Ecoli 0.2.0

.deprecated/deprecated_complete_collection.yml

@@ -0,0 +1,75 @@
+!!omap
+- metaData:
+    id: "Ecoli-GEM"
+    name: "The Consensus Genome-Scale Metabolic Model of Escherichia coli"
+    date: "2025-06-16"
+    version: ""
+    github: "https://github.com/SysBioChalmers/Ecoli-GEM"
+- metabolites:
+- reactions:
+  - !!omap
+    - id: GLYCK
+    - name: Glycerate kinase
+    - metabolites: !!omap
+      - 3pg_c: 1.0
+      - adp_c: 1.0
+      - atp_c: -1.0
+      - glyc__R_c: -1.0
+      - h_c: 1.0
+    - lower_bound: 0.0
+    - upper_bound: 1000.0
+    - gene_reaction_rule: b0514
+    - subsystem: Glyoxylate Metabolism
+    - annotation: !!omap
+      - bigg.reaction: GLYCK
+      - biocyc: META:GLY3KIN-RXN
+      - ec-code: 2.7.1.31
+      - kegg.reaction: R01514
+      - metanetx.reaction: MNXR100328
+      - reactome.reaction:
+        - R-MMU-6799495
+        - R-TGU-6799495
+        - R-DME-6799495
+        - R-GGA-6799495
+        - R-RNO-6799495
+        - R-XTR-6799495
+        - R-DRE-6799495
+        - R-HSA-6799495
+        - R-SSC-6799495
+        - R-BTA-6799495
+        - R-CEL-6799495
+        - R-CFA-6799495
+      - rhea:
+        - '23518'
+        - '23519'
+        - '23516'
+        - '23517'
+      - sabiork: '428'
+      - sbo: SBO:0000176
+      - seed.reaction: rxn01102
+  - !!omap
+    - id: XYLI2
+    - name: Xylose isomerase
+    - metabolites: !!omap
+      - fru_c: 1.0
+      - glc__D_c: -1.0
+    - lower_bound: -1000.0
+    - upper_bound: 1000.0
+    - gene_reaction_rule: b3565
+    - subsystem: Alternate Carbon Metabolism
+    - annotation: !!omap
+      - bigg.reaction: XYLI2
+      - biocyc: META:GLUCISOM-RXN
+      - ec-code: 5.3.1.5
+      - kegg.reaction: R00307
+      - metanetx.reaction: MNXR105254
+      - rhea:
+        - '28546'
+        - '28547'
+        - '28549'
+        - '28548'
+      - sabiork: '800'
+      - sbo: SBO:0000176
+      - seed.reaction: rxn00223
+- genes:
+- compartments:

code/curations/curation_remove_XYLI2.py

@@ -0,0 +1,48 @@
+import cobra
+from rebuild_groups import rebuild_groups_from_subsystems
+
+# Load and rebuild model
+model_path = 'path_to_repository/Ecoli-GEM/model/Ecoli-GEM.yml'
+model = cobra.io.load_yaml_model(model_path)
+rebuild_groups_from_subsystems(model)
+
+# Metabolites of XYLI2
+metabolites = [met.id for met in model.reactions.XYLI2.metabolites]
+
+# remove XYLI2
+print(model.reactions.XYLI2.reaction)
+print(model.reactions.XYLI1.reaction)
+model.remove_reactions(['XYLI2'])
+
+# Check other reactions for XYLI2 metabolites
+for met_id in metabolites:
+    met = model.metabolites.get_by_id(met_id)
+    print(f"\nMetabolite: {met.id} ({met.name})")
+    for rxn in met.reactions:
+        print(f" - {rxn.id}: {rxn.reaction}")
+
+def orphan_check(met_id):
+    met = model.metabolites.get_by_id(met_id)
+    producing = [r for r in met.reactions if met in r.products]
+    consuming = [r for r in met.reactions if met in r.reactants]
+    print(f"\n{met_id} -> Produced by: {len(producing)} reactions, Consumed by: {len(consuming)} reactions")
+
+for met_id in metabolites:
+    orphan_check(met_id)
+# Metabolite results
+# fru_c -> Produced by: 2 reactions, Consumed by: 1 reactions
+# glc__D_c -> Produced by: 19 reactions, Consumed by: 2 reactions
+# Conclusion: No dead-end reactions produced, keep all metabolites
+
+
+# XYLI1 annotation
+print(model.reactions.XYLI1.reaction)
+print(model.reactions.XYLI1.annotation)
+# Was MNXR105253
+model.reactions.XYLI1.annotation["metanetx.reaction"] = "MNXR146751"
+
+# Save model
+output_path='path_to_output_dir/Ecoli-GEM.yml'
+cobra.io.save_yaml_model(model, output_path, sort='True')
+
+

code/curations/curations_Bernstein_2023.py

@@ -0,0 +1,17 @@
+import cobra
+from rebuild_groups import rebuild_groups_from_subsystems
+
+# Load and rebuild model
+model_path = 'path_to_repository/Ecoli-GEM/model/Ecoli-GEM.yml'
+model = cobra.io.load_yaml_model(model_path)
+rebuild_groups_from_subsystems(model)
+
+#GHMT2r irreversible
+print(model.reactions.GHMT2r.bounds)
+model.reactions.GHMT2r.lower_bound = 0
+
+# Save model
+output_path='path_to_output_dir/Ecoli-GEM.yml'
+cobra.io.save_yaml_model(model, output_path, sort='True')
+
+

code/curations/curations_Carrao_2024.py

@@ -0,0 +1,69 @@
+import cobra
+from rebuild_groups import rebuild_groups_from_subsystems
+
+# Load and rebuild model
+model_path = 'path_to_repository/Ecoli-GEM/model/Ecoli-GEM.yml'
+model = cobra.io.load_yaml_model(model_path)
+rebuild_groups_from_subsystems(model)
+
+# pntAB (THD2pp)
+print(model.reactions.THD2pp.reaction)
+model.reactions.THD2pp.add_metabolites({"h_c": -1, "h_p": 1})
+print(model.reactions.THD2pp.reaction)
+
+# glxK (b0514) to GLYCK2 & remove GLYCK
+print(model.reactions.GLYCK2.gene_reaction_rule)
+model.reactions.GLYCK2.gene_reaction_rule = '(b3124 or b0514)'
+print(model.reactions.GLYCK2.gene_reaction_rule)
+
+# Metabolites of GLYCK
+metabolites = [met.id for met in model.reactions.GLYCK.metabolites]
+
+# remove GLYCK
+print(model.reactions.GLYCK.reaction)
+print(model.reactions.GLYCK2.reaction)
+model.remove_reactions(['GLYCK'])
+
+# Check other reactions for GLYCK metabolites
+for met_id in metabolites:
+    met = model.metabolites.get_by_id(met_id)
+    print(f"\nMetabolite: {met.id} ({met.name})")
+    for rxn in met.reactions:
+        print(f" - {rxn.id}: {rxn.reaction}")
+
+def orphan_check(met_id):
+    met = model.metabolites.get_by_id(met_id)
+    producing = [r for r in met.reactions if met in r.products]
+    consuming = [r for r in met.reactions if met in r.reactants]
+    print(f"\n{met_id} -> Produced by: {len(producing)} reactions, Consumed by: {len(consuming)} reactions")
+
+for met_id in metabolites:
+    orphan_check(met_id)
+
+# Metabolite results
+# 3pg_c -> Produced by: 2 reactions, Consumed by: 2 reactions
+# adp_c -> Produced by: 279 reactions, Consumed by: 8 reactions
+# atp_c -> Produced by: 4 reactions, Consumed by: 345 reactions
+# glyc__R_c -> Produced by: 5 reactions, Consumed by: 2 reactions
+# h_c -> Produced by: 786 reactions, Consumed by: 293 reactions
+# Conclusion: No dead-end reactions produced, keep all metabolites
+
+# HSDy 
+print(model.reactions.HSDy.bounds)
+print(model.reactions.HSDy.reversibility)
+print(model.reactions.HSDy.reaction)
+model.reactions.HSDy.lower_bound = 0
+print(model.reactions.HSDy.bounds)
+
+# SUCCt1pp
+print(model.reactions.SUCCt1pp.bounds)
+print(model.reactions.SUCCt1pp.reversibility)
+print(model.reactions.SUCCt1pp.reaction)
+model.reactions.SUCCt1pp.lower_bound = 0
+print(model.reactions.SUCCt1pp.bounds)
+
+# Save model
+output_path='path_to_output_dir/Ecoli-GEM.yml'
+cobra.io.save_yaml_model(model, output_path, sort='True')
+
+

code/curations/curations_Mao_2022.py

@@ -0,0 +1,67 @@
+import cobra
+from rebuild_groups import rebuild_groups_from_subsystems
+
+# Load and rebuild model
+model_path = 'path_to_repository/Ecoli-GEM/model/Ecoli-GEM.yml'
+model = cobra.io.load_yaml_model(model_path)
+rebuild_groups_from_subsystems(model)
+
+print(model.reactions.FMNRx2.gene_reaction_rule)
+# From b3844 or b0937 or (b2764 and b2763)
+model.reactions.FMNRx2.gene_reaction_rule = '(b0937 or b3844 or b2764)'
+
+print(model.reactions.ARGabcpp.gene_reaction_rule)
+# From (b2308 and b2306 and b2310 and b2307) or (b0864 and b0860 and b0863 and b0862 and b0861)
+model.reactions.ARGabcpp.gene_reaction_rule = '( b2310 and b2308 and b2306 and b2307 ) or ( b0862 and b0860 and b0864 and b0861 ) or ( b0862 and b0864 and b0863 and b0861 )'
+
+print(model.reactions.ECAP1pp.gene_reaction_rule)
+# From b3785 and b3793
+model.reactions.ECAP1pp.gene_reaction_rule = '( b3785 and b3793 and b3792 )'
+
+print(model.reactions.ECAP2pp.gene_reaction_rule)
+# From b3785 and b3793
+model.reactions.ECAP2pp.gene_reaction_rule = '( b3785 and b3793 and b3792 )'
+
+print(model.reactions.ECAP3pp.gene_reaction_rule)
+# From b3785 and b3793
+model.reactions.ECAP3pp.gene_reaction_rule = '( b3785 and b3793 and b3792 )'
+
+print(model.reactions.FADRx2.gene_reaction_rule)
+# From b2764 and b2763
+model.reactions.FADRx2.gene_reaction_rule = '( b2764 )'
+
+print(model.reactions.BWCOGDS1.gene_reaction_rule)
+# From (b3857 and b3856) or b3857
+model.reactions.BWCOGDS1.gene_reaction_rule = '( b3857 )'
+
+print(model.reactions.BWCOGDS2.gene_reaction_rule)
+# From (b3857 and b3856) or b3857
+model.reactions.BWCOGDS2.gene_reaction_rule = '( b3857 )'
+
+print(model.reactions.THZPSN3.gene_reaction_rule)
+# From b0423 and b3990 and b2530 and b3992 and b4407
+model.reactions.THZPSN3.gene_reaction_rule = '( b3992 and b3990 and b0423 and b2530 and b4407 and b3991 )'
+
+print(model.reactions.BMOGDS1.gene_reaction_rule)
+# From b3857 or (b3857 and b3856)
+model.reactions.BMOGDS1.gene_reaction_rule = '( b3857 )'
+
+print(model.reactions.BMOGDS2.gene_reaction_rule)
+# From (b3857 and b3856) or b3857
+model.reactions.BMOGDS2.gene_reaction_rule = '( b3857 )'
+
+print(model.reactions.MOGDS.gene_reaction_rule)
+# From (b3857 and b3856) or b3857
+model.reactions.MOGDS.gene_reaction_rule = '( b3857 )'
+
+print(model.reactions.get_by_id('3NTD4pp').gene_reaction_rule)
+# From b4213 or b0383 or b0383
+model.reactions.get_by_id('3NTD4pp').gene_reaction_rule = '( b0383 or b4213 or b2744 )'
+
+print(model.reactions.GLUDy.gene_reaction_rule)
+# From b1761 or (b3213 and b3212)
+model.reactions.GLUDy.gene_reaction_rule = '( b1761 )'
+
+# Save model
+output_path='path_to_output_dir/Ecoli-GEM.yml'
+cobra.io.save_yaml_model(model, output_path, sort='True')

data/testResults/macaw_results.csv

@@ -623,7 +623,7 @@ CYSItpp,cysi__L_c --> cysi__L_p,cysi__L_c;cysi__L_p,ok,ok,ok,N/A
 CYSS,acser_c + h2s_c --> ac_c + cys__L_c + h_c,ok,ok,ok,ok,N/A
 CYSSADS,3sala_c + 2.0 h_c --> ala__L_c + so2_c,3sala_c;so2_c,ok,ok,ok,N/A
 CYSTA,akg_c + cys__L_c --> glu__L_c + mercppyr_c,mercppyr_c,ok,ok,ok,N/A
-CYSTL,cyst__L_c + h2o_c --> hcys__L_c + nh4_c + pyr_c,ok,ok,ok,ok,N/A
+CYSTL,cyst__L_c + h2o_c --> hcys__L_c + nh4_c + pyr_c,cyst__L_c,ok,ok,ok,N/A
 CYSabc2pp,atp_c + cys__L_c + h2o_c --> adp_c + cys__L_p + h_c + pi_c,ok,ok,ok,CYSabcpp,N/A
 CYSabcpp,atp_c + cys__L_p + h2o_c --> adp_c + cys__L_c + h_c + pi_c,ok,ok,ok,CYSabc2pp,N/A
 CYStex,cys__L_e <=> cys__L_p,only when going forwards,ok,ok,ok,N/A
@@ -1037,7 +1037,7 @@ EX_hdca_e,hdca_e --> ,hdca_e,ok,ok,ok,N/A
 EX_hdcea_e,hdcea_e --> ,hdcea_e,ok,ok,ok,N/A
 EX_hg2_e,hg2_e --> ,hg2_e,ok,ok,ok,N/A
 EX_his__L_e,his__L_e --> ,ok,ok,ok,ok,N/A
-EX_hom__L_e,hom__L_e --> ,ok,ok,ok,ok,N/A
+EX_hom__L_e,hom__L_e --> ,hom__L_e,ok,ok,ok,N/A
 EX_hxa_e,hxa_e --> ,ok,ok,ok,ok,N/A
 EX_hxan_e,hxan_e --> ,ok,ok,ok,ok,N/A
 EX_idon__L_e,idon__L_e --> ,ok,ok,ok,ok,N/A
@@ -1404,7 +1404,7 @@ GGGABAH,gg4abut_c + h2o_c --> 4abut_c + glu__L_c,ok,ok,ok,ok,N/A
 GGPTRCO,ggptrc_c + h2o_c + o2_c --> ggbutal_c + h2o2_c + nh4_c,ok,ok,ok,ok,N/A
 GGPTRCS,atp_c + glu__L_c + ptrc_c --> adp_c + ggptrc_c + h_c + pi_c,ok,ok,ok,ok,N/A
 GHBDHx,h_c + nadh_c + sucsal_c <=> ghb_c + nad_c,ghb_c,ok,ok,ok,N/A
-GHMT2r,ser__L_c + thf_c <=> gly_c + h2o_c + mlthf_c,ok,ok,ok,ok,N/A
+GHMT2r,ser__L_c + thf_c --> gly_c + h2o_c + mlthf_c,ok,ok,ok,ok,N/A
 GK1,atp_c + gmp_c <=> adp_c + gdp_c,ok,ok,ok,ok,N/A
 GLBRAN2,glycogen_c --> bglycogen_c,ok,ok,GLDBRAN2,GLDBRAN2,N/A
 GLCATr,accoa_c + glc__D_c <=> acglc__D_c + coa_c,acglc__D_c,ok,ok,ok,N/A
@@ -1467,7 +1467,6 @@ GLYC3Ptex,glyc3p_e <=> glyc3p_p,only when going forwards,ok,ok,ok,N/A
 GLYCAt2rpp,glyc__R_p + h_p <=> glyc__R_c + h_c,only when going forwards,ok,ok,ok,N/A
 GLYCAtex,glyc__R_e <=> glyc__R_p,only when going forwards,ok,ok,ok,N/A
 GLYCDx,glyc_c + nad_c --> dha_c + h_c + nadh_c,ok,ok,ok,ok,N/A
-GLYCK,atp_c + glyc__R_c --> 3pg_c + adp_c + h_c,ok,ok,ok,ok,N/A
 GLYCK2,atp_c + glyc__R_c --> 2pg_c + adp_c + h_c,ok,ok,ok,ok,N/A
 GLYCL,gly_c + nad_c + thf_c --> co2_c + mlthf_c + nadh_c + nh4_c,ok,ok,ok,ok,N/A
 GLYCLTDx,glx_c + h_c + nadh_c --> glyclt_c + nad_c,ok,ok,ok,ok,N/A
@@ -1590,8 +1589,8 @@ HKNDDH,h2o_c + hkndd_c --> h_c + op4en_c + succ_c,hkndd_c;op4en_c,ok,ok,ok,N/A
 HKNTDH,h2o_c + hkntd_c --> fum_c + h_c + op4en_c,hkntd_c;op4en_c,ok,ok,ok,N/A
 HMBS,h2o_c + 4.0 ppbng_c --> hmbil_c + 4.0 nh4_c,ok,ok,ok,ok,N/A
 HMPK1,4ahmmp_c + atp_c --> 4ampm_c + adp_c + h_c,4ahmmp_c,ok,ok,ok,N/A
-HOMt2pp,h_p + hom__L_c --> h_c + hom__L_p,ok,ok,ok,ok,N/A
-HOMtex,hom__L_e <=> hom__L_p,only when going forwards,ok,ok,ok,N/A
+HOMt2pp,h_p + hom__L_c --> h_c + hom__L_p,hom__L_c;hom__L_p,ok,ok,ok,N/A
+HOMtex,hom__L_e <=> hom__L_p,hom__L_e;hom__L_p,ok,ok,ok,N/A
 HOPNTAL,4h2opntn_c --> acald_c + pyr_c,4h2opntn_c,ok,ok,ok,N/A
 HPACOAT,34dphacoa_c + h2o_c --> 34dhpha_c + coa_c + h_c,34dhpha_c;34dphacoa_c,ok,ok,ok,N/A
 HPPK2,6hmhpt_c + atp_c --> 6hmhptpp_c + amp_c + h_c,ok,ok,ok,ok,N/A
@@ -1602,9 +1601,9 @@ HPYRI,hpyr_c <=> 2h3oppan_c,ok,ok,ok,ok,N/A
 HPYRP,3php_c + h2o_c --> hpyr_c + pi_c,ok,ok,ok,ok,N/A
 HPYRRx,h_c + hpyr_c + nadh_c --> glyc__R_c + nad_c,ok,ok,ok,ok,N/A
 HPYRRy,h_c + hpyr_c + nadph_c --> glyc__R_c + nadp_c,ok,ok,ok,ok,N/A
-HSDy,hom__L_c + nadp_c <=> aspsa_c + h_c + nadph_c,only when going forwards,ok,ok,ok,N/A
-HSK,atp_c + hom__L_c --> adp_c + h_c + phom_c,ok,ok,ok,ok,N/A
-HSST,hom__L_c + succoa_c --> coa_c + suchms_c,ok,ok,ok,ok,N/A
+HSDy,hom__L_c + nadp_c --> aspsa_c + h_c + nadph_c,hom__L_c,ok,ok,ok,N/A
+HSK,atp_c + hom__L_c --> adp_c + h_c + phom_c,hom__L_c;phom_c,ok,ok,ok,N/A
+HSST,hom__L_c + succoa_c --> coa_c + suchms_c,hom__L_c;suchms_c,ok,ok,ok,N/A
 HSTPT,glu__L_c + imacp_c --> akg_c + hisp_c,ok,ok,ok,ok,N/A
 HXAND,h2o_c + hxan_c + nad_c --> h_c + nadh_c + xan_c,ok,ok,ok,ok,N/A
 HXAtex,hxa_e <=> hxa_p,only when going forwards,ok,ok,ok,N/A
@@ -2473,7 +2472,7 @@ SHCHF,fe2_c + scl_c --> 3.0 h_c + sheme_c,ok,ok,ok,ok,N/A
 SHGO,S2hglut_c + o2_c --> akg_c + h2o2_c,ok,ok,ok,ok,N/A
 SHK3Dr,3dhsk_c + h_c + nadph_c <=> nadp_c + skm_c,only when going backwards,ok,ok,ok,N/A
 SHKK,atp_c + skm_c --> adp_c + h_c + skm5p_c,ok,ok,ok,ok,N/A
-SHSL1,cys__L_c + suchms_c --> cyst__L_c + h_c + succ_c,ok,ok,ok,ok,N/A
+SHSL1,cys__L_c + suchms_c --> cyst__L_c + h_c + succ_c,cyst__L_c;suchms_c,ok,ok,ok,N/A
 SKMt2pp,h_p + skm_p --> h_c + skm_c,skm_p,ok,ok,ok,N/A
 SKMtex,skm_e <=> skm_p,skm_e;skm_p,ok,ok,ok,N/A
 SLNTabcpp,atp_c + h2o_c + slnt_p --> adp_c + h_c + pi_c + slnt_c,slnt_c;slnt_p,ok,ok,ok,N/A
@@ -2501,7 +2500,7 @@ SSALy,h2o_c + nadp_c + sucsal_c --> 2.0 h_c + nadph_c + succ_c,ok,ok,ok,ok,N/A
 SUCASPtpp,asp__L_p + succ_c <=> asp__L_c + succ_p,ok,ok,ok,ok,N/A
 SUCBZL,atp_c + coa_c + sucbz_c --> amp_c + ppi_c + sbzcoa_c,ok,ok,ok,ok,N/A
 SUCBZS,2shchc_c --> h2o_c + sucbz_c,ok,ok,ok,ok,N/A
-SUCCt1pp,succ_p <=> succ_c,ok,ok,ok,ok,N/A
+SUCCt1pp,succ_p --> succ_c,ok,ok,ok,ok,N/A
 SUCCt2_2pp,2.0 h_p + succ_p --> 2.0 h_c + succ_c,ok,ok,ok,SUCCt2_3pp,N/A
 SUCCt2_3pp,3.0 h_p + succ_p --> 3.0 h_c + succ_c,ok,ok,ok,SUCCt2_2pp,N/A
 SUCCtex,succ_e <=> succ_p,only when going forwards,ok,ok,ok,N/A
@@ -2539,7 +2538,7 @@ TDSR1,dsbcox_p + dsbdrd_c --> dsbcrd_p + dsbdox_c,dsbcox_p;dsbcrd_p;dsbdox_c;dsb
 TDSR2,dsbdrd_c + dsbgox_p --> dsbdox_c + dsbgrd_p,dsbdox_c;dsbdrd_c;dsbgox_p;dsbgrd_p,ok,ok,ok,N/A
 TEO2M,amet_c + teo2_c --> ahcys_c + mteo2_c,mteo2_c;teo2_c,ok,ok,ok,N/A
 TGBPA,tagdp__D_c <=> dhap_c + g3p_c,tagdp__D_c,ok,ok,ok,N/A
-THD2pp,2.0 h_p + nadh_c + nadp_c --> 2.0 h_c + nad_c + nadph_c,ok,ok,ok,ok,N/A
+THD2pp,h_p + nadh_c + nadp_c --> h_c + nad_c + nadph_c,ok,ok,ok,ok,N/A
 THDPS,h2o_c + succoa_c + thdp_c --> coa_c + sl2a6o_c,ok,ok,ok,ok,N/A
 THFAT,h2o_c + methf_c --> 5fthf_c + h_c,ok,ok,FOMETRi,FOMETRi,N/A
 THIORDXi,h2o2_c + trdrd_c --> 2.0 h2o_c + trdox_c,ok,ok,ok,ok,N/A
@@ -2553,7 +2552,7 @@ THRA2,athr__L_c --> acald_c + gly_c,ok,ok,ok,ok,N/A
 THRD,nad_c + thr__L_c --> 2aobut_c + h_c + nadh_c,ok,ok,ok,ok,N/A
 THRD_L,thr__L_c --> 2obut_c + nh4_c,ok,ok,ok,ok,N/A
 THRPtex,thrp_e <=> thrp_p,thrp_e;thrp_p,ok,ok,ok,N/A
-THRS,h2o_c + phom_c --> pi_c + thr__L_c,ok,ok,ok,ok,N/A
+THRS,h2o_c + phom_c --> pi_c + thr__L_c,phom_c,ok,ok,ok,N/A
 THRabcpp,atp_c + h2o_c + thr__L_p --> adp_c + h_c + pi_c + thr__L_c,ok,ok,ok,ok,N/A
 THRt2pp,h_p + thr__L_c --> h_c + thr__L_p,ok,ok,ok,THRt2rpp,N/A
 THRt2rpp,h_p + thr__L_p --> h_c + thr__L_c,ok,ok,ok,THRt2pp,N/A
@@ -2697,7 +2696,6 @@ XTSNt2rpp,h_p + xtsn_p <=> h_c + xtsn_c,only when going forwards,ok,ok,ok,N/A
 XTSNtex,xtsn_e <=> xtsn_p,only when going forwards,ok,ok,ok,N/A
 XYHDL,h2o_c + iprimv_c --> glc__D_c + xyl__D_c,iprimv_c;xyl__D_c,ok,ok,ok,N/A
 XYLI1,xyl__D_c <=> xylu__D_c,xyl__D_c;xylu__D_c,ok,ok,ok,N/A
-XYLI2,glc__D_c <=> fru_c,ok,ok,ok,ok,N/A
 XYLK,atp_c + xylu__D_c --> adp_c + h_c + xu5p__D_c,xylu__D_c,ok,ok,ok,N/A
 XYLK2,atp_c + xylu__L_c --> adp_c + h_c + xu5p__L_c,xu5p__L_c;xylu__L_c,ok,ok,ok,N/A
 XYLUt2pp,h_p + xylu__L_p --> h_c + xylu__L_c,xylu__L_c;xylu__L_p,ok,ok,ok,N/A

data/testResults/macaw_summary.md

@@ -1,7 +1,7 @@
 Starting dead-end test...
- - Found 682 dead-end metabolites.
- - Found 866 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
- - Found 246 reversible reactions that can only carry steady-state fluxes in a single direction due to dead-ends.
+ - Found 688 dead-end metabolites.
+ - Found 875 reactions incapable of sustaining steady-state fluxes in either direction due to these dead-ends.
+ - Found 244 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.
  - Found 77 reactions that were some type of duplicate: