferase"
@@ -245971,6 +245955,25 @@
       - references: "PMID:11080211;PMID:1356223;PMID:14583610;PMID:16213501;PMID:7595668;PMID:8838581;PMID:9053810"
       - subsystem: "Alanine, aspartate and glutamate metabolism"
       - confidence_score: 0
+    - !!omap
+      - id: "MAR20192"
+      - name: "Transport of 1,2-D-glucosyl-5-D-(galactosyloxy)-L-lysine-procollagen (Cytosol to Extracellular)"
+      - metabolites: !!omap
+          - MAM00232c: -1
+          - MAM00232e: 1
+      - lower_bound: 0
+      - upper_bound: 1000
+      - subsystem: "Transport reactions"
+      - confidence_score: 0
+    - !!omap
+      - id: "MAR20193"
+      - name: "Exchange of 1,2-D-glucosyl-5-D-(galactosyloxy)-L-lysine-procollagen"
+      - metabolites: !!omap
+          - MAM00232e: -1
+      - lower_bound: -1000
+      - upper_bound: 1000
+      - subsystem: "Exchange/demand reactions"
+      - confidence_score: 0
 - genes:
     - !!omap
       - id: "ENSG00000000419"

diff --git a/model/metabolites.tsv b/model/metabolites.tsv
@@ -430,6 +430,7 @@ MAM00229c	MAM00229		C19591							M00229	MNXM9522	m00229c	m00229c
 MAM00230c	MAM00230					107838		CE2152		CE2152	MNXM32042	m00230c	m00230c
 MAM00231c	MAM00231							CE5629		CE5629	MNXM32113	m00231c	m00231c
 MAM00232c	MAM00232		C04759							M00232	MNXM91041	m00232c	m00232c
+MAM00232e	MAM00232		C04759								MNXM91041		
 MAM00233c	MAM00233		C00641		CHEBI:17815		LMGL02010000		HC02085	HC02085	MNXM59	m00233c	m00233c
 MAM00234e	MAM00234		C00641		CHEBI:17815		LMGL02010000			M00234	MNXM59	m00234s	m00234s
 MAM00235c	MAM00235		C00641		CHEBI:17815		LMGL02010000		HC02056	HC02056	MNXM59	m00235c	m00235c
@@ -4756,7 +4757,6 @@ MAM02764c	MAM02764		C03428		CHEBI:15442				HC01118	HC01118	MNXM591	m02764c	m0276
 MAM02765c	MAM02765	pd3	C07711	HMDB0006500		11199982				pd3	MNXM7697	m02765c	m02765c
 MAM02766x	MAM02766	prist		HMDB0000795	CHEBI:51340	123929	LMPR0104010022	CE0932		prist	MNXM3342	m02766p	m02766p
 MAM02767c	MAM02767		C01211		CHEBI:51807					M02767	MNXM5281	m02767c	m02767c
-MAM02768c	MAM02768	pcollglys	C16740						HC00904	pcollglys	MNXM149166	m02768c	m02768c
 MAM02769c	MAM02769	prgstrn	C00410	HMDB0001830	CHEBI:17026	5994	LMST02030135			prgstrn	MNXM162773;MNXM307	m02769c	m02769c
 MAM02769r	MAM02769	prgstrn	C00410	HMDB0001830	CHEBI:17026	5994	LMST02030135			prgstrn	MNXM162773;MNXM307	m02769r	m02769r
 MAM02769e	MAM02769	prgstrn	C00410	HMDB0001830	CHEBI:17026	5994	LMST02030135			prgstrn	MNXM162773;MNXM307	m02769s	m02769s

diff --git a/model/reactions.tsv b/model/reactions.tsv
@@ -4988,7 +4988,6 @@ MAR09549	R04481					HMR_9549	MNXR108915	HMR_9549	RCR14813		0		RHEA:36419	HMR_954
 MAR09550	R05182					HMR_9550	MNXR109379	HMR_9550	RCR14814		0		RHEA:23908	HMR_9550
 MAR09551	R05635					HMR_9551	MNXR109727	HMR_9551	RCR14150		0		RHEA:24420	HMR_9551
 MAR09552	R05777					HMR_9552	MNXR109829	HMR_9552	RCR14151		0			HMR_9552
-MAR09553		PCLYSOX				PCLYSOX	MNXR102412	HMR_9553	RCR14815		0			HMR_9553
 MAR09801	R03378					HMR_9801	MNXR100675	HMR_9801	RCR14816		0		RHEA:19049	HMR_9801
 MAR09807	R10270					HMR_9807	MNXR95619	HMR_9807	RCR14152		0		RHEA:34091	HMR_9807
 MAR09554	R05792					HMR_9554	MNXR109840	HMR_9554	RCR14817		0			HMR_9554
@@ -12876,3 +12875,5 @@ MAR20188											0
 MAR20189											0			
 MAR20190											0			
 MAR20191	R00253	GLNS	R00253C	r0077		GLNS	MNXR100024	HMR_3890	RCR10506		0		RHEA:16169	HMR_3890
+MAR20192											0			
+MAR20193											0