diff --git a/.deprecated/deprecated_complete_collection.yml b/.deprecated/deprecated_complete_collection.yml
new file mode 100644
index 0000000..c9476b3
--- /dev/null
+++ b/.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:
diff --git a/code/curations/curation_remove_XYLI2.py b/code/curations/curation_remove_XYLI2.py
new file mode 100644
index 0000000..6b660d4
--- /dev/null
+++ b/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')
+
+
diff --git a/code/curations/curations_Bernstein_2023.py b/code/curations/curations_Bernstein_2023.py
new file mode 100644
index 0000000..306c14a
--- /dev/null
+++ b/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')
+
+
diff --git a/code/curations/curations_Carrao_2024.py b/code/curations/curations_Carrao_2024.py
new file mode 100644
index 0000000..0c82d7e
--- /dev/null
+++ b/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')
+
+
diff --git a/code/curations/curations_Mao_2022.py b/code/curations/curations_Mao_2022.py
new file mode 100644
index 0000000..e542f92
--- /dev/null
+++ b/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')
diff --git a/data/testResults/macaw_results.csv b/data/testResults/macaw_results.csv
index af26c9e..02486c1 100644
--- a/data/testResults/macaw_results.csv
+++ b/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
diff --git a/data/testResults/macaw_summary.md b/data/testResults/macaw_summary.md
index 6b05e3b..e575b3f 100644
--- a/data/testResults/macaw_summary.md
+++ b/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:
diff --git a/model/Ecoli-GEM.yml b/model/Ecoli-GEM.yml
index b54d859..76cae28 100644
--- a/model/Ecoli-GEM.yml
+++ b/model/Ecoli-GEM.yml
@@ -2,7 +2,7 @@
 - metaData:
     id: "Ecoli-GEM"
     name: "The Consensus Genome-Scale Metabolic Model of Escherichia coli"
-    date: "2025-05-15"
+    date: "2025-06-11"
     version: ""
     github: "https://github.com/SysBioChalmers/Ecoli-GEM"
 - metabolites:
@@ -319,8 +319,7 @@
         - CHEBI:14902
         - CHEBI:26286
         - CHEBI:16109
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/7987e84d-4979-49a1-974e-6d9a36411041
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/7987e84d-4979-49a1-974e-6d9a36411041
       - kegg.compound: C02457
       - metanetx.chemical: MNXM2861
       - sabiork: '2417'
@@ -1947,8 +1946,7 @@
         - CHEBI:21210
         - CHEBI:37012
         - CHEBI:58671
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/a5f22d9e-2c03-4186-94c9-b4a32eb48adb
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/a5f22d9e-2c03-4186-94c9-b4a32eb48adb
       - kegg.compound: C11822
       - metanetx.chemical: MNXM2124
       - sbo: SBO:0000247
@@ -2854,8 +2852,7 @@
       - chebi:
         - CHEBI:63252
         - CHEBI:63251
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3dfebe6c-c2b9-490b-8a0b-a10c16c4700f
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3dfebe6c-c2b9-490b-8a0b-a10c16c4700f
       - kegg.compound: C19975
       - metanetx.chemical: MNXM2851
       - sbo: SBO:0000247
@@ -3126,8 +3123,7 @@
         - CHEBI:11727
         - CHEBI:42422
         - CHEBI:1431
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/f2e806ef-76ea-4ddf-bf89-db7737caa79b
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/f2e806ef-76ea-4ddf-bf89-db7737caa79b
       - hmdb: HMDB00707
       - kegg.compound: C01179
       - metanetx.chemical: MNXM153
@@ -3524,8 +3520,7 @@
         - CHEBI:71038
         - CHEBI:34002
         - CHEBI:70990
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/5bf44b24-e859-4cb6-9efd-d350969bc5f5
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/5bf44b24-e859-4cb6-9efd-d350969bc5f5
       - hmdb:
         - HMDB62352
         - HMDB12475
@@ -3552,8 +3547,7 @@
         - CHEBI:11048
         - CHEBI:39978
         - CHEBI:57316
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/52913599-1749-4913-8cc4-b6c15d72ad5e
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/52913599-1749-4913-8cc4-b6c15d72ad5e
       - hmdb: HMDB62259
       - kegg.compound: C01144
       - lipidmaps: LMFA07050153
@@ -3950,8 +3944,7 @@
         - CHEBI:20071
         - CHEBI:33404
         - CHEBI:16510
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/bd10562a-7c1b-4ef8-a422-80f89844ef72
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/bd10562a-7c1b-4ef8-a422-80f89844ef72
       - hmdb: HMDB00700
       - kegg.compound: C01013
       - metanetx.chemical: MNXM872
@@ -3975,8 +3968,7 @@
         - CHEBI:20071
         - CHEBI:33404
         - CHEBI:16510
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/bd10562a-7c1b-4ef8-a422-80f89844ef72
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/bd10562a-7c1b-4ef8-a422-80f89844ef72
       - hmdb: HMDB00700
       - kegg.compound: C01013
       - metanetx.chemical: MNXM872
@@ -4000,8 +3992,7 @@
         - CHEBI:20071
         - CHEBI:33404
         - CHEBI:16510
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/bd10562a-7c1b-4ef8-a422-80f89844ef72
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/bd10562a-7c1b-4ef8-a422-80f89844ef72
       - hmdb: HMDB00700
       - kegg.compound: C01013
       - metanetx.chemical: MNXM872
@@ -4022,8 +4013,7 @@
         - CHEBI:17871
         - CHEBI:20078
         - CHEBI:11835
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/6458b515-6bde-43bf-a85a-1f4c966ad3e6
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/6458b515-6bde-43bf-a85a-1f4c966ad3e6
       - hmdb: HMDB03453
       - kegg.compound: C00969
       - metanetx.chemical: MNXM1526
@@ -4140,8 +4130,7 @@
         - CHEBI:20115
         - CHEBI:1584
         - CHEBI:16530
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/dee66401-4b7f-4203-8ee3-fa61f1f45f03
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/dee66401-4b7f-4203-8ee3-fa61f1f45f03
       - hmdb:
         - HMDB04260
         - HMDB00019
@@ -4528,8 +4517,7 @@
       - chebi:
         - CHEBI:63253
         - CHEBI:63255
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/6ee3d25d-86c2-4734-a684-74b0f8510d20
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/6ee3d25d-86c2-4734-a684-74b0f8510d20
       - kegg.compound: C19945
       - lipidmaps: LMFA07050236
       - metanetx.chemical: MNXM3852
@@ -4629,8 +4617,7 @@
         - CHEBI:1664
         - CHEBI:224037
         - CHEBI:11889
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/aa80c146-8c4c-4ce4-9276-0d8d56942369
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/aa80c146-8c4c-4ce4-9276-0d8d56942369
       - hmdb:
         - HMDB00996
         - HMDB60179
@@ -4703,8 +4690,7 @@
         - CHEBI:11961
         - CHEBI:59888
         - CHEBI:20318
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e90ecce1-b9b5-49f9-85d9-b83421426cbb
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e90ecce1-b9b5-49f9-85d9-b83421426cbb
       - hmdb: HMDB00112
       - kegg.compound: C00334
       - kegg.drug: D00058
@@ -4737,8 +4723,7 @@
         - CHEBI:11961
         - CHEBI:59888
         - CHEBI:20318
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e90ecce1-b9b5-49f9-85d9-b83421426cbb
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e90ecce1-b9b5-49f9-85d9-b83421426cbb
       - hmdb: HMDB00112
       - kegg.compound: C00334
       - kegg.drug: D00058
@@ -4771,8 +4756,7 @@
         - CHEBI:11961
         - CHEBI:59888
         - CHEBI:20318
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e90ecce1-b9b5-49f9-85d9-b83421426cbb
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e90ecce1-b9b5-49f9-85d9-b83421426cbb
       - hmdb: HMDB00112
       - kegg.compound: C00334
       - kegg.drug: D00058
@@ -4829,8 +4813,7 @@
         - CHEBI:20315
         - CHEBI:17836
         - CHEBI:1783
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a5ad09dc-a75c-4ad4-8917-a62ebefdc941
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a5ad09dc-a75c-4ad4-8917-a62ebefdc941
       - hmdb: HMDB01392
       - kegg.compound: C00568
       - kegg.drug: D02456
@@ -4901,8 +4884,7 @@
         - CHEBI:1781
         - CHEBI:16892
         - CHEBI:20312
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/05e806c1-5e9c-4cd7-b31a-1cff94880c8a
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/05e806c1-5e9c-4cd7-b31a-1cff94880c8a
       - kegg.compound: C01279
       - metanetx.chemical: MNXM874
       - sabiork: '5497'
@@ -4955,8 +4937,7 @@
         - CHEBI:44726
         - CHEBI:17847
         - CHEBI:11981
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b1f893aa-04c5-4a93-b65f-6b42cd0dc97f
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b1f893aa-04c5-4a93-b65f-6b42cd0dc97f
       - hmdb:
         - HMDB13762
         - HMDB01858
@@ -6169,8 +6150,7 @@
         - CHEBI:12764
         - CHEBI:57688
         - CHEBI:8956
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d4e9e4f7-3585-4e9c-92d7-3860ef127777
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d4e9e4f7-3585-4e9c-92d7-3860ef127777
       - hmdb:
         - HMDB01550
         - HMDB62625
@@ -6198,8 +6178,7 @@
         - CHEBI:42833
         - CHEBI:22486
         - CHEBI:13766
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/f730ed9b-d11c-482f-a9ba-ac22fc782cc2
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/f730ed9b-d11c-482f-a9ba-ac22fc782cc2
       - kegg.compound: C06735
       - metanetx.chemical: MNXM2212
       - sabiork: '2912'
@@ -6222,8 +6201,7 @@
         - CHEBI:11756
         - CHEBI:41333
         - CHEBI:57286
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e8a0c5c5-e9b1-4f85-94c1-d3d04866d6c9
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e8a0c5c5-e9b1-4f85-94c1-d3d04866d6c9
       - hmdb:
         - HMDB01484
         - HMDB11665
@@ -6254,8 +6232,7 @@
         - CHEBI:17906
         - CHEBI:13767
         - CHEBI:42849
-      - envipath: 
-          5882df9c-dae1-4d80-a40e-db4724271456/compound/c7d3904a-a2ab-4e04-8933-d57d61dca653
+      - envipath: 5882df9c-dae1-4d80-a40e-db4724271456/compound/c7d3904a-a2ab-4e04-8933-d57d61dca653
       - hmdb:
         - HMDB60177
         - HMDB02134
@@ -6615,8 +6592,7 @@
         - CHEBI:19414
         - CHEBI:21602
         - CHEBI:32578
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/685af208-3a2e-4b98-875d-0c9154d9272c
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/685af208-3a2e-4b98-875d-0c9154d9272c
       - kegg.compound: C06332
       - metanetx.chemical: MNXM1939
       - sbo: SBO:0000247
@@ -6637,8 +6613,7 @@
         - CHEBI:13712
         - CHEBI:2408
         - CHEBI:40470
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/57bd5e24-9d14-4b91-bc60-64c8ea6c2d11
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/57bd5e24-9d14-4b91-bc60-64c8ea6c2d11
       - hmdb: HMDB01206
       - kegg.compound: C00024
       - lipidmaps:
@@ -6668,8 +6643,7 @@
         - CHEBI:27957
         - CHEBI:5796
         - CHEBI:24666
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/090b3a12-aba4-4202-9b9c-f30232d329f0
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/090b3a12-aba4-4202-9b9c-f30232d329f0
       - hmdb: HMDB06961
       - kegg.compound: C05235
       - metanetx.chemical: MNXM1744
@@ -7375,8 +7349,7 @@
         - CHEBI:32805
         - CHEBI:23308
         - CHEBI:10482
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/643481e5-a35b-477e-8665-70f4dca66baa
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/643481e5-a35b-477e-8665-70f4dca66baa
       - hmdb:
         - HMDB00461
         - HMDB00072
@@ -8323,8 +8296,7 @@
         - CHEBI:10343
         - CHEBI:57966
         - CHEBI:41050
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/0352ab69-1208-420e-b7c9-87b5b436f4df
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/0352ab69-1208-420e-b7c9-87b5b436f4df
       - hmdb: HMDB00056
       - kegg.compound: C00099
       - kegg.drug: D07561
@@ -8352,8 +8324,7 @@
         - CHEBI:10343
         - CHEBI:57966
         - CHEBI:41050
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/0352ab69-1208-420e-b7c9-87b5b436f4df
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/0352ab69-1208-420e-b7c9-87b5b436f4df
       - hmdb: HMDB00056
       - kegg.compound: C00099
       - kegg.drug: D07561
@@ -8381,8 +8352,7 @@
         - CHEBI:10343
         - CHEBI:57966
         - CHEBI:41050
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/0352ab69-1208-420e-b7c9-87b5b436f4df
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/0352ab69-1208-420e-b7c9-87b5b436f4df
       - hmdb: HMDB00056
       - kegg.compound: C00099
       - kegg.drug: D07561
@@ -9273,8 +9243,7 @@
         - CHEBI:13841
         - CHEBI:22577
         - CHEBI:2757
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec511e59-d2cf-482d-ae9f-7f4dd74818c2
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ec511e59-d2cf-482d-ae9f-7f4dd74818c2
       - hmdb: HMDB01123
       - kegg.compound: C00108
       - metanetx.chemical: MNXM188
@@ -9431,8 +9400,7 @@
         - CHEBI:10963
         - CHEBI:19030
         - CHEBI:303
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/d0a37a0c-a6b5-45b9-b8cd-3d633776e4a3
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/d0a37a0c-a6b5-45b9-b8cd-3d633776e4a3
       - hmdb: HMDB12136
       - kegg.compound:
         - C05771
@@ -10110,8 +10078,7 @@
         - CHEBI:29243
         - CHEBI:29866
         - CHEBI:29242
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/42d95b9b-3aca-45eb-a99d-ef775cb20524
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/42d95b9b-3aca-45eb-a99d-ef775cb20524
       - hmdb: HMDB11620
       - kegg.compound: C06697
       - metanetx.chemical: MNXM658
@@ -10141,8 +10108,7 @@
         - CHEBI:29243
         - CHEBI:29866
         - CHEBI:29242
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/42d95b9b-3aca-45eb-a99d-ef775cb20524
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/42d95b9b-3aca-45eb-a99d-ef775cb20524
       - hmdb: HMDB11620
       - kegg.compound: C06697
       - metanetx.chemical: MNXM658
@@ -10172,8 +10138,7 @@
         - CHEBI:29243
         - CHEBI:29866
         - CHEBI:29242
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/42d95b9b-3aca-45eb-a99d-ef775cb20524
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/42d95b9b-3aca-45eb-a99d-ef775cb20524
       - hmdb: HMDB11620
       - kegg.compound: C06697
       - metanetx.chemical: MNXM658
@@ -10202,8 +10167,7 @@
         - CHEBI:2844
         - CHEBI:22629
         - CHEBI:18231
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/090d280e-0ebf-4fab-bb54-3a3933e7a5fe
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/090d280e-0ebf-4fab-bb54-3a3933e7a5fe
       - hmdb: HMDB12190
       - kegg.compound:
         - C01478
@@ -10239,8 +10203,7 @@
         - CHEBI:40853
         - CHEBI:29992
         - CHEBI:40900
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/4b0cdcb0-137a-4ddc-8e5c-2b55ea238c15
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/4b0cdcb0-137a-4ddc-8e5c-2b55ea238c15
       - hmdb:
         - HMDB62186
         - HMDB62501
@@ -10285,8 +10248,7 @@
         - CHEBI:40853
         - CHEBI:29992
         - CHEBI:40900
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/4b0cdcb0-137a-4ddc-8e5c-2b55ea238c15
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/4b0cdcb0-137a-4ddc-8e5c-2b55ea238c15
       - hmdb:
         - HMDB62186
         - HMDB62501
@@ -10331,8 +10293,7 @@
         - CHEBI:40853
         - CHEBI:29992
         - CHEBI:40900
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/4b0cdcb0-137a-4ddc-8e5c-2b55ea238c15
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/4b0cdcb0-137a-4ddc-8e5c-2b55ea238c15
       - hmdb:
         - HMDB62186
         - HMDB62501
@@ -10472,8 +10433,7 @@
         - CHEBI:13921
         - CHEBI:41612
         - CHEBI:58669
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c0e5f008-6d8b-4b94-a265-03d19ff197f4
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c0e5f008-6d8b-4b94-a265-03d19ff197f4
       - hmdb:
         - HMDB62466
         - HMDB02009
@@ -10582,8 +10542,7 @@
         - CHEBI:3233
         - CHEBI:15743
         - CHEBI:13923
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/242f8a4e-2a91-4c5f-a129-d044d115b969
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/242f8a4e-2a91-4c5f-a129-d044d115b969
       - hmdb: HMDB03543
       - kegg.compound: C01412
       - metanetx.chemical: MNXM1017
@@ -10606,8 +10565,7 @@
         - CHEBI:3235
         - CHEBI:15517
         - CHEBI:13926
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dcfe6e71-5e24-4086-91a3-076df362da44
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dcfe6e71-5e24-4086-91a3-076df362da44
       - hmdb: HMDB01088
       - kegg.compound: C00136
       - lipidmaps: LMFA07050292
@@ -11350,8 +11308,7 @@
         - CHEBI:60087
         - CHEBI:48690
         - CHEBI:60088
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/98ef2d5b-75f7-4313-90f9-30f649403e35
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/98ef2d5b-75f7-4313-90f9-30f649403e35
       - metanetx.chemical: MNXM1636
       - sbo: SBO:0000247
   - !!omap
@@ -11421,8 +11378,7 @@
         - CHEBI:49071
         - CHEBI:60108
         - CHEBI:61451
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/916b6989-0170-4531-998d-de0420436691
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/916b6989-0170-4531-998d-de0420436691
       - kegg.compound: C12622
       - metanetx.chemical: MNXM2161
       - sbo: SBO:0000247
@@ -12515,8 +12471,7 @@
         - CHEBI:15346
         - CHEBI:3771
         - CHEBI:13294
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/19310484-6aa5-4dcf-b1da-855a8c21ecfd
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/19310484-6aa5-4dcf-b1da-855a8c21ecfd
       - hmdb:
         - HMDB01423
         - HMDB62184
@@ -13464,8 +13419,7 @@
         - CHEBI:29195
         - CHEBI:23422
         - CHEBI:28024
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/20a1ab57-2ac5-44c6-8390-60706fcc3fa1
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/20a1ab57-2ac5-44c6-8390-60706fcc3fa1
       - hmdb: HMDB02078
       - kegg.compound: C01417
       - metanetx.chemical: MNXM1191
@@ -13488,8 +13442,7 @@
         - CHEBI:29195
         - CHEBI:23422
         - CHEBI:28024
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/20a1ab57-2ac5-44c6-8390-60706fcc3fa1
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/20a1ab57-2ac5-44c6-8390-60706fcc3fa1
       - hmdb: HMDB02078
       - kegg.compound: C01417
       - metanetx.chemical: MNXM1191
@@ -13512,8 +13465,7 @@
         - CHEBI:29195
         - CHEBI:23422
         - CHEBI:28024
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/20a1ab57-2ac5-44c6-8390-60706fcc3fa1
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/20a1ab57-2ac5-44c6-8390-60706fcc3fa1
       - hmdb: HMDB02078
       - kegg.compound: C01417
       - metanetx.chemical: MNXM1191
@@ -14593,8 +14545,7 @@
         - CHEBI:41874
         - CHEBI:14188
         - CHEBI:14501
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/74d61ac3-3daa-4b6c-b746-ada3812ec3c7
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/74d61ac3-3daa-4b6c-b746-ada3812ec3c7
       - hmdb: HMDB03571
       - kegg.compound: C01832
       - lipidmaps:
@@ -14737,8 +14688,7 @@
       - chebi:
         - CHEBI:71259
         - CHEBI:26634
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/827fc514-4527-4f8f-8df2-fe7ba01da727
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/827fc514-4527-4f8f-8df2-fe7ba01da727
       - kegg.compound: C18870
       - metanetx.chemical: MNXM7767
       - reactome.compound: '5357667'
@@ -14856,8 +14806,7 @@
         - CHEBI:16016
         - CHEBI:39809
         - CHEBI:5453
-      - envipath: 
-          4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/88a6ccc5-fd05-4708-9244-5bc7a155dbbf
+      - envipath: 4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/88a6ccc5-fd05-4708-9244-5bc7a155dbbf
       - hmdb: HMDB01882
       - kegg.compound: C00184
       - kegg.drug: D07841
@@ -14880,8 +14829,7 @@
         - CHEBI:16016
         - CHEBI:39809
         - CHEBI:5453
-      - envipath: 
-          4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/88a6ccc5-fd05-4708-9244-5bc7a155dbbf
+      - envipath: 4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/88a6ccc5-fd05-4708-9244-5bc7a155dbbf
       - hmdb: HMDB01882
       - kegg.compound: C00184
       - kegg.drug: D07841
@@ -14904,8 +14852,7 @@
         - CHEBI:16016
         - CHEBI:39809
         - CHEBI:5453
-      - envipath: 
-          4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/88a6ccc5-fd05-4708-9244-5bc7a155dbbf
+      - envipath: 4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/88a6ccc5-fd05-4708-9244-5bc7a155dbbf
       - hmdb: HMDB01882
       - kegg.compound: C00184
       - kegg.drug: D07841
@@ -14964,8 +14911,7 @@
         - CHEBI:58642
         - CHEBI:48681
         - CHEBI:32356
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ca1afb6b-2124-4ca0-9740-8c757c0ea104
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ca1afb6b-2124-4ca0-9740-8c757c0ea104
       - hmdb: HMDB32057
       - kegg.compound: C12623
       - metanetx.chemical: MNXM1130
@@ -15147,8 +15093,7 @@
         - CHEBI:1419
         - CHEBI:19919
         - CHEBI:11718
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/41182ed7-9bc7-4ca9-82dc-53a07e6cc91d
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/41182ed7-9bc7-4ca9-82dc-53a07e6cc91d
       - kegg.compound: C04044
       - metanetx.chemical: MNXM826
       - sabiork: '7038'
@@ -15557,8 +15502,7 @@
         - CHEBI:23800
         - CHEBI:14175
         - CHEBI:14168
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/26c081a5-2c2d-4e64-bd11-0d80376989ba
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/26c081a5-2c2d-4e64-bd11-0d80376989ba
       - hmdb: HMDB02303
       - kegg.compound: C00580
       - metanetx.chemical: MNXM444
@@ -15581,8 +15525,7 @@
         - CHEBI:23800
         - CHEBI:14175
         - CHEBI:14168
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/26c081a5-2c2d-4e64-bd11-0d80376989ba
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/26c081a5-2c2d-4e64-bd11-0d80376989ba
       - hmdb: HMDB02303
       - kegg.compound: C00580
       - metanetx.chemical: MNXM444
@@ -15605,8 +15548,7 @@
         - CHEBI:23800
         - CHEBI:14175
         - CHEBI:14168
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/26c081a5-2c2d-4e64-bd11-0d80376989ba
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/26c081a5-2c2d-4e64-bd11-0d80376989ba
       - hmdb: HMDB02303
       - kegg.compound: C00580
       - metanetx.chemical: MNXM444
@@ -15627,8 +15569,7 @@
         - CHEBI:4612
         - CHEBI:42138
         - CHEBI:28262
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/455cdb68-acf9-42fe-a3f8-420236744cc5
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/455cdb68-acf9-42fe-a3f8-420236744cc5
       - hmdb: HMDB02151
       - kegg.compound: C11143
       - kegg.drug: D01043
@@ -15649,8 +15590,7 @@
         - CHEBI:4612
         - CHEBI:42138
         - CHEBI:28262
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/455cdb68-acf9-42fe-a3f8-420236744cc5
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/455cdb68-acf9-42fe-a3f8-420236744cc5
       - hmdb: HMDB02151
       - kegg.compound: C11143
       - kegg.drug: D01043
@@ -15671,8 +15611,7 @@
         - CHEBI:4612
         - CHEBI:42138
         - CHEBI:28262
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/455cdb68-acf9-42fe-a3f8-420236744cc5
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/455cdb68-acf9-42fe-a3f8-420236744cc5
       - hmdb: HMDB02151
       - kegg.compound: C11143
       - kegg.drug: D01043
@@ -15724,8 +15663,7 @@
         - CHEBI:43686
         - CHEBI:18243
         - CHEBI:59905
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/47cc810c-1f1f-4351-82ca-b97abf5dc03c
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/47cc810c-1f1f-4351-82ca-b97abf5dc03c
       - hmdb: HMDB00073
       - kegg.compound: C03758
       - kegg.drug: D07870
@@ -15757,8 +15695,7 @@
         - CHEBI:43686
         - CHEBI:18243
         - CHEBI:59905
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/47cc810c-1f1f-4351-82ca-b97abf5dc03c
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/47cc810c-1f1f-4351-82ca-b97abf5dc03c
       - hmdb: HMDB00073
       - kegg.compound: C03758
       - kegg.drug: D07870
@@ -18653,8 +18590,7 @@
         - CHEBI:29806
         - CHEBI:22958
         - CHEBI:24122
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/709035ec-4868-4de8-9095-06428f6be14b
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/709035ec-4868-4de8-9095-06428f6be14b
       - hmdb: HMDB00134
       - kegg.compound: C00122
       - kegg.drug: D02308
@@ -18689,8 +18625,7 @@
         - CHEBI:29806
         - CHEBI:22958
         - CHEBI:24122
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/709035ec-4868-4de8-9095-06428f6be14b
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/709035ec-4868-4de8-9095-06428f6be14b
       - hmdb: HMDB00134
       - kegg.compound: C00122
       - kegg.drug: D02308
@@ -18725,8 +18660,7 @@
         - CHEBI:29806
         - CHEBI:22958
         - CHEBI:24122
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/709035ec-4868-4de8-9095-06428f6be14b
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/709035ec-4868-4de8-9095-06428f6be14b
       - hmdb: HMDB00134
       - kegg.compound: C00122
       - kegg.drug: D02308
@@ -20549,8 +20483,7 @@
         - CHEBI:386065
         - CHEBI:16724
         - CHEBI:20401
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a41e6b76-b462-49d4-ae42-391ef00bf98c
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a41e6b76-b462-49d4-ae42-391ef00bf98c
       - hmdb:
         - HMDB15507
         - HMDB00710
@@ -22798,8 +22731,7 @@
         - CHEBI:14372
         - CHEBI:24443
         - CHEBI:5563
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/b5208daa-3750-4745-b4ed-179fb9d4fcfd
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/b5208daa-3750-4745-b4ed-179fb9d4fcfd
       - hmdb: HMDB00132
       - kegg.compound: C00242
       - metanetx.chemical: MNXM259
@@ -22823,8 +22755,7 @@
         - CHEBI:14372
         - CHEBI:24443
         - CHEBI:5563
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/b5208daa-3750-4745-b4ed-179fb9d4fcfd
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/b5208daa-3750-4745-b4ed-179fb9d4fcfd
       - hmdb: HMDB00132
       - kegg.compound: C00242
       - metanetx.chemical: MNXM259
@@ -22848,8 +22779,7 @@
         - CHEBI:14372
         - CHEBI:24443
         - CHEBI:5563
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/b5208daa-3750-4745-b4ed-179fb9d4fcfd
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/b5208daa-3750-4745-b4ed-179fb9d4fcfd
       - hmdb: HMDB00132
       - kegg.compound: C00242
       - metanetx.chemical: MNXM259
@@ -23646,8 +23576,7 @@
         - CHEBI:24541
         - CHEBI:24550
         - CHEBI:29889
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc7314a1-8e9a-410f-be4f-f7d8bf32b1cb
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc7314a1-8e9a-410f-be4f-f7d8bf32b1cb
       - hmdb:
         - HMDB60083
         - HMDB00220
@@ -23690,8 +23619,7 @@
         - CHEBI:24541
         - CHEBI:24550
         - CHEBI:29889
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc7314a1-8e9a-410f-be4f-f7d8bf32b1cb
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc7314a1-8e9a-410f-be4f-f7d8bf32b1cb
       - hmdb:
         - HMDB60083
         - HMDB00220
@@ -23734,8 +23662,7 @@
         - CHEBI:24541
         - CHEBI:24550
         - CHEBI:29889
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc7314a1-8e9a-410f-be4f-f7d8bf32b1cb
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc7314a1-8e9a-410f-be4f-f7d8bf32b1cb
       - hmdb:
         - HMDB60083
         - HMDB00220
@@ -23902,8 +23829,7 @@
         - CHEBI:16793
         - CHEBI:49640
         - CHEBI:5714
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/79a26c21-7769-4377-9880-413b45e89afe
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/79a26c21-7769-4377-9880-413b45e89afe
       - hmdb: HMDB03625
       - kegg.compound: C00703
       - metanetx.chemical: MNXM1562
@@ -23925,8 +23851,7 @@
         - CHEBI:16793
         - CHEBI:49640
         - CHEBI:5714
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/79a26c21-7769-4377-9880-413b45e89afe
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/79a26c21-7769-4377-9880-413b45e89afe
       - hmdb: HMDB03625
       - kegg.compound: C00703
       - metanetx.chemical: MNXM1562
@@ -23948,8 +23873,7 @@
         - CHEBI:16793
         - CHEBI:49640
         - CHEBI:5714
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/79a26c21-7769-4377-9880-413b45e89afe
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/79a26c21-7769-4377-9880-413b45e89afe
       - hmdb: HMDB03625
       - kegg.compound: C00703
       - metanetx.chemical: MNXM1562
@@ -24191,8 +24115,7 @@
         - CHEBI:61449
         - CHEBI:66936
         - CHEBI:11589
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/29315147-9cf6-4642-ac32-ecd4eb00a7fe
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/29315147-9cf6-4642-ac32-ecd4eb00a7fe
       - kegg.compound: C04479
       - metanetx.chemical: MNXM1693
       - sabiork: '7342'
@@ -24209,8 +24132,7 @@
       - chebi:
         - CHEBI:61450
         - CHEBI:61467
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d982e35d-ed93-4304-b42e-a1933826f3c6
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d982e35d-ed93-4304-b42e-a1933826f3c6
       - kegg.compound: C12624
       - metanetx.chemical: MNXM2040
       - sbo: SBO:0000247
@@ -24267,8 +24189,7 @@
         - CHEBI:58758
         - CHEBI:40619
         - CHEBI:34963
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/fee99d5c-735f-4808-89ec-dbadb58f766c
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/fee99d5c-735f-4808-89ec-dbadb58f766c
       - hmdb: HMDB04662
       - kegg.compound: C14180
       - metanetx.chemical: MNXM1051
@@ -24463,8 +24384,7 @@
         - CHEBI:17120
         - CHEBI:5702
         - CHEBI:24569
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/e4df503e-0f40-4bad-8885-76774b301631
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/e4df503e-0f40-4bad-8885-76774b301631
       - hmdb:
         - HMDB00535
         - HMDB61883
@@ -24492,8 +24412,7 @@
         - CHEBI:17120
         - CHEBI:5702
         - CHEBI:24569
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/e4df503e-0f40-4bad-8885-76774b301631
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/e4df503e-0f40-4bad-8885-76774b301631
       - hmdb:
         - HMDB00535
         - HMDB61883
@@ -24521,8 +24440,7 @@
         - CHEBI:17120
         - CHEBI:5702
         - CHEBI:24569
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/e4df503e-0f40-4bad-8885-76774b301631
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/e4df503e-0f40-4bad-8885-76774b301631
       - hmdb:
         - HMDB00535
         - HMDB61883
@@ -25873,8 +25791,7 @@
         - CHEBI:340
         - CHEBI:17167
         - CHEBI:18683
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/40a73f79-ca1a-42bb-a386-b7c5f7d72f1d
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/40a73f79-ca1a-42bb-a386-b7c5f7d72f1d
       - hmdb:
         - HMDB06949
         - HMDB06458
@@ -26964,8 +26881,7 @@
         - CHEBI:18167
         - CHEBI:17306
         - CHEBI:25144
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/943ae27f-7875-4bcd-948d-1551ec9aa1ca
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/943ae27f-7875-4bcd-948d-1551ec9aa1ca
       - kegg.compound:
         - C00897
         - C00208
@@ -27004,8 +26920,7 @@
         - CHEBI:18167
         - CHEBI:17306
         - CHEBI:25144
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/943ae27f-7875-4bcd-948d-1551ec9aa1ca
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/943ae27f-7875-4bcd-948d-1551ec9aa1ca
       - kegg.compound:
         - C00897
         - C00208
@@ -27044,8 +26959,7 @@
         - CHEBI:18167
         - CHEBI:17306
         - CHEBI:25144
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/943ae27f-7875-4bcd-948d-1551ec9aa1ca
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/943ae27f-7875-4bcd-948d-1551ec9aa1ca
       - kegg.compound:
         - C00897
         - C00208
@@ -27211,8 +27125,7 @@
         - CHEBI:25146
         - CHEBI:43937
         - CHEBI:27931
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/7d7cf31a-30a5-4368-8802-9269424379b6
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/7d7cf31a-30a5-4368-8802-9269424379b6
       - hmdb: HMDB01262
       - kegg.compound: C01835
       - metanetx.chemical: MNXM468
@@ -27235,8 +27148,7 @@
         - CHEBI:25146
         - CHEBI:43937
         - CHEBI:27931
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/7d7cf31a-30a5-4368-8802-9269424379b6
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/7d7cf31a-30a5-4368-8802-9269424379b6
       - hmdb: HMDB01262
       - kegg.compound: C01835
       - metanetx.chemical: MNXM468
@@ -27259,8 +27171,7 @@
         - CHEBI:25146
         - CHEBI:43937
         - CHEBI:27931
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/7d7cf31a-30a5-4368-8802-9269424379b6
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/7d7cf31a-30a5-4368-8802-9269424379b6
       - hmdb: HMDB01262
       - kegg.compound: C01835
       - metanetx.chemical: MNXM468
@@ -27509,8 +27420,7 @@
         - CHEBI:21057
         - CHEBI:33930
         - CHEBI:12999
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c5f931e8-e7f7-4b73-bed6-48662796fe18
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c5f931e8-e7f7-4b73-bed6-48662796fe18
       - hmdb: HMDB00169
       - kegg.compound: C00159
       - metanetx.chemical: MNXM182
@@ -27540,8 +27450,7 @@
         - CHEBI:21057
         - CHEBI:33930
         - CHEBI:12999
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c5f931e8-e7f7-4b73-bed6-48662796fe18
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c5f931e8-e7f7-4b73-bed6-48662796fe18
       - hmdb: HMDB00169
       - kegg.compound: C00159
       - metanetx.chemical: MNXM182
@@ -27571,8 +27480,7 @@
         - CHEBI:21057
         - CHEBI:33930
         - CHEBI:12999
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c5f931e8-e7f7-4b73-bed6-48662796fe18
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c5f931e8-e7f7-4b73-bed6-48662796fe18
       - hmdb: HMDB00169
       - kegg.compound: C00159
       - metanetx.chemical: MNXM182
@@ -27855,8 +27763,7 @@
         - CHEBI:57678
         - CHEBI:11847
         - CHEBI:20104
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/867afe4f-221e-465f-b082-bf34bbb99022
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/867afe4f-221e-465f-b082-bf34bbb99022
       - hmdb: HMDB01368
       - kegg.compound: C00957
       - metanetx.chemical: MNXM1214
@@ -27957,8 +27864,7 @@
         - CHEBI:16643
         - CHEBI:13141
         - CHEBI:43990
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/44a61812-39ff-48f9-bf09-8398e8723d5e
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/44a61812-39ff-48f9-bf09-8398e8723d5e
       - hmdb:
         - HMDB00696
         - HMDB33951
@@ -28006,8 +27912,7 @@
         - CHEBI:16643
         - CHEBI:13141
         - CHEBI:43990
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/44a61812-39ff-48f9-bf09-8398e8723d5e
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/44a61812-39ff-48f9-bf09-8398e8723d5e
       - hmdb:
         - HMDB00696
         - HMDB33951
@@ -28055,8 +27960,7 @@
         - CHEBI:16643
         - CHEBI:13141
         - CHEBI:43990
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/44a61812-39ff-48f9-bf09-8398e8723d5e
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/44a61812-39ff-48f9-bf09-8398e8723d5e
       - hmdb:
         - HMDB00696
         - HMDB33951
@@ -29002,8 +28906,7 @@
         - CHEBI:6813
         - CHEBI:27376
         - CHEBI:25224
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/08e4702f-d7fe-43da-9a21-5771459eab73
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/08e4702f-d7fe-43da-9a21-5771459eab73
       - kegg.compound: C11145
       - metanetx.chemical: MNXM1485
       - sbo: SBO:0000247
@@ -29021,8 +28924,7 @@
         - CHEBI:6813
         - CHEBI:27376
         - CHEBI:25224
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/08e4702f-d7fe-43da-9a21-5771459eab73
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/08e4702f-d7fe-43da-9a21-5771459eab73
       - kegg.compound: C11145
       - metanetx.chemical: MNXM1485
       - sbo: SBO:0000247
@@ -29040,8 +28942,7 @@
         - CHEBI:6813
         - CHEBI:27376
         - CHEBI:25224
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/08e4702f-d7fe-43da-9a21-5771459eab73
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/08e4702f-d7fe-43da-9a21-5771459eab73
       - kegg.compound: C11145
       - metanetx.chemical: MNXM1485
       - sbo: SBO:0000247
@@ -29070,8 +28971,7 @@
         - CHEBI:11643
         - CHEBI:6875
         - CHEBI:17158
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/87b7fac4-f224-43ab-81f4-b95330450174
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/87b7fac4-f224-43ab-81f4-b95330450174
       - hmdb: HMDB01167
       - kegg.compound: C00546
       - metanetx.chemical: MNXM310
@@ -29332,8 +29232,7 @@
         - CHEBI:7598
         - CHEBI:17045
         - CHEBI:44250
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/27f4cd6e-d42f-484e-8813-ef9e60aa5bf0
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/27f4cd6e-d42f-484e-8813-ef9e60aa5bf0
       - hmdb: HMDB35807
       - kegg.compound: C00887
       - kegg.drug: D00102
@@ -29356,8 +29255,7 @@
         - CHEBI:7598
         - CHEBI:17045
         - CHEBI:44250
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/27f4cd6e-d42f-484e-8813-ef9e60aa5bf0
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/27f4cd6e-d42f-484e-8813-ef9e60aa5bf0
       - hmdb: HMDB35807
       - kegg.compound: C00887
       - kegg.drug: D00102
@@ -29380,8 +29278,7 @@
         - CHEBI:7598
         - CHEBI:17045
         - CHEBI:44250
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/27f4cd6e-d42f-484e-8813-ef9e60aa5bf0
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/27f4cd6e-d42f-484e-8813-ef9e60aa5bf0
       - hmdb: HMDB35807
       - kegg.compound: C00887
       - kegg.drug: D00102
@@ -29677,8 +29574,7 @@
       - sbo: SBO:0000247
   - !!omap
     - id: nadhx__S_c
-    - name: Adenosine 
-        5'-(3-{5-[(2S)-5-carbamoyl-2-hydroxy-3,4-dihydropyridin-1-yl]-5-deoxy-?-D-ribofuranosyl}
+    - name: Adenosine 5'-(3-{5-[(2S)-5-carbamoyl-2-hydroxy-3,4-dihydropyridin-1-yl]-5-deoxy-?-D-ribofuranosyl}
         dihydrogen diphosphate)
     - compartment: c
     - charge: -2
@@ -30188,8 +30084,7 @@
         - CHEBI:7585
         - CHEBI:44396
         - CHEBI:25567
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/84af9b8c-5f58-4093-85cb-964ba8ed40b7
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/84af9b8c-5f58-4093-85cb-964ba8ed40b7
       - hmdb: HMDB02786
       - kegg.compound: C00088
       - metanetx.chemical: MNXM107
@@ -30212,8 +30107,7 @@
         - CHEBI:7585
         - CHEBI:44396
         - CHEBI:25567
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/84af9b8c-5f58-4093-85cb-964ba8ed40b7
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/84af9b8c-5f58-4093-85cb-964ba8ed40b7
       - hmdb: HMDB02786
       - kegg.compound: C00088
       - metanetx.chemical: MNXM107
@@ -30236,8 +30130,7 @@
         - CHEBI:7585
         - CHEBI:44396
         - CHEBI:25567
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/84af9b8c-5f58-4093-85cb-964ba8ed40b7
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/84af9b8c-5f58-4093-85cb-964ba8ed40b7
       - hmdb: HMDB02786
       - kegg.compound: C00088
       - metanetx.chemical: MNXM107
@@ -30264,8 +30157,7 @@
         - CHEBI:17632
         - CHEBI:48107
         - CHEBI:25545
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/706be27f-b4cf-4022-b2ef-04cec5197ca5
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/706be27f-b4cf-4022-b2ef-04cec5197ca5
       - hmdb:
         - HMDB02878
         - HMDB01853
@@ -30294,8 +30186,7 @@
         - CHEBI:17632
         - CHEBI:48107
         - CHEBI:25545
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/706be27f-b4cf-4022-b2ef-04cec5197ca5
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/706be27f-b4cf-4022-b2ef-04cec5197ca5
       - hmdb:
         - HMDB02878
         - HMDB01853
@@ -30324,8 +30215,7 @@
         - CHEBI:17632
         - CHEBI:48107
         - CHEBI:25545
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/706be27f-b4cf-4022-b2ef-04cec5197ca5
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/706be27f-b4cf-4022-b2ef-04cec5197ca5
       - hmdb:
         - HMDB02878
         - HMDB01853
@@ -30536,8 +30426,7 @@
         - CHEBI:23833
         - CHEBI:25366
         - CHEBI:10745
-      - envipath: 
-          5882df9c-dae1-4d80-a40e-db4724271456/compound/d5d12248-82d3-4cf3-b7d0-2e3d096768b4
+      - envipath: 5882df9c-dae1-4d80-a40e-db4724271456/compound/d5d12248-82d3-4cf3-b7d0-2e3d096768b4
       - hmdb: HMDB01377
       - kegg.compound: C00007
       - kegg.drug: D00003
@@ -30579,8 +30468,7 @@
         - CHEBI:23833
         - CHEBI:25366
         - CHEBI:10745
-      - envipath: 
-          5882df9c-dae1-4d80-a40e-db4724271456/compound/d5d12248-82d3-4cf3-b7d0-2e3d096768b4
+      - envipath: 5882df9c-dae1-4d80-a40e-db4724271456/compound/d5d12248-82d3-4cf3-b7d0-2e3d096768b4
       - hmdb: HMDB01377
       - kegg.compound: C00007
       - kegg.drug: D00003
@@ -30622,8 +30510,7 @@
         - CHEBI:23833
         - CHEBI:25366
         - CHEBI:10745
-      - envipath: 
-          5882df9c-dae1-4d80-a40e-db4724271456/compound/d5d12248-82d3-4cf3-b7d0-2e3d096768b4
+      - envipath: 5882df9c-dae1-4d80-a40e-db4724271456/compound/d5d12248-82d3-4cf3-b7d0-2e3d096768b4
       - hmdb: HMDB01377
       - kegg.compound: C00007
       - kegg.drug: D00003
@@ -30806,8 +30693,7 @@
         - CHEBI:14681
         - CHEBI:15533
         - CHEBI:57386
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/803b8f43-e64d-427d-a22e-a38aca2708eb
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/803b8f43-e64d-427d-a22e-a38aca2708eb
       - hmdb:
         - HMDB06257
         - HMDB01070
@@ -30846,8 +30732,7 @@
         - CHEBI:45710
         - CHEBI:25629
         - CHEBI:28842
-      - envipath: 
-          5882df9c-dae1-4d80-a40e-db4724271456/compound/c0fae385-4844-4700-ba7a-96b6726ed216
+      - envipath: 5882df9c-dae1-4d80-a40e-db4724271456/compound/c0fae385-4844-4700-ba7a-96b6726ed216
       - hmdb: HMDB00827
       - kegg.compound: C01530
       - kegg.drug: D00119
@@ -30875,8 +30760,7 @@
         - CHEBI:45710
         - CHEBI:25629
         - CHEBI:28842
-      - envipath: 
-          5882df9c-dae1-4d80-a40e-db4724271456/compound/c0fae385-4844-4700-ba7a-96b6726ed216
+      - envipath: 5882df9c-dae1-4d80-a40e-db4724271456/compound/c0fae385-4844-4700-ba7a-96b6726ed216
       - hmdb: HMDB00827
       - kegg.compound: C01530
       - kegg.drug: D00119
@@ -30904,8 +30788,7 @@
         - CHEBI:45710
         - CHEBI:25629
         - CHEBI:28842
-      - envipath: 
-          5882df9c-dae1-4d80-a40e-db4724271456/compound/c0fae385-4844-4700-ba7a-96b6726ed216
+      - envipath: 5882df9c-dae1-4d80-a40e-db4724271456/compound/c0fae385-4844-4700-ba7a-96b6726ed216
       - hmdb: HMDB00827
       - kegg.compound: C01530
       - kegg.drug: D00119
@@ -31551,8 +31434,7 @@
         - CHEBI:57348
         - CHEBI:11872
         - CHEBI:1632
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/07216e0c-6bda-4477-b3ee-a2bda11a0800
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/07216e0c-6bda-4477-b3ee-a2bda11a0800
       - hmdb: HMDB60378
       - kegg.compound: C02232
       - lipidmaps: LMFA07050237
@@ -31598,8 +31480,7 @@
         - CHEBI:14708
         - CHEBI:18058
         - CHEBI:58363
-      - envipath: 
-          5882df9c-dae1-4d80-a40e-db4724271456/compound/39b30a97-8fc7-4a71-be89-c591d56a8f6a
+      - envipath: 5882df9c-dae1-4d80-a40e-db4724271456/compound/39b30a97-8fc7-4a71-be89-c591d56a8f6a
       - kegg.compound: C01444
       - metanetx.chemical: MNXM3329
       - sabiork: '3029'
@@ -32791,8 +32672,7 @@
         - CHEBI:14780
         - CHEBI:15537
         - CHEBI:57390
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc20356c-1455-4c1c-8260-b86508a89a3d
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/dc20356c-1455-4c1c-8260-b86508a89a3d
       - hmdb: HMDB06503
       - kegg.compound: C00582
       - metanetx.chemical: MNXM502
@@ -33073,8 +32953,7 @@
         - CHEBI:26007
         - CHEBI:18005
         - CHEBI:12821
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/1a2c1780-502b-43c6-8d45-759953ea5e07
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/1a2c1780-502b-43c6-8d45-759953ea5e07
       - hmdb:
         - HMDB00205
         - HMDB31629
@@ -33314,8 +33193,7 @@
         - CHEBI:7898
         - CHEBI:15525
         - CHEBI:14732
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/683c12f9-18f4-4439-a718-0877aa11b9ae
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/683c12f9-18f4-4439-a718-0877aa11b9ae
       - hmdb:
         - HMDB01338
         - HMDB59623
@@ -33598,8 +33476,7 @@
         - CHEBI:26295
         - CHEBI:8479
         - CHEBI:15539
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/4e032169-05c6-49aa-9422-d081d81bc1a6
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/4e032169-05c6-49aa-9422-d081d81bc1a6
       - hmdb: HMDB01275
       - kegg.compound: C00100
       - lipidmaps: LMFA07050364
@@ -34088,8 +33965,7 @@
       - seed.compound: cpd19185
   - !!omap
     - id: prfp_c
-    - name: 
-        1-(5-Phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide
+    - name: 1-(5-Phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide
     - compartment: c
     - charge: -4
     - formula: C15H21N5O15P2
@@ -34110,8 +33986,7 @@
       - seed.compound: cpd02979
   - !!omap
     - id: prlp_c
-    - name: 
-        5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]-1-(5-phosphoribosyl)imidazole-4-carboxamide
+    - name: 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]-1-(5-phosphoribosyl)imidazole-4-carboxamide
     - compartment: c
     - charge: -4
     - formula: C15H21N5O15P2
@@ -34331,8 +34206,7 @@
         - CHEBI:8488
         - CHEBI:15513
         - CHEBI:57367
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/04437fe9-7f67-491c-bfba-52e7b1b43ed6
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/04437fe9-7f67-491c-bfba-52e7b1b43ed6
       - hmdb:
         - HMDB06507
         - HMDB02307
@@ -34752,8 +34626,7 @@
         - CHEBI:8669
         - CHEBI:14978
         - CHEBI:131533
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a8e03eef-0f65-4f7e-aaaa-c85331fbebe6
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a8e03eef-0f65-4f7e-aaaa-c85331fbebe6
       - hmdb:
         - HMDB62696
         - HMDB01431
@@ -34780,8 +34653,7 @@
         - CHEBI:8669
         - CHEBI:14978
         - CHEBI:131533
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a8e03eef-0f65-4f7e-aaaa-c85331fbebe6
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a8e03eef-0f65-4f7e-aaaa-c85331fbebe6
       - hmdb:
         - HMDB62696
         - HMDB01431
@@ -34808,8 +34680,7 @@
         - CHEBI:8669
         - CHEBI:14978
         - CHEBI:131533
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a8e03eef-0f65-4f7e-aaaa-c85331fbebe6
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a8e03eef-0f65-4f7e-aaaa-c85331fbebe6
       - hmdb:
         - HMDB62696
         - HMDB01431
@@ -34860,8 +34731,7 @@
         - CHEBI:26423
         - CHEBI:17310
         - CHEBI:8667
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/049709c3-768e-468f-b435-40e990942002
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/049709c3-768e-468f-b435-40e990942002
       - hmdb: HMDB01545
       - kegg.compound: C00250
       - metanetx.chemical: MNXM311
@@ -34885,8 +34755,7 @@
         - CHEBI:26423
         - CHEBI:17310
         - CHEBI:8667
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/049709c3-768e-468f-b435-40e990942002
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/049709c3-768e-468f-b435-40e990942002
       - hmdb: HMDB01545
       - kegg.compound: C00250
       - metanetx.chemical: MNXM311
@@ -34910,8 +34779,7 @@
         - CHEBI:26423
         - CHEBI:17310
         - CHEBI:8667
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/049709c3-768e-468f-b435-40e990942002
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/049709c3-768e-468f-b435-40e990942002
       - hmdb: HMDB01545
       - kegg.compound: C00250
       - metanetx.chemical: MNXM311
@@ -34933,8 +34801,7 @@
         - CHEBI:26429
         - CHEBI:16709
         - CHEBI:8671
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/344a84bd-2fbd-4e3b-903e-556786d111e2
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/344a84bd-2fbd-4e3b-903e-556786d111e2
       - hmdb:
         - HMDB02075
         - HMDB00239
@@ -34959,8 +34826,7 @@
         - CHEBI:26429
         - CHEBI:16709
         - CHEBI:8671
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/344a84bd-2fbd-4e3b-903e-556786d111e2
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/344a84bd-2fbd-4e3b-903e-556786d111e2
       - hmdb:
         - HMDB02075
         - HMDB00239
@@ -34985,8 +34851,7 @@
         - CHEBI:26429
         - CHEBI:16709
         - CHEBI:8671
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/344a84bd-2fbd-4e3b-903e-556786d111e2
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/344a84bd-2fbd-4e3b-903e-556786d111e2
       - hmdb:
         - HMDB02075
         - HMDB00239
@@ -36065,8 +35930,7 @@
         - CHEBI:15075
         - CHEBI:9088
         - CHEBI:33490
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/7ce756a8-39aa-4c50-aa82-5a7c7fe07bdc
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/7ce756a8-39aa-4c50-aa82-5a7c7fe07bdc
       - hmdb: HMDB62761
       - kegg.compound: C05697
       - metanetx.chemical: MNXM2282
@@ -36089,8 +35953,7 @@
         - CHEBI:15075
         - CHEBI:9088
         - CHEBI:33490
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/7ce756a8-39aa-4c50-aa82-5a7c7fe07bdc
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/7ce756a8-39aa-4c50-aa82-5a7c7fe07bdc
       - hmdb: HMDB62761
       - kegg.compound: C05697
       - metanetx.chemical: MNXM2282
@@ -36113,8 +35976,7 @@
         - CHEBI:15075
         - CHEBI:9088
         - CHEBI:33490
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/7ce756a8-39aa-4c50-aa82-5a7c7fe07bdc
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/7ce756a8-39aa-4c50-aa82-5a7c7fe07bdc
       - hmdb: HMDB62761
       - kegg.compound: C05697
       - metanetx.chemical: MNXM2282
@@ -36141,8 +36003,7 @@
         - CHEBI:30485
         - CHEBI:16503
         - CHEBI:47675
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/1e71e9cf-365f-47bc-a252-f0e75f597818
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/1e71e9cf-365f-47bc-a252-f0e75f597818
       - hmdb: HMDB11110
       - kegg.compound: C01528
       - metanetx.chemical: MNXM92652
@@ -36168,8 +36029,7 @@
         - CHEBI:16144
         - CHEBI:58618
         - CHEBI:29269
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/2375fd0c-e578-4771-9d3f-030d6dc30c7c
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/2375fd0c-e578-4771-9d3f-030d6dc30c7c
       - hmdb:
         - HMDB06407
         - HMDB03840
@@ -36284,8 +36144,7 @@
         - CHEBI:45677
         - CHEBI:6301
         - CHEBI:9116
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/207ebcd7-f859-4b01-8a69-9b99fb380595
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/207ebcd7-f859-4b01-8a69-9b99fb380595
       - hmdb:
         - HMDB00589
         - HMDB00187
@@ -36340,8 +36199,7 @@
         - CHEBI:45677
         - CHEBI:6301
         - CHEBI:9116
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/207ebcd7-f859-4b01-8a69-9b99fb380595
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/207ebcd7-f859-4b01-8a69-9b99fb380595
       - hmdb:
         - HMDB00589
         - HMDB00187
@@ -36396,8 +36254,7 @@
         - CHEBI:45677
         - CHEBI:6301
         - CHEBI:9116
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/207ebcd7-f859-4b01-8a69-9b99fb380595
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/207ebcd7-f859-4b01-8a69-9b99fb380595
       - hmdb:
         - HMDB00589
         - HMDB00187
@@ -36642,8 +36499,7 @@
         - CHEBI:29924
         - CHEBI:9090
         - CHEBI:15077
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/853ba2d0-3106-4c3e-9578-b095546ea194
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/853ba2d0-3106-4c3e-9578-b095546ea194
       - hmdb: HMDB11119
       - kegg.compound: C05684
       - kegg.drug: D05814
@@ -36666,8 +36522,7 @@
         - CHEBI:29924
         - CHEBI:9090
         - CHEBI:15077
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/853ba2d0-3106-4c3e-9578-b095546ea194
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/853ba2d0-3106-4c3e-9578-b095546ea194
       - hmdb: HMDB11119
       - kegg.compound: C05684
       - kegg.drug: D05814
@@ -36690,8 +36545,7 @@
         - CHEBI:29924
         - CHEBI:9090
         - CHEBI:15077
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/853ba2d0-3106-4c3e-9578-b095546ea194
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/853ba2d0-3106-4c3e-9578-b095546ea194
       - hmdb: HMDB11119
       - kegg.compound: C05684
       - kegg.drug: D05814
@@ -36713,8 +36567,7 @@
         - CHEBI:18422
         - CHEBI:9351
         - CHEBI:8992
-      - envipath: 
-          4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/739d918d-f0e0-4b19-900c-7abb204b45c0
+      - envipath: 4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/739d918d-f0e0-4b19-900c-7abb204b45c0
       - hmdb: HMDB34834
       - kegg.compound: C09306
       - kegg.drug: D05961
@@ -36736,8 +36589,7 @@
         - CHEBI:18422
         - CHEBI:9351
         - CHEBI:8992
-      - envipath: 
-          4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/739d918d-f0e0-4b19-900c-7abb204b45c0
+      - envipath: 4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/739d918d-f0e0-4b19-900c-7abb204b45c0
       - hmdb: HMDB34834
       - kegg.compound: C09306
       - kegg.drug: D05961
@@ -36759,8 +36611,7 @@
         - CHEBI:18422
         - CHEBI:9351
         - CHEBI:8992
-      - envipath: 
-          4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/739d918d-f0e0-4b19-900c-7abb204b45c0
+      - envipath: 4fd7f3e0-dd25-43ac-9453-dda3e52396e4/compound/739d918d-f0e0-4b19-900c-7abb204b45c0
       - hmdb: HMDB34834
       - kegg.compound: C09306
       - kegg.drug: D05961
@@ -36905,8 +36756,7 @@
         - CHEBI:45687
         - CHEBI:26836
         - CHEBI:45696
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/cf4fcd19-f2cb-4d92-aa67-323762e3b269
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/cf4fcd19-f2cb-4d92-aa67-323762e3b269
       - hmdb: HMDB01448
       - kegg.compound: C00059
       - kegg.drug: D05963
@@ -36942,8 +36792,7 @@
         - CHEBI:45687
         - CHEBI:26836
         - CHEBI:45696
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/cf4fcd19-f2cb-4d92-aa67-323762e3b269
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/cf4fcd19-f2cb-4d92-aa67-323762e3b269
       - hmdb: HMDB01448
       - kegg.compound: C00059
       - kegg.drug: D05963
@@ -36979,8 +36828,7 @@
         - CHEBI:45687
         - CHEBI:26836
         - CHEBI:45696
-      - envipath: 
-          650babc9-9d68-4b73-9332-11972ca26f7b/compound/cf4fcd19-f2cb-4d92-aa67-323762e3b269
+      - envipath: 650babc9-9d68-4b73-9332-11972ca26f7b/compound/cf4fcd19-f2cb-4d92-aa67-323762e3b269
       - hmdb: HMDB01448
       - kegg.compound: C00059
       - kegg.drug: D05963
@@ -37349,8 +37197,7 @@
         - CHEBI:9310
         - CHEBI:45541
         - CHEBI:26811
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/359075fb-98d9-458d-ba82-db4020e753f3
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/359075fb-98d9-458d-ba82-db4020e753f3
       - hmdb: HMDB01022
       - kegg.compound: C00091
       - lipidmaps: LMFA07050370
@@ -37996,8 +37843,7 @@
         - CHEBI:9550
         - CHEBI:26954
         - CHEBI:15234
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e06445a5-0756-47c6-b6f7-64c74b192ecc
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e06445a5-0756-47c6-b6f7-64c74b192ecc
       - hmdb: HMDB01453
       - kegg.compound: C01755
       - metanetx.chemical: MNXM762
@@ -38023,8 +37869,7 @@
         - CHEBI:9550
         - CHEBI:26954
         - CHEBI:15234
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e06445a5-0756-47c6-b6f7-64c74b192ecc
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e06445a5-0756-47c6-b6f7-64c74b192ecc
       - hmdb: HMDB01453
       - kegg.compound: C01755
       - metanetx.chemical: MNXM762
@@ -38050,8 +37895,7 @@
         - CHEBI:9550
         - CHEBI:26954
         - CHEBI:15234
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e06445a5-0756-47c6-b6f7-64c74b192ecc
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/e06445a5-0756-47c6-b6f7-64c74b192ecc
       - hmdb: HMDB01453
       - kegg.compound: C01755
       - metanetx.chemical: MNXM762
@@ -38262,8 +38106,7 @@
     - annotation: !!omap
       - bigg.metabolite: thm
       - chebi: CHEBI:33283
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d00080d5-971d-4e5f-973a-226a589d76df
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d00080d5-971d-4e5f-973a-226a589d76df
       - kegg.drug: D08580
       - metanetx.chemical: MNXM161565
       - sabiork: '2032'
@@ -38278,8 +38121,7 @@
     - annotation: !!omap
       - bigg.metabolite: thm
       - chebi: CHEBI:33283
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d00080d5-971d-4e5f-973a-226a589d76df
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d00080d5-971d-4e5f-973a-226a589d76df
       - kegg.drug: D08580
       - metanetx.chemical: MNXM161565
       - sabiork: '2032'
@@ -38294,8 +38136,7 @@
     - annotation: !!omap
       - bigg.metabolite: thm
       - chebi: CHEBI:33283
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d00080d5-971d-4e5f-973a-226a589d76df
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d00080d5-971d-4e5f-973a-226a589d76df
       - kegg.drug: D08580
       - metanetx.chemical: MNXM161565
       - sabiork: '2032'
@@ -38409,8 +38250,7 @@
         - CHEBI:45983
         - CHEBI:32832
         - CHEBI:26986
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b570a573-71c2-4661-a517-6ac1b121dc59
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b570a573-71c2-4661-a517-6ac1b121dc59
       - hmdb: HMDB00167
       - kegg.compound: C00188
       - kegg.drug: D00041
@@ -38447,8 +38287,7 @@
         - CHEBI:45983
         - CHEBI:32832
         - CHEBI:26986
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b570a573-71c2-4661-a517-6ac1b121dc59
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b570a573-71c2-4661-a517-6ac1b121dc59
       - hmdb: HMDB00167
       - kegg.compound: C00188
       - kegg.drug: D00041
@@ -38485,8 +38324,7 @@
         - CHEBI:45983
         - CHEBI:32832
         - CHEBI:26986
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b570a573-71c2-4661-a517-6ac1b121dc59
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b570a573-71c2-4661-a517-6ac1b121dc59
       - hmdb: HMDB00167
       - kegg.compound: C00188
       - kegg.drug: D00041
@@ -38702,8 +38540,7 @@
         - CHEBI:58389
         - CHEBI:27127
         - CHEBI:27125
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3311ee4e-2800-486b-9556-983f5d367c23
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3311ee4e-2800-486b-9556-983f5d367c23
       - hmdb: HMDB00906
       - kegg.compound: C00565
       - metanetx.chemical: MNXM352
@@ -38727,8 +38564,7 @@
         - CHEBI:58389
         - CHEBI:27127
         - CHEBI:27125
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3311ee4e-2800-486b-9556-983f5d367c23
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3311ee4e-2800-486b-9556-983f5d367c23
       - hmdb: HMDB00906
       - kegg.compound: C00565
       - metanetx.chemical: MNXM352
@@ -38752,8 +38588,7 @@
         - CHEBI:58389
         - CHEBI:27127
         - CHEBI:27125
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3311ee4e-2800-486b-9556-983f5d367c23
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3311ee4e-2800-486b-9556-983f5d367c23
       - hmdb: HMDB00906
       - kegg.compound: C00565
       - metanetx.chemical: MNXM352
@@ -38776,8 +38611,7 @@
         - CHEBI:27126
         - CHEBI:9733
         - CHEBI:15263
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c203aa4e-eb3d-491f-80bc-2b014da6482f
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c203aa4e-eb3d-491f-80bc-2b014da6482f
       - hmdb: HMDB00925
       - kegg.compound: C01104
       - metanetx.chemical: MNXM437
@@ -38800,8 +38634,7 @@
         - CHEBI:27126
         - CHEBI:9733
         - CHEBI:15263
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c203aa4e-eb3d-491f-80bc-2b014da6482f
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c203aa4e-eb3d-491f-80bc-2b014da6482f
       - hmdb: HMDB00925
       - kegg.compound: C01104
       - metanetx.chemical: MNXM437
@@ -38824,8 +38657,7 @@
         - CHEBI:27126
         - CHEBI:9733
         - CHEBI:15263
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c203aa4e-eb3d-491f-80bc-2b014da6482f
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c203aa4e-eb3d-491f-80bc-2b014da6482f
       - hmdb: HMDB00925
       - kegg.compound: C01104
       - metanetx.chemical: MNXM437
@@ -39236,8 +39068,7 @@
         - CHEBI:45922
         - CHEBI:5587
         - CHEBI:33542
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/32b1f2ad-32ba-4271-9c86-f4bb1c35e35d
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/32b1f2ad-32ba-4271-9c86-f4bb1c35e35d
       - hmdb:
         - HMDB00257
         - HMDB60293
@@ -39270,8 +39101,7 @@
         - CHEBI:45922
         - CHEBI:5587
         - CHEBI:33542
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/32b1f2ad-32ba-4271-9c86-f4bb1c35e35d
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/32b1f2ad-32ba-4271-9c86-f4bb1c35e35d
       - hmdb:
         - HMDB00257
         - HMDB60293
@@ -39304,8 +39134,7 @@
         - CHEBI:45922
         - CHEBI:5587
         - CHEBI:33542
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/32b1f2ad-32ba-4271-9c86-f4bb1c35e35d
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/32b1f2ad-32ba-4271-9c86-f4bb1c35e35d
       - hmdb:
         - HMDB00257
         - HMDB60293
@@ -39580,8 +39409,7 @@
         - CHEBI:17895
         - CHEBI:18186
         - CHEBI:32785
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/974bd9b7-53fb-48cd-aaf3-6bd3196c0365
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/974bd9b7-53fb-48cd-aaf3-6bd3196c0365
       - hmdb:
         - HMDB00647
         - HMDB00158
@@ -39629,8 +39457,7 @@
         - CHEBI:17895
         - CHEBI:18186
         - CHEBI:32785
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/974bd9b7-53fb-48cd-aaf3-6bd3196c0365
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/974bd9b7-53fb-48cd-aaf3-6bd3196c0365
       - hmdb:
         - HMDB00647
         - HMDB00158
@@ -39678,8 +39505,7 @@
         - CHEBI:17895
         - CHEBI:18186
         - CHEBI:32785
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/974bd9b7-53fb-48cd-aaf3-6bd3196c0365
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/974bd9b7-53fb-48cd-aaf3-6bd3196c0365
       - hmdb:
         - HMDB00647
         - HMDB00158
@@ -39836,8 +39662,7 @@
       - seed.compound: cpd15576
   - !!omap
     - id: uaagmda_c
-    - name: 
-        Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-ala-D-glu-meso-2,6-diaminopimeloyl-D-ala-D-ala
+    - name: Undecaprenyl-diphospho-N-acetylmuramoyl-(N-acetylglucosamine)-L-ala-D-glu-meso-2,6-diaminopimeloyl-D-ala-D-ala
     - compartment: c
     - charge: -4
     - formula: C95H152N8O28P2
@@ -40026,8 +39851,7 @@
       - seed.compound: cpd03732
   - !!omap
     - id: uagmda_c
-    - name: 
-        Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine
+    - name: Undecaprenyl-diphospho-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine
     - compartment: c
     - charge: -4
     - formula: C87H139N7O23P2
@@ -40689,8 +40513,7 @@
       - sbo: SBO:0000247
   - !!omap
     - id: ugmda_c
-    - name: 
-        UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine
+    - name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine
     - compartment: c
     - charge: -4
     - formula: C41H61N9O28P2
@@ -40712,8 +40535,7 @@
         - cpd02968
   - !!omap
     - id: um4p_c
-    - name: 
-        UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine
+    - name: UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine
     - compartment: c
     - charge: -4
     - formula: C38H56N8O27P2
@@ -40851,8 +40673,7 @@
       - seed.compound: cpd15581
   - !!omap
     - id: unagamuf_c
-    - name: Undecaprenyl-diphospho 
-        N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose
+    - name: Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose
     - compartment: c
     - charge: -3
     - formula: C79H126N3O22P2
@@ -40864,8 +40685,7 @@
       - seed.compound: cpd15582
   - !!omap
     - id: unagamuf_p
-    - name: Undecaprenyl-diphospho 
-        N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose
+    - name: Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose
     - compartment: p
     - charge: -3
     - formula: C79H126N3O22P2
@@ -41524,8 +41344,7 @@
         - CHEBI:48517
         - CHEBI:17712
         - CHEBI:27317
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3cf4dbf8-ae84-49e6-b294-b5138cb94f75
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3cf4dbf8-ae84-49e6-b294-b5138cb94f75
       - hmdb: HMDB00292
       - kegg.compound: C00385
       - metanetx.chemical: MNXM174
@@ -41549,8 +41368,7 @@
         - CHEBI:48517
         - CHEBI:17712
         - CHEBI:27317
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3cf4dbf8-ae84-49e6-b294-b5138cb94f75
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3cf4dbf8-ae84-49e6-b294-b5138cb94f75
       - hmdb: HMDB00292
       - kegg.compound: C00385
       - metanetx.chemical: MNXM174
@@ -41574,8 +41392,7 @@
         - CHEBI:48517
         - CHEBI:17712
         - CHEBI:27317
-      - envipath: 
-          32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3cf4dbf8-ae84-49e6-b294-b5138cb94f75
+      - envipath: 32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/3cf4dbf8-ae84-49e6-b294-b5138cb94f75
       - hmdb: HMDB00292
       - kegg.compound: C00385
       - metanetx.chemical: MNXM174
@@ -43782,7 +43599,7 @@
       - pi_p: 1.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: b4213 or b0383 or b0383
+    - gene_reaction_rule: b0383 or b4213 or b2744
     - subsystem: Nucleotide Salvage Pathway
     - annotation: !!omap
       - bigg.reaction: 3NTD4pp
@@ -51116,8 +50933,8 @@
       - pi_c: 1.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: (b2308 and b2306 and b2310 and b2307) or (b0864 and b0860
-        and b0863 and b0862 and b0861)
+    - 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)
     - subsystem: Transport, Inner Membrane
     - annotation: !!omap
       - bigg.reaction: ARGabcpp
@@ -52593,7 +52410,7 @@
       - ppi_c: 1.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: b3857 or (b3857 and b3856)
+    - gene_reaction_rule: b3857
     - subsystem: Cofactor and Prosthetic Group Biosynthesis
     - annotation: !!omap
       - bigg.reaction: BMOGDS1
@@ -52610,7 +52427,7 @@
       - ppi_c: 1.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: (b3857 and b3856) or b3857
+    - gene_reaction_rule: b3857
     - subsystem: Cofactor and Prosthetic Group Biosynthesis
     - annotation: !!omap
       - bigg.reaction: BMOGDS2
@@ -52862,7 +52679,7 @@
       - ppi_c: 1.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: (b3857 and b3856) or b3857
+    - gene_reaction_rule: b3857
     - subsystem: Cofactor and Prosthetic Group Biosynthesis
     - annotation: !!omap
       - bigg.reaction: BWCOGDS1
@@ -52879,7 +52696,7 @@
       - ppi_c: 1.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: (b3857 and b3856) or b3857
+    - gene_reaction_rule: b3857
     - subsystem: Cofactor and Prosthetic Group Biosynthesis
     - annotation: !!omap
       - bigg.reaction: BWCOGDS2
@@ -60822,7 +60639,7 @@
       - unagamuf_p: -2.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: b3785 and b3793
+    - gene_reaction_rule: b3785 and b3793 and b3792
     - subsystem: Lipopolysaccharide Biosynthesis / Recycling
     - annotation: !!omap
       - bigg.reaction: ECAP1pp
@@ -60839,7 +60656,7 @@
       - unagamuf_p: -1.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: b3785 and b3793
+    - gene_reaction_rule: b3785 and b3793 and b3792
     - subsystem: Lipopolysaccharide Biosynthesis / Recycling
     - annotation: !!omap
       - bigg.reaction: ECAP2pp
@@ -60856,7 +60673,7 @@
       - unagamuf_p: -1.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: b3785 and b3793
+    - gene_reaction_rule: b3785 and b3793 and b3792
     - subsystem: Lipopolysaccharide Biosynthesis / Recycling
     - annotation: !!omap
       - bigg.reaction: ECAP3pp
@@ -69170,7 +68987,7 @@
       - nadph_c: -1.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: b2764 and b2763
+    - gene_reaction_rule: b2764
     - subsystem: Cofactor and Prosthetic Group Biosynthesis
     - annotation: !!omap
       - bigg.reaction: FADRx2
@@ -70850,7 +70667,7 @@
       - nadph_c: -1.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: b3844 or b0937 or (b2764 and b2763)
+    - gene_reaction_rule: b0937 or b3844 or b2764
     - subsystem: Cofactor and Prosthetic Group Biosynthesis
     - annotation: !!omap
       - bigg.reaction: FMNRx2
@@ -73469,7 +73286,7 @@
       - mlthf_c: 1.0
       - ser__L_c: -1.0
       - thf_c: -1.0
-    - lower_bound: -1000.0
+    - lower_bound: 0
     - upper_bound: 1000.0
     - gene_reaction_rule: b2551
     - subsystem: Glycine and Serine Metabolism
@@ -74272,7 +74089,7 @@
       - nh4_c: 1.0
     - lower_bound: -1000.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: b1761 or (b3213 and b3212)
+    - gene_reaction_rule: b1761
     - subsystem: Glutamate Metabolism
     - annotation: !!omap
       - bigg.reaction: GLUDy
@@ -75026,46 +74843,6 @@
       - sabiork: '1322'
       - sbo: SBO:0000176
       - seed.reaction: rxn00762
-  - !!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: GLYCK2
     - name: Glycerate kinase
@@ -75077,7 +74854,7 @@
       - h_c: 1.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: b3124
+    - gene_reaction_rule: b3124 or b0514
     - subsystem: Glycine and Serine Metabolism
     - annotation: !!omap
       - bigg.reaction: GLYCK2
@@ -79152,7 +78929,7 @@
       - hom__L_c: -1.0
       - nadp_c: -1.0
       - nadph_c: 1.0
-    - lower_bound: -1000.0
+    - lower_bound: 0.0
     - upper_bound: 1000.0
     - gene_reaction_rule: b3940 or b0002
     - subsystem: Threonine and Lysine Metabolism
@@ -86440,7 +86217,7 @@
       - ppi_c: 1.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: (b3857 and b3856) or b3857
+    - gene_reaction_rule: b3857
     - subsystem: Cofactor and Prosthetic Group Biosynthesis
     - annotation: !!omap
       - bigg.reaction: MOGDS
@@ -95951,8 +95728,7 @@
       - sbo: SBO:0000176
   - !!omap
     - id: PRMICI
-    - name: 
-        1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide
+    - name: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide
         isomerase
     - metabolites: !!omap
       - prfp_c: -1.0
@@ -100388,7 +100164,7 @@
     - metabolites: !!omap
       - succ_c: 1.0
       - succ_p: -1.0
-    - lower_bound: -1000.0
+    - lower_bound: 0.0
     - upper_bound: 1000.0
     - gene_reaction_rule: b1206
     - subsystem: Transport, Inner Membrane
@@ -101246,8 +101022,8 @@
     - id: THD2pp
     - name: NAD(P) transhydrogenase (periplasm)
     - metabolites: !!omap
-      - h_c: 2.0
-      - h_p: -2.0
+      - h_c: 1.0
+      - h_p: -1.0
       - nad_c: 1.0
       - nadh_c: -1.0
       - nadp_c: -1.0
@@ -101749,7 +101525,7 @@
       - ppi_c: 1.0
     - lower_bound: 0.0
     - upper_bound: 1000.0
-    - gene_reaction_rule: b0423 and b3990 and b2530 and b3992 and b4407
+    - gene_reaction_rule: b3992 and b3990 and b0423 and b2530 and b4407 and b3991
     - subsystem: Cofactor and Prosthetic Group Biosynthesis
     - annotation: !!omap
       - bigg.reaction: THZPSN3
@@ -103261,8 +103037,7 @@
       - seed.reaction: rxn00293
   - !!omap
     - id: UAGPT3
-    - name: 
-        UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol
+    - name: UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol
         N-acetylglucosamine transferase
     - metabolites: !!omap
       - h_c: 1.0
@@ -103879,8 +103654,7 @@
       - seed.reaction: rxn00327
   - !!omap
     - id: UGMDDS
-    - name: 
-        UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine
+    - name: UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine
         synthetase
     - metabolites: !!omap
       - adp_c: 1.0
@@ -103985,8 +103759,7 @@
       - sbo: SBO:0000176
   - !!omap
     - id: UM4PCP
-    - name: 
-        UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine
+    - name: UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine
         L,D-carboxypeptidase
     - metabolites: !!omap
       - ala__D_c: 1.0
@@ -105127,7 +104900,7 @@
       - biocyc: META:XYLISOM-RXN
       - ec-code: 5.3.1.5
       - kegg.reaction: R01432
-      - metanetx.reaction: MNXR105253
+      - metanetx.reaction: MNXR146751
       - rhea:
         - '22818'
         - '22816'
@@ -105135,30 +104908,6 @@
         - '22817'
       - sbo: SBO:0000176
       - seed.reaction: rxn01044
-  - !!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
   - !!omap
     - id: XYLK
     - name: Xylulokinase