diff --git a/memote_report.html b/memote_report.html
index 6448af1..bfea948 100644
--- a/memote_report.html
+++ b/memote_report.html
@@ -20,7 +20,7 @@
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-    window.data = {"meta":{"timestamp":"2025-06-09 08:06:22.368380","platform":"Linux","release":"6.11.0-1014-azure","python":"3.9.16","packages":{"memote":"0.13.0","click":"8.1.3","click-configfile":"0.2.3","click-log":"0.4.0","six":"1.16.0","future":"0.18.3","pytest":"7.2.2","gitpython":"3.1.31","pandas":"1.5.3","Jinja2":"3.1.2","cookiecutter":"2.1.1","cobra":"0.26.2","ruamel.yaml":"0.17.21","travis-encrypt":"1.1.2","sympy":"1.11.1","sqlalchemy":"2.0.5.post1","requests":"2.28.2","importlib-resources":"5.12.0","numpydoc":"1.5.0","pylru":"1.2.1","goodtables":"2.5.4","depinfo":"1.7.0","black ; extra == 'development'":"not installed","isort ; extra == 'development'":"not installed","tox ; extra == 'development'":"not installed","pip":"23.0.1","setuptools":"67.6.0","wheel":"0.38.4"}},"tests":{"test_metabolite_annotation_presence":{"duration":0.0010978339999994091,"result":"passed","title":"Presence of Metabolite Annotation","summary":"This test checks if any annotations at all are present in the SBML\nannotations field for each metabolite, irrespective of the type of\nannotation i.e. specific database  cross-references, ontology terms,\nadditional information. For this test to pass the model is expected to\nhave metabolites and each of them should have some form of annotation.\n\nImplementation:\nCheck if the annotation attribute of each cobra.Metabolite object of the\nmodel is unset or empty.","message":"A total of 0 metabolites (0.00%) lack any form of annotation:","data":[],"format_type":"count","metric":0.0},"test_reaction_annotation_presence":{"duration":0.0018274900000037064,"result":"passed","title":"Presence of Reaction Annotation","summary":"This test checks if any annotations at all are present in the SBML\nannotations field for each reaction, irrespective of the type of\nannotation i.e. specific database  cross-references, ontology terms,\nadditional information. For this test to pass the model is expected to\nhave reactions and each of them should have some form of annotation.\n\nImplementation:\nCheck if the annotation attribute of each cobra.Reaction object of the\nmodel is unset or empty.","message":"A total of 0 reactions (0.00%) lack any form of annotation:","data":[],"format_type":"count","metric":0.0},"test_gene_product_annotation_presence":{"duration":0.000862844000003804,"result":"passed","title":"Presence of Gene Annotation","summary":"This test checks if any annotations at all are present in the SBML\nannotations field (extended by FBC package) for each gene product,\nirrespective of the type of annotation i.e. specific database,\ncross-references, ontology terms, additional information. For this test to\npass the model is expected to have genes and each of them should have some\nform of annotation.\n\nImplementation:\nCheck if the annotation attribute of each cobra.Gene object of the\nmodel is unset or empty.","message":"A total of 0 genes (0.00%) lack any form of         annotation:","data":[],"format_type":"count","metric":0.0},"test_metabolite_annotation_overview":{"duration":{"pubchem.compound":0.0014413969999935716,"kegg.compound":0.0011466650000002687,"seed.compound":0.0011413450000006264,"inchikey":0.0012248819999953753,"inchi":0.0010191470000009417,"chebi":0.0010452659999984348,"hmdb":0.000972660000002179,"reactome":0.0009606779999984383,"metanetx.chemical":0.0007615640000011581,"bigg.metabolite":0.0006762749999964512,"biocyc":0.0008988720000004946},"result":{"pubchem.compound":"failed","kegg.compound":"failed","seed.compound":"failed","inchikey":"failed","inchi":"failed","chebi":"failed","hmdb":"failed","reactome":"failed","metanetx.chemical":"failed","bigg.metabolite":"passed","biocyc":"failed"},"title":"Metabolite Annotations Per Database","summary":"Specific database cross-references are paramount to mapping information.\nTo provide references to as many databases as possible helps to make the\nmetabolic model more accessible to other researchers. This does not only\nfacilitate the use of a model in a broad array of computational pipelines,\nit also promotes the metabolic model itself to become an organism-specific\nknowledge base.\n\nFor this test to pass, each metabolite annotation should contain\ncross-references to a number of databases. The currently selection is\nlisted in `annotation.py`, but an ongoing discussion can be found at\nhttps://github.com/opencobra/memote/issues/332. For each database this\ntest checks for the presence of its corresponding namespace ID to comply\nwith the MIRIAM guidelines i.e. they have to match those defined on\nhttps://identifiers.org/.\n\nSince each database is quite different and some potentially incomplete, it\nmay not be feasible to achieve 100% coverage for each of them. Generally\nit should be possible, however, to obtain cross-references to at least\none of the databases for all metabolites consistently.\n\nImplementation:\nCheck if the keys of the annotation attribute of each cobra.Metabolite of\nthe model match with a selection of common biochemical databases. The\nannotation  attribute of cobrapy components is a dictionary of\nkey:value pairs.","message":{"pubchem.compound":"The following 1877 metabolites (100.00%) lack annotation for\npubchem.compound:         10fthf_c, 12dgr120_c, 12dgr120_p,\n12dgr140_c, 12dgr140_p, ...","kegg.compound":"The following 527 metabolites (28.08%) lack annotation for\nkegg.compound:         12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p,\n12dgr141_c, ...","seed.compound":"The following 275 metabolites (14.65%) lack annotation for\nseed.compound:         12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p,\n12dgr141_c, ...","inchikey":"The following 1877 metabolites (100.00%) lack annotation for inchikey:\n10fthf_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...","inchi":"The following 1877 metabolites (100.00%) lack annotation for inchi:\n10fthf_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...","chebi":"The following 438 metabolites (23.34%) lack annotation for chebi:\n12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, 12dgr141_c, ...","hmdb":"The following 817 metabolites (43.53%) lack annotation for hmdb:\n12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, 12dgr141_c, ...","reactome":"The following 1877 metabolites (100.00%) lack annotation for reactome:\n10fthf_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...","metanetx.chemical":"The following 73 metabolites (3.89%) lack annotation for\nmetanetx.chemical:         2ddara_c, 2hptcl_c, 2hptcoa_c, 34dphacoa_c,\n3hbz_c, ...","bigg.metabolite":"The following 0 metabolites (0.00%) lack annotation for\nbigg.metabolite:","biocyc":"The following 378 metabolites (20.14%) lack annotation for biocyc:\n12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, 12dgr141_c, 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Annotations Per Database","summary":"Specific database cross-references are paramount to mapping information.\nTo provide references to as many databases as possible helps to make the\nmetabolic model more accessible to other researchers. This does not only\nfacilitate the use of a model in a broad array of computational pipelines,\nit also promotes the metabolic model itself to become an organism-specific\nknowledge base.\n\nFor this test to pass, each reaction annotation should contain\ncross-references to a number of databases. The currently selection is\nlisted in `annotation.py`, but an ongoing discussion can be found at\nhttps://github.com/opencobra/memote/issues/332. For each database this\ntest checks for the presence of its corresponding namespace ID to comply\nwith the MIRIAM guidelines i.e. they have to match those defined on\nhttps://identifiers.org/.\n\nSince each database is quite different and some potentially incomplete, it\nmay not be feasible to achieve 100% coverage for each of them. Generally\nit should be possible, however, to obtain cross-references to at least\none of the databases for all reactions consistently.\n\nImplementation:\nCheck if the keys of the annotation attribute of each cobra.Reaction of\nthe model match with a selection of common biochemical databases. The\nannotation  attribute of cobrapy components is a dictionary of\nkey:value pairs.","message":{"rhea":"The following 1535 reactions (56.60%) lack annotation for rhea:\n12DGR120tipp, 12DGR140tipp, 12DGR141tipp, 12DGR160tipp, 12DGR161tipp,\n...","kegg.reaction":"The following 1966 reactions (72.49%) lack annotation for\nkegg.reaction:         12DGR120tipp, 12DGR140tipp, 12DGR141tipp,\n12DGR160tipp, 12DGR161tipp, ...","seed.reaction":"The following 846 reactions (31.19%) lack annotation for\nseed.reaction:         12DGR120tipp, 12DGR140tipp, 12DGR141tipp,\n12DGR160tipp, 12DGR161tipp, ...","metanetx.reaction":"The following 151 reactions (5.57%) lack annotation for\nmetanetx.reaction:         13PPDH2, 23DOGULNt4pp, 2DDARAA, 2DGLCptspp,\n2DGLCtex, ...","bigg.reaction":"The following 0 reactions (0.00%) lack annotation for bigg.reaction:","reactome":"The following 2712 reactions (100.00%) lack annotation for reactome:\n12DGR120tipp, 12DGR140tipp, 12DGR141tipp, 12DGR160tipp, 12DGR161tipp,\n...","ec-code":"The following 1616 reactions (59.59%) lack annotation for ec-code:\n12DGR120tipp, 12DGR140tipp, 12DGR141tipp, 12DGR160tipp, 12DGR161tipp,\n...","brenda":"The following 2712 reactions (100.00%) lack annotation for brenda:\n12DGR120tipp, 12DGR140tipp, 12DGR141tipp, 12DGR160tipp, 12DGR161tipp,\n...","biocyc":"The following 1621 reactions (59.77%) lack annotation for biocyc:\n12DGR120tipp, 12DGR140tipp, 12DGR141tipp, 12DGR160tipp, 12DGR161tipp,\n..."},"data":{"rhea":["12DGR120tipp","12DGR140tipp","12DGR141tipp","12DGR160tipp","12DGR161tipp","12DGR180tipp","12DGR181tipp","12PPDRtex","12PPDRtpp","12PPDStex","12PPDStpp","13PPDH2","14GLUCANabcpp","14GLUCANtexi","23CAMPtex","23CCMPtex","23CGMPtex","23CUMPtex","23DAPPAt2pp","23DAPPAtex","23DOGULNt4pp","26DAHtex","2AGPA120tipp","2AGPA140tipp","2AGPA141tipp","2AGPA160tipp","2AGPA161tipp","2AGPA180tipp","2AGPA181tipp","2AGPE120tipp","2AGPE140tipp","2AGPE141tipp","2AGPE160tipp","2AGPE161tipp","2AGPE180tipp","2AGPE181tipp","2AGPEAT120","2AGPEAT140","2AGPEAT141","2AGPEAT160","2AGPEAT161","2AGPEAT180","2AGPEAT181","2AGPG120tipp","2AGPG140tipp","2AGPG141tipp","2AGPG160tipp","2AGPG161tipp","2AGPG180tipp","2AGPG181tipp","2AGPGAT120","2AGPGAT140","2AGPGAT141","2AGPGAT160","2AGPGAT161","2AGPGAT180","2AGPGAT181","2DDARAA","2DGLCptspp","2DGLCtex","2DGULRGx","2DGULRGy","2DGULRx","2DGULRy","2HESR","2HPTCOAT","2MAHMP","34dhpactex","3AMPtex","3CMPtex","3GMPtex","3HAD100","3HAD120","3HAD121","3HAD140","3HAD141","3HAD160","3HAD161","3HAD180","3HAD181","3HAD40","3HAD60","3HAD80","3HBZCT","3HPADHi","3HPPtpp","3OAR100","3OAR120","3OAR121","3OAR140","3OAR141","3OAR160","3OAR161","3OAR180","3OAR181","3OAR40","3OAR60","3OAR80","3OAS100","3OAS120","3OAS121","3OAS140","3OAS141","3OAS160","3OAS161","3OAS180","3OAS181","3OAS60","3OAS80","3PEPTabcpp","3PEPTtex","3SLAR","3UMPtex","4ABZGLUH","4ABZGLUtex","4ABZGLUtr","4HBZt3pp","4HOXPACDtex","4HTHRA","4PCP","4PCPpp","4PEPTabcpp","4PEPTtex","5DGLCNtex","5DKGR","5MTRtpp","6D6SFK","6D6SPA","AACPS1","AACPS2","AACPS3","AACPS4","AACPS5","AACPS6","AACPS7","AACPS8","AACPS9","AADDGT","AAMYL","AAMYLpp","AB6PGH","ACACT3r","ACACT5r","ACACt2pp","ACALDtex","ACALDtpp","ACCOAL","ACGAL1PPpp","ACGAL1Ptex","ACGALtex","ACGAM1PPpp","ACGAM1Ptex","ACGAMT","ACGAptspp","ACGAtex","ACMANAptspp","ACMANAtex","ACMUMptspp","ACMUMtex","ACOAD1fr","ACOAD2f","ACOAD4f","ACOATA","ACOLIPAabctex","ACOXT","ACP1p","ACPPAT120","ACPPAT140","ACPPAT141","ACPPAT160","ACPPAT161","ACPPAT180","ACPPAT181","ACPS1","ACt2rpp","ACt4pp","ADEtex","ADNtex","ADOCBIK","ADOCBLS","ADOCBLabcpp","ADOCBLtonex","ADPRDP","AGM3PA","AGM3PApp","AGM3PH","AGM3Pt2pp","AGM4PA","AGM4PApp","AGM4PCP","AGM4PCPpp","AGM4PH","AGM4Pt2pp","AGMH","AGMt2pp","AGMtex","AGPAT120","AGPAT140","AGPAT141","AGPAT160","AGPAT161","AGPAT180","AGPAT181","AGt3","AHGDx","AI2K","AI2abcpp","AI2tex","AI2tpp","AKGtex","ALAALAabcpp","ALAALAtex","ALAabcpp","ALAtex","ALAtpp","ALDD3y","ALDD4","ALLK","ALLTAMH2","ALLTNt2rpp","ALLTNtex","ALLULPE","ALLabcpp","ALLtex","ALPATE160pp","ALPATG160pp","ALR2x","ALR4x","AM3PA","AM4PA","AM4PCP","AMALT1","AMALT2","AMALT3","AMALT4","AMPMS2","AMPN","AMPNTAT","AMPtex","ANHGMtex","ANHMK","AOXSr2","APG3PAT120","APG3PAT140","APG3PAT141","APG3PAT160","APG3PAT161","APG3PAT180","APG3PAT181","APH120","APH140","APH141","APH160","APH161","APH180","APH181","ARAI","ARBTNR1","ARBTNR2","ARBTNR3","ARBTNabcpp","ARBTNexs","ARBTNtex","ARBTNtonex","ARBTNtpp","ARBabcpp","ARBt2rpp","ARBt3ipp","ARBtex","ARGt3pp","ARHGDx","ARMEPNS","ASCBptspp","ASCBtex","ASNt2rpp","ASNtex","ASO3tex","ASPt2_3pp","ASPt2pp","ASPtex","ASPtpp","ASR","ATPS4rpp","BALAtex","BGLA1","BIOMASS_Ec_iML1515_WT_75p37M","BIOMASS_Ec_iML1515_core_75p37M","BMOCOS","BMOGDS1","BMOGDS2","BTNt2ipp","BTS5","BUTCT","BUTSO3abcpp","BUTSO3tex","BUTt2rpp","BUTtex","BWCOGDS1","BWCOGDS2","BWCOS","CA2t3pp","CADVtpp","CBIAT","CBItonex","CBIuabcpp","CBL1abcpp","CBL1tonex","CBLAT","CDAPPA120","CDAPPA140","CDAPPA141","CDAPPA160","CDAPPA161","CDAPPA180","CDAPPA181","CDGUNPD","CDPPH","CELBpts","CFAS160E","CFAS160G","CFAS180E","CFAS180G","CGLYabcpp","CGLYtex","CH4t2pp","CH4tex","CHLt3pp","CHOLATEtpp","CHOLID","CHTBSptspp","CHTBStex","CITt3pp","CLBtex","CLIPAabctex","CLPNH120pp","CLPNH140pp","CLPNH141pp","CLPNH160pp","CLPNH161pp","CLPNH180pp","CLPNH181pp","CLPNS120pp","CLPNS140pp","CLPNS141pp","CLPNS160pp","CLPNS161pp","CLPNS180pp","CLPNS181pp","CLtipp","CMPN","CMPtex","CMtpp","CO2tex","CO2tpp","COBALT2t3pp","COLIPAKpp","COLIPAPabctex","COLIPAabcpp","COLIPAabctex","CPGNR1","CPGNR2","CPGNR3","CPGNUtex","CPGNUtpp","CPGNabcpp","CPGNexs","CPGNtonex","CPL","CPMPS","CRNCAL2","CRNDabcpp","CRNDt2rpp","CRNt2rpp","CRNt8pp","CS1tex","CSNtex","CTBTabcpp","CTBTt2rpp","CTECOAI6","CTECOAI7","CTECOAI8","CURR","CUt2pp","CUt3","CUtex","CXSAMS","CYANtex","CYNTtex","CYSDabcpp","CYSDtex","CYSItex","CYSItpp","CYSSADS","CYTBD2pp","CYTBDpp","CYTBO3_4pp","CYTDtex","DAAD","DADNtex","DAGK120","DAGK140","DAGK141","DAGK160","DAGK161","DAGK180","DAGK181","DALAtex","DAMPtex","DAPabcpp","DAPtex","DASYN120","DASYN140","DASYN141","DASYN160","DASYN161","DASYN180","DASYN181","DATPHs","DB4PS","DC6PDA","DCAtex","DCMPtex","DCYTtex","DDCAtexi","DDGLCNtex","DGMPtex","DGSNt2pp","DGSNtex","DGUNC","DHAtex","DHAtpp","DHBSH","DHBSZ3FEabcpp","DHCINDO","DHCURR","DHDPRy","DHGLYH","DHMPTR","DHNCOAS","DHNCOAT","DHNPTE","DHPStex","DHPStr","DHPTPE","DIMPtex","DINStex","DKGLCNR1","DMPPS","DMSOR1pp","DMSOR2pp","DMStex","DM_5drib_c","DM_aacald_c","DM_amob_c","DM_oxam_c","DOPAte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Annotations Per Database","summary":"Specific database cross-references are paramount to mapping information.\nTo provide references to as many databases as possible helps to make the\nmetabolic model more accessible to other researchers. This does not only\nfacilitate the use of a model in a broad array of computational pipelines,\nit also promotes the metabolic model itself to become an organism-specific\nknowledge base.\n\nFor this test to pass, each gene annotation should contain\ncross-references to a number of databases. The currently selection is\nlisted in `annotation.py`, but an ongoing discussion can be found at\nhttps://github.com/opencobra/memote/issues/332. For each database this\ntest checks for the presence of its corresponding namespace ID to comply\nwith the MIRIAM guidelines i.e. they have to match those defined on\nhttps://identifiers.org/.\n\nSince each database is quite different and some potentially incomplete, it\nmay not be feasible to achieve 100% coverage for each of them. Generally\nit should be possible, however, to obtain cross-references to at least\none of the databases for all gene products consistently.\n\nImplementation:\nCheck if the keys of the annotation attribute of each cobra.Gene of\nthe model match with a selection of common genome databases. The\nannotation  attribute of cobrapy components is a dictionary of\nkey:value pairs.","message":{"refseq":"The following 1516 genes (100.00%) lack annotation for refseq:\nb0002, b0003, b0004, b0007, b0008, ...","uniprot":"The following 1 genes (0.07%) lack annotation for uniprot:\ns0001","ecogene":"The following 1 genes (0.07%) lack annotation for ecogene:\ns0001","kegg.genes":"The following 1516 genes (100.00%) lack annotation for kegg.genes:\nb0002, b0003, b0004, b0007, b0008, ...","ncbigi":"The following 3 genes (0.20%) lack annotation for ncbigi:\nb2092, b4104, s0001","ncbigene":"The following 1 genes (0.07%) lack annotation for ncbigene:\ns0001","ncbiprotein":"The following 1516 genes (100.00%) lack annotation for ncbiprotein:\nb0002, b0003, b0004, b0007, b0008, ...","ccds":"The following 1516 genes (100.00%) lack annotation for ccds:\nb0002, b0003, b0004, b0007, b0008, ...","hprd":"The following 1516 genes (100.00%) lack annotation for hprd:\nb0002, b0003, b0004, b0007, b0008, ...","asap":"The following 1 genes (0.07%) lack annotation for asap:         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Annotation Conformity Per Database","summary":"To identify databases and the identifiers belonging to them, computational\ntools rely on the presence of specific patterns. Only when these patterns\ncan be identified consistently is an ID truly machine-readable. This test\nchecks if the database cross-references in metabolite annotations conform\nto patterns defined according to the MIRIAM guidelines, i.e. matching\nthose that are defined at https://identifiers.org/.\n\nThe required formats, i.e., regex patterns are further outlined in\n`annotation.py`. This test does not carry out a web query for the composed\nURI, it merely controls that the regex patterns match the identifiers.\n\nImplementation:\nFor those metabolites whose annotation keys match any of the tested\ndatabases, check if the corresponding values match the identifier pattern\nof each database.","message":{"pubchem.compound":"There are no metabolite annotations for the pubchem.compound database.","kegg.compound":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nkegg.compound         database:","seed.compound":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nseed.compound         database:","inchikey":"There are no metabolite annotations for the inchikey database.","inchi":"There are no metabolite annotations for the inchi database.","chebi":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the chebi\ndatabase:","hmdb":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the hmdb\ndatabase:","reactome":"There are no metabolite annotations for the reactome database.","metanetx.chemical":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nmetanetx.chemical         database:","bigg.metabolite":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nbigg.metabolite         database:","biocyc":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the biocyc\ndatabase:"},"data":{"pubchem.compound":[],"kegg.compound":[],"seed.compound":[],"inchikey":[],"inchi":[],"chebi":[],"hmdb":[],"reactome":[],"metanetx.chemical":[],"bigg.metabolite":[],"biocyc":[]},"format_type":"percent","metric":{"pubchem.compound":1.0,"kegg.compound":0.0,"seed.compound":0.0,"inchikey":1.0,"inchi":1.0,"chebi":0.0,"hmdb":0.0,"reactome":1.0,"metanetx.chemical":0.0,"bigg.metabolite":0.0,"biocyc":0.0},"score":{"pubchem.compound":0.0,"kegg.compound":1.0,"seed.compound":1.0,"inchikey":0.0,"inchi":0.0,"chebi":1.0,"hmdb":1.0,"reactome":0.0,"metanetx.chemical":1.0,"bigg.metabolite":1.0,"biocyc":1.0}},"test_reaction_annotation_wrong_ids":{"duration":{"rhea":0.0062848589999973115,"kegg.reaction":0.003338947000003145,"seed.reaction":0.004333177999995996,"metanetx.reaction":0.004044437000004564,"bigg.reaction":0.003716212999997026,"reactome":0.001029517000006308,"ec-code":0.0036302219999981844,"brenda":0.0011068100000031222,"biocyc":0.0030045909999998344},"result":{"rhea":"failed","kegg.reaction":"passed","seed.reaction":"passed","metanetx.reaction":"passed","bigg.reaction":"passed","reactome":"failed","ec-code":"failed","brenda":"failed","biocyc":"passed"},"title":"Reaction Annotation Conformity Per Database","summary":"To identify databases and the identifiers belonging to them, computational\ntools rely on the presence of specific patterns. Only when these patterns\ncan be identified consistently is an ID truly machine-readable. This test\nchecks if the database cross-references in reaction annotations conform\nto patterns defined according to the MIRIAM guidelines, i.e. matching\nthose that are defined at https://identifiers.org/.\n\nThe required formats, i.e., regex patterns are further outlined in\n`annotation.py`. This test does not carry out a web query for the composed\nURI, it merely controls that the regex patterns match the identifiers.\n\nImplementation:\nFor those reaction whose annotation keys match any of the tested\ndatabases, check if the corresponding values match the identifier pattern\nof each database.","message":{"rhea":"A total of 51 reaction annotations (1.88%) do not match the\nregular expression patterns defined on identifiers.org for the rhea\ndatabase: ARGabcpp, ASO3t8pp, ASPabcpp, CD2abcpp, CHLabcpp, ...","kegg.reaction":"A total of 0 reaction annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nkegg.reaction         database:","seed.reaction":"A total of 0 reaction annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nseed.reaction         database:","metanetx.reaction":"A total of 0 reaction annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nmetanetx.reaction         database:","bigg.reaction":"A total of 0 reaction annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nbigg.reaction         database:","reactome":"There are no reaction annotations for the reactome database.","ec-code":"A total of 53 reaction annotations (1.95%) do not match the\nregular expression patterns defined on identifiers.org for the ec-code\ndatabase: 4HTHRK, 5DGLCNR, AACPS7, AACPS9, AHGDx, ...","brenda":"There are no reaction annotations for the brenda database.","biocyc":"A total of 0 reaction annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the biocyc\ndatabase:"},"data":{"rhea":["ARGabcpp","ASO3t8pp","ASPabcpp","CD2abcpp","CHLabcpp","COBALT2abcpp","CRNabcpp","CU1abcpp","CU2abcpp","CYSabc2pp","CYSabcpp","FDH4pp","FE3abcpp","GLNabcpp","GLUabcpp","GLYBabcpp","GLYC2Pabcpp","GLYC3Pabcpp","GTHRDabc2pp","GTHRDabcpp","HISabcpp","HYD1pp","HYD2pp","ILEabcpp","K2L4Aabcpp","Kabcpp","LEUabcpp","LIPAabcpp","LYSabcpp","MALTabcpp","METDabcpp","METabcpp","MG2uabcpp","MOBDabcpp","NI2abcpp","NI2uabcpp","NO3R1pp","NO3R2pp","ORNabcpp","PHEMEabcpp","PIuabcpp","PROabcpp","PTRCabcpp","RIBabcpp","SPMDabcpp","SULabcpp","TAURabcpp","TSULabcpp","TUNGSabcpp","VALabcpp","XYLabcpp"],"kegg.reaction":[],"seed.reaction":[],"metanetx.reaction":[],"bigg.reaction":[],"reactome":[],"ec-code":["4HTHRK","5DGLCNR","AACPS7","AACPS9","AHGDx","ALKP","ALLULPE","ALR2","AP4AS","APCS","ASCBPL","ASPO5","CHOLD","CRNCAR","CU1Opp","CU2abcpp","DHPTPE","DKGLCNR2y","DNMPPA","DXYLK","ENTERES","F6PA","FALDH2","FBA3","FDMO2","GALCTLO","GART","GDMANE","GLTPD","GLUTRS","GTHRDHpp","HCYSMT","HEPT1","HEPT2","HOPNTAL","HPYRRy","IDONt2rpp","IG3PS","MACPD","MALTTRabcpp","MALTTTRabcpp","NTP10","NTP12","OBTFL","PDH","PFK_3","PPDOy","PPM","PTHRpp","TDP","TRSARr","ThDPAT","UDCPDPS"],"brenda":[],"biocyc":[]},"format_type":"percent","metric":{"rhea":0.018805309734513276,"kegg.reaction":0.0,"seed.reaction":0.0,"metanetx.reaction":0.0,"bigg.reaction":0.0,"reactome":1.0,"ec-code":0.019542772861356934,"brenda":1.0,"biocyc":0.0},"score":{"rhea":0.9811946902654867,"kegg.reaction":1.0,"seed.reaction":1.0,"metanetx.reaction":1.0,"bigg.reaction":1.0,"reactome":0.0,"ec-code":0.980457227138643,"brenda":0.0,"biocyc":1.0}},"test_gene_product_annotation_wrong_ids":{"duration":{"refseq":0.0009146610000030364,"uniprot":0.0023442459999998277,"ecogene":0.001871712999999886,"kegg.genes":0.000559256000002506,"ncbigi":0.0020234059999992837,"ncbigene":0.0018647180000002095,"ncbiprotein":0.0005913270000021953,"ccds":0.0006143389999948567,"hprd":0.0006905420000009599,"asap":0.0018104769999993664},"result":{"refseq":"failed","uniprot":"passed","ecogene":"passed","kegg.genes":"failed","ncbigi":"failed","ncbigene":"passed","ncbiprotein":"failed","ccds":"failed","hprd":"failed","asap":"passed"},"title":"Gene Annotation Conformity Per Database","summary":"To identify databases and the identifiers belonging to them, computational\ntools rely on the presence of specific patterns. Only when these patterns\ncan be identified consistently is an ID truly machine-readable. This test\nchecks if the database cross-references in reaction annotations conform\nto patterns defined according to the MIRIAM guidelines, i.e. matching\nthose that are defined at https://identifiers.org/.\n\nThe required formats, i.e., regex patterns are further outlined in\n`annotation.py`. This test does not carry out a web query for the composed\nURI, it merely controls that the regex patterns match the identifiers.\n\nImplementation:\nFor those genes whose annotation keys match any of the tested\ndatabases, check if the corresponding values match the identifier pattern\nof each database.","message":{"refseq":"There are no gene annotations for the refseq database.","uniprot":"A total of 0 gene annotations (0.00%) do not match the         regular\nexpression patterns defined on identifiers.org for the uniprot\ndatabase:","ecogene":"A total of 0 gene annotations (0.00%) do not match the         regular\nexpression patterns defined on identifiers.org for the ecogene\ndatabase:","kegg.genes":"There are no gene annotations for the kegg.genes database.","ncbigi":"A total of 1513 gene annotations (99.80%) do not match the\nregular expression patterns defined on identifiers.org for the ncbigi\ndatabase: b0002, b0003, b0004, b0007, b0008, ...","ncbigene":"A total of 0 gene annotations (0.00%) do not match the         regular\nexpression patterns defined on identifiers.org for the ncbigene\ndatabase:","ncbiprotein":"There are no gene annotations for the ncbiprotein database.","ccds":"There are no gene annotations for the ccds database.","hprd":"There are no gene annotations for the hprd database.","asap":"A total of 0 gene annotations (0.00%) do not match the         regular\nexpression patterns defined on identifiers.org for the 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Metabolite Identifier Namespace","summary":"In well-annotated models it is no problem if the pool of main identifiers\nfor metabolites consists of identifiers from several databases. However,\nin models that lack appropriate annotations, it may hamper the ability of\nother researchers to use it. Running the model through a computational\npipeline may be difficult without first consolidating the namespace.\n\nHence, this test checks if the main metabolite identifiers can be\nattributed to one single namespace based on the regex patterns defined at\nhttps://identifiers.org/\n\nImplementation:\nGenerate a table with each column corresponding to one\ndatabase from the selection and each row to a metabolite identifier. A\nBoolean entry indicates whether the identifier matches the regular\nexpression of the corresponding database. Since the Biocyc pattern matches\nbroadly, we assume that any instance of an identifier matching to Biocyc\nAND any other database pattern is a false positive match for Biocyc and\nthus set it to ``false``. Sum the positive matches for each database and\nassume that the largest set is the 'main' identifier namespace.","message":"0 metabolite identifiers (0.00%) deviate from the largest found\nnamespace (bigg.metabolite):","data":[],"format_type":"count","metric":0.0},"test_reaction_id_namespace_consistency":{"duration":0.018947359999998525,"result":"passed","title":"Uniform Reaction Identifier Namespace","summary":"In well-annotated models it is no problem if the pool of main identifiers\nfor reactions consists of identifiers from several databases. However,\nin models that lack appropriate annotations, it may hamper the ability of\nother researchers to use it. Running the model through a computational\npipeline may be difficult without first consolidating the namespace.\n\nHence, this test checks if the main reaction identifiers can be\nattributed to one single namespace based on the regex patterns defined at\nhttps://identifiers.org/\n\nImplementation:\nGenerate a pandas.DataFrame with each column corresponding to one\ndatabase from the selection and each row to the reaction ID. A boolean\nentry indicates whether the metabolite ID matches the regex pattern\nof the corresponding database. Since the Biocyc pattern matches quite,\nassume that any instance of an identifier matching to Biocyc\nAND any other DB pattern is a false positive match for Biocyc and then set\nthe boolean to ``false``. Sum the positive matches for each database and\nassume that the largest set is the 'main' identifier namespace.","message":"0 reaction identifiers (0.00%) deviate from the largest found\nnamespace (bigg.reaction):","data":[],"format_type":"count","metric":0.0},"test_model_id_presence":{"duration":0.0003173440000026062,"result":"failed","title":"Model Identifier","summary":"The MIRIAM guidelines require a model to be identified via an ID.\nFurther, the ID will be displayed on the memote snapshot\nreport, which helps to distinguish the output clearly.\n\nImplementation:\nCheck if the cobra.Model object has a non-empty \"id\"\nattribute, this value is parsed from the \"id\" attribute of the <model> tag\nin the SBML file e.g. <model fbc:strict=\"true\" id=\"iJO1366\">.","message":"The model ID is ","data":"","format_type":"raw","metric":1.0},"test_genes_presence":{"duration":0.0005223570000012501,"result":"passed","title":"Total Genes","summary":"A metabolic model can still be a useful tool without any\ngenes, however there are certain methods which rely on the presence of\ngenes and, more importantly, the corresponding gene-protein-reaction\nrules. 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without Formula","summary":"To be able to ensure that reactions are mass-balanced, all model\nmetabolites ought to be provided with a chemical formula. Since it may be\ndifficult to obtain formulas for certain metabolites this test serves as a\nmere report. Models can still be stoichiometrically consistent even\nwhen chemical formulas are not defined for each metabolite.\n\nImplementation:\nCheck if each cobra.Metabolite has a non-empty \"formula\"\nattribute. This attribute is set by the parser if there is an\nfbc:chemicalFormula attribute for the corresponding species in the\nSBML.","message":"There are a total of 0         metabolites (0.00%) without a formula:","data":[],"format_type":"count","metric":0.0},"test_metabolites_charge_presence":{"duration":0.00045776599999669543,"result":"passed","title":"Metabolites without Charge","summary":"To be able to ensure that reactions are charge-balanced, all model\nmetabolites ought to be provided with a charge. Since it may be\ndifficult to obtain charges for certain metabolites this test serves as a\nmere report. Models can still be stoichiometrically consistent even\nwhen charge information is not defined for each metabolite.\n\nImplementation:\nCheck if each cobra.Metabolite has a non-empty \"charge\"\nattribute. This attribute is set by the parser if there is an\nfbc:charge attribute for the corresponding species in the\nSBML.","message":"There are a total of 0         metabolites (0.00%) without a charge:","data":[],"format_type":"count","metric":0.0},"test_gene_protein_reaction_rule_presence":{"duration":0.00992484900000079,"result":"failed","title":"Reactions without GPR","summary":"Gene-Protein-Reaction rules express which gene has what function.\nThe presence of this annotation is important to justify the existence\nof reactions in the model, and is required to conduct in silico gene\ndeletion studies. However, reactions without GPR may also be valid:\nSpontaneous reactions, or known reactions with yet undiscovered genes\nlikely lack GPR.\n\nImplementation:\nCheck if each cobra.Reaction has a non-empty\n\"gene_reaction_rule\" attribute, which is set by the parser if there is an\nfbc:geneProductAssociation defined for the corresponding reaction in the\nSBML.","message":"There are a total of 109 reactions (4.02%) without GPR:\nCH4tex, URIC, FECRMR3, BIOMASS_Ec_iML1515_core_75p37M, URAtpp, ...","data":["CH4tex","URIC","FECRMR3","BIOMASS_Ec_iML1515_core_75p37M","URAtpp","FE3HOXUtpp","ARBTNtex","CPGNUtex","LIPOt2pp","CITt3pp","FEOXAMUtpp","CPGNR3","ARBTNR1","MOX","CLPNH120pp","ARBTNtpp","NMNN","12PPDRtpp","FEOXAMUtex","BIOMASS_Ec_iML1515_WT_75p37M","5MTRtpp","12DGR120tipp","12DGR181tipp","12PPDStpp","12DGR140tipp","OMMBLHX3","CDGS","CLPNH181pp","LALDO3","METSOX2abcpp","AACTOOR","CLPNH180pp","FECRMUtpp","ATPM","12DGR141tipp","HEX4","FE3HOXR1","GUR1PPpp","PHEMEtiex","12DGR180tipp","PYDAMtpp","ThDPAT","FTHFLi","DXYLONtpp","QUIN2tpp","PYDXNtpp","MALt3pp","ETHAt2pp","OXAMTC","FEENTERR3","CLPNH140pp","12DGR160tipp","CLPNH160pp","UDCPPtppi","CPGNR2","DNMPPA","CPGNR1","DHBSH","OPHHX3","FE3HOXUtex","12DGR161tipp","DAPabcpp","GUACYC","FE3HOXR2","SELGTHR3","FECRMR1","PACALDt2rpp","CPGNUtpp","PYDXtpp","FEENTERR2","ALDD4","DHAtpp","NACtpp","FE3abcpp","THYMt3pp","PDX5PO2","CYSDabcpp","O16GLCT2","ARBTNR2","23DAPPAt2pp","PYRt2rpp","HYPOE","FEENTERR1","NADN","H2SO","R1PK","ACGAL1PPpp","ACGAM1PPpp","3HPPtpp","CLPNH141pp","NADPPPS","FE3HOXR3","CH4t2pp","MINOHPtexi","FECRMUtex","SELGTHR2","MG2t3_2pp","ARBTNR3","BTNt2ipp","FECRMR2","XANtpp","SELGTHR","DHORDfum","CMPN","METSOX1abcpp","NMNt7pp","PPALtpp","CLPNH161pp","ARBTNtonex"],"format_type":"count","metric":0.04019174041297935},"test_ngam_presence":{"duration":0.29041595399999665,"result":"passed","title":"Non-Growth Associated Maintenance Reaction","summary":"The Non-Growth Associated Maintenance reaction (NGAM) is an\nATP-hydrolysis reaction added to metabolic models to represent energy\nexpenses that the cell invests in continuous processes independent of\nthe growth rate. Memote tries to infer this reaction from a list of\nbuzzwords, and the stoichiometry and components of a simple ATP-hydrolysis\nreaction.\n\nImplementation:\nFrom the list of all reactions that convert ATP to ADP select the reactions\nthat match the irreversible reaction \"ATP + H2O -> ADP + HO4P + H+\",\nwhose metabolites are situated within the main model compartment.\nThe main model compartment is assumed to be the cytosol, yet, if that\ncannot be identified, it is assumed to be the compartment with the most\nmetabolites. The resulting list of reactions is then filtered further by\nattempting to match the reaction name with any of the following buzzwords\n('maintenance', 'atpm', 'requirement', 'ngam', 'non-growth', 'associated').\nIf this is possible only the filtered reactions are returned, if not the\nlist is returned as is.","message":"A total of 1 NGAM reactions could be identified:         ATPM","data":["ATPM"],"format_type":"count","metric":0.0},"test_metabolic_coverage":{"duration":0.0002193099999985293,"result":"passed","title":"Metabolic Coverage","summary":"The degree of metabolic coverage indicates the modeling detail of a\ngiven reconstruction calculated by dividing the total amount of\nreactions by the amount of genes. Models with a 'high level of modeling\ndetail have ratios >1, and models with a low level of detail have\nratios <1. This difference arises as models with basic or intermediate\nlevels of detail are assumed to include many reactions in which several\ngene products and their enzymatic transformations are ‘lumped’.\n\nImplementation:\nDivides the amount reactions by the amount of genes. Raises an error\nif the model does not contain either reactions or genes.","message":"The degree of metabolic coverage is 1.8.","data":[2712,1516],"format_type":"percent","metric":1.7889182058047493},"test_compartments_presence":{"duration":0.0008552709999989361,"result":"passed","title":"Total Compartments","summary":"While simplified metabolic models may be perfectly viable, generally\nacross the tree of life organisms contain at least one distinct\ncompartment: the cytosol or cytoplasm. In the case of prokaryotes there is\nusually a periplasm, and eurkaryotes are more complex. In addition to the\ninternal compartment, a metabolic model also reflects the extracellular\nenvironment i.e. the medium/ metabolic context in which the modelled cells\ngrow. Hence, in total, at least two compartments can be expected from a\nmetabolic model.\n\nImplementation:\nCheck if the cobra.Model object has a non-empty \"compartments\"\nattribute, this list is populated from the list of sbml:listOfCompartments\nwhich should contain at least two sbml:compartment elements.","message":"A total of 3 compartments are defined in the model: c, p, e","data":["c","p","e"],"format_type":"count","metric":0.0},"test_protein_complex_presence":{"duration":0.05994172000000475,"result":"passed","title":"Enzyme Complexes","summary":"Based on the gene-protein-reaction (GPR) rules, it is possible to infer\nwhether a reaction is catalyzed by a single gene product, isozymes or by a\nheteromeric protein complex. This test checks that at least one\nsuch heteromeric protein complex is defined in any GPR of the model. For\nS. cerevisiae it could be shown that \"essential proteins tend to [cluster]\ntogether in essential complexes\"\n(https://doi.org/10.1074%2Fmcp.M800490-MCP200).\n\nThis might also be a relevant metric for other organisms.\n\nImplementation:\nIdentify GPRs which contain at least one logical AND that combines two\ndifferent gene products.","message":"A total of 309 reactions are catalyzed by complexes defined\nthrough GPR rules in the model.","data":["14GLUCANabcpp","23DOGULNt4pp","2DGLCptspp","3PEPTabcpp","4ABZGLUH","4HBZt3pp","4PEPTabcpp","AACPS1","AACPS2","AACPS3","AACPS4","AACPS5","AACPS6","AACPS7","AACPS8","AACPS9","ACACCT","ACCOAC","ACGAptspp","ACHBS","ACLS","ACMANAptspp","ACMUMptspp","ACOATA","ACOLIPAabctex","ACPPAT120","ACPPAT140","ACPPAT141","ACPPAT160","ACPPAT161","ACPPAT180","ACPPAT181","ADCS","ADOCBLabcpp","ADOCBLtonex","AGt3","AI2abcpp","AKGDH","ALAALAabcpp","ALAabcpp","ALLabcpp","ALPATE160pp","ALPATG160pp","ANS","ARBTNabcpp","ARBTptspp","ARBabcpp","ARGabcpp","ARMEPNS","ASCBptspp","ASPCT","ASPabcpp","ASR","ATPS4rpp","BMOGDS1","BUTCT","BUTSO3abcpp","CBItonex","CBIuabcpp","CBL1abcpp","CBL1tonex","CBPS","CELBpts","CGLYabcpp","CHLabcpp","CHTBSptspp","CINNDO","CITL","CLIPAabctex","CMtpp","COLIPAPabctex","COLIPAabctex","CPGNabcpp","CPGNtonex","CPMPS","CRNDabcpp","CRNabcpp","CTBTabcpp","CUt3","CYSabc2pp","CYSabcpp","CYTBD2pp","CYTBDpp","CYTBO3_4pp","DHAPT","DHBSZ3FEabcpp","DMSOR1","DMSOR1pp","DMSOR2","DMSOR2pp","DOXRBCNtpp","DSBAO1","DSBAO2","DSBDR","DURADx","ECA4COLIPAabctex","ECAP1pp","ECAP2pp","ECAP3pp","ENLIPAabctex","ETHAAL","ETHSO3abcpp","FADRx2","FDH4pp","FDH5pp","FE3DCITabcpp","FE3DCITtonex","FE3DHBZStonex","FE3HOXabcpp","FE3HOXtonex","FECRMabcpp","FECRMtonex","FEENTERabcpp","FEENTERtonex","FEOXAMabcpp","FEOXAMtonex","FHL","FLDR2","FLVR","FMNRx2","FRD2","FRD3","FRUpts2pp","FRUptspp","FUSAtpp","G3PAT120","G3PAT140","G3PAT141","G3PAT160","G3PAT161","G3PAT180","G3PAT181","G3PCabcpp","G3PD5","G3PD6","G3PD7","G3PEabcpp","G3PGabcpp","G3PIabcpp","G3PSabcpp","GALTptspp","GALabcpp","GAMptspp","GLCabcpp","GLCptspp","GLNabcpp","GLUDy","GLUSy","GLUabcpp","GLYBabcpp","GLYC2Pabcpp","GLYC3Pabcpp","GLYCL","GLYCTO2","GLYCTO3","GLYCTO4","GTHRDabc2pp","GTHRDabcpp","HISabcpp","HXAND","HXCT","HYD1pp","HYD2pp","HYD3pp","I2FE2SR","I2FE2SS","I2FE2SS2","I2FE2ST","I4FE4ST","IG3PS","ILEabcpp","INDOLEt2pp","IPPMIa","IPPMIb","ISETACabcpp","K2L4Aabctex","Kabcpp","Kt2pp","LEUabcpp","LIPAabctex","LYSabcpp","L_LACD2","L_LACD3","MALTHXabcpp","MALTPTabcpp","MALTTRabcpp","MALTTTRabcpp","MALTabcpp","MALTptspp","MANGLYCptspp","MANptspp","MCOATA","MCTP1App","MCTP2App","MECDPDH5","MEPNabcpp","METDabcpp","METSOXR1","METSOXR2","METabcpp","MINCYCtpp","MNLptspp","MOADSUx","MOBDabcpp","MPTG","MPTG2","MPTS","MSO3abcpp","NADH16pp","NADH17pp","NADH18pp","NADHPO","NHFRBO","NI2uabcpp","NO3R1bpp","NO3R1pp","NO3R2bpp","NO3R2pp","NOVBCNtpp","NTRIR2x","NTRIR3pp","NTRIR4pp","O16A4COLIPAabctex","O16AP1pp","O16AP2pp","O16AP3pp","OBTFL","ORNabcpp","OXDHCOAT","PACCOAE","PAPSR","PAPSR2","PDH","PDX5PS","PFL","PHEMEabcpp","PIuabcpp","POR5","PPPNDO","PROGLYabcpp","PROabcpp","PTRCabcpp","PUACGAMS","PUACGAMtr","PYROX","RFAMPtpp","RIBabcpp","RNDR1","RNDR1b","RNDR2","RNDR2b","RNDR3","RNDR3b","RNDR4","RNDR4b","RNTR1c2","RNTR2c2","RNTR3c2","RNTR4c2","S2FE2SR","S2FE2SS","S2FE2SS2","S2FE2ST","S4FE4SR","S4FE4ST","SADT2","SBTptspp","SCYSDS","SELR","SELabcpp","SLNTabcpp","SPMDabcpp","SPMDt3pp","SUCDi","SUCOAS","SUCptspp","SULFACabcpp","SULR","SULabcpp","TARTD","TAURabcpp","TDSR1","TDSR2","TGBPA","THD2pp","THIORDXi","THMabcpp","THRabcpp","THZPSN3","TMAOR1","TMAOR1pp","TMAOR2","TMAOR2pp","TRDR","TREptspp","TRPS1","TRPS2","TRPS3","TSULabcpp","TTRCYCtpp","TUNGSabcpp","UAGAAT","ULA4Ntppi","VALabcpp","VALt3pp","XAND","XYLUt2pp","XYLabcpp","ZNabcpp"],"format_type":"count","metric":0.11393805309734513},"test_find_pure_metabolic_reactions":{"duration":0.031094176999999945,"result":"passed","title":"Purely Metabolic Reactions","summary":"If a reaction is neither a transport reaction, a biomass reaction nor a\nboundary reaction, it is counted as a purely metabolic reaction. This test\nrequires the presence of metabolite formula to be able to identify\ntransport reactions. This test is passed when the model contains at least\none purely metabolic reaction i.e. a conversion of one metabolite into\nanother.\n\nImplementation:\nFrom the list of all reactions, those that are boundary, transport and\nbiomass reactions are removed and the remainder assumed to be pure\nmetabolic reactions. Boundary reactions are identified using the attribute\ncobra.Model.boundary. Please read the description of \"Transport Reactions\"\nand \"Biomass Reaction Identified\" to learn how they are identified.","message":"A total of 1542 (56.86%) purely metabolic reactions are defined in\nthe model, this excludes transporters, exchanges, or pseudo-reactions:\nNTPP5, URIC, RNTR3c2, HACD3, NTPP4, 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Metabolic Reactions with Constraints","summary":"If a reaction is neither a transport reaction, a biomass reaction nor a\nboundary reaction, it is counted as a purely metabolic reaction. This test\nrequires the presence of metabolite formula to be able to identify\ntransport reactions. This test simply reports the number of purely\nmetabolic reactions that have fixed constraints and does not have any\nmandatory 'pass' criteria.\n\nImplementation: From the pool of pure metabolic reactions identify\nreactions which are constrained to values other than the model's minimal or\nmaximal possible bounds.","message":"A total of 2 (0.13%) purely metabolic reactions have fixed\nconstraints in the model, this excludes transporters, exchanges, or\npseudo-reactions: 6.86 <= ATPM <= 1000.0, 0.0 <= FHL <= 0.0","data":["6.86 <= ATPM <= 1000.0","0.0 <= FHL <= 0.0"],"format_type":"count","metric":0.0012970168612191958},"test_find_transport_reactions":{"duration":0.0004988929999996117,"result":"passed","title":"Transport Reactions","summary":"Cellular metabolism in any organism usually involves the transport of\nmetabolites across a lipid bi-layer. This test reports how many\nof these reactions, which transports metabolites from one compartment\nto another, are present in the model, as at least one transport reaction\nmust be present for cells to take up nutrients and/or excrete waste.\n\nImplementation:\nA transport reaction is defined as follows:\n1. It contains metabolites from at least 2 compartments and\n2. at least 1 metabolite undergoes no chemical reaction, i.e.,\nthe formula and/or annotation stays the same on both sides of the equation.\n\nA notable exception is transport via PTS, which also contains the following\nrestriction:\n3. The transported metabolite(s) are transported into a compartment through\nthe exchange of a phosphate.\n\nAn example of transport via PTS would be\npep(c) + glucose(e) -> glucose-6-phosphate(c) + pyr(c)\n\nReactions similar to transport via PTS (referred to as \"modified transport\nreactions\") follow a similar pattern:\nA(x) + B-R(y) -> A-R(y) + B(y)\n\nSuch modified transport reactions can be detected, but only when the\nformula is defined for all metabolites in a particular reaction. If this\nis not the case, transport reactions are identified through annotations,\nwhich cannot detect modified transport reactions.","message":"A total of 831 (30.64%) transport reactions are defined in the\nmodel, this excludes purely metabolic reactions, exchanges, or\npseudo-reactions: UREAtpp, MSO3abcpp, CYSItpp, PIt2rpp, COLIPAPabctex,\n...","data":["UREAtpp","MSO3abcpp","CYSItpp","PIt2rpp","COLIPAPabctex","CYSabc2pp","GLCRtex","CHOLATEtpp","FE3HOXtonex","GMPtex","PHEtex","CHLt3pp","TDSR2","DAPtex","MALTabcpp","TDSR1","XMPtex","4PEPTabcpp","FMNtex","DADNtex","PSURItpp","THRabcpp","PE181abcpp","MALTTRtexi","HPPPNt2rpp","THRt2pp","COBALT2t3pp","DALAt2pp","MALTTRabcpp","GBBTNtex","QUIN2tex","K2L4Aabcpp","UDPGtex","PHEtipp","GLYCtex","PHEMEabcpp","HPPPNtex","TYRt2rpp","METSOX2abcpp","CHLtex","THD2pp","GLCURt2rpp","DALAtex","14GLUCANtexi","GUAt2pp","23CAMPtex","PA181abcpp","G3PCabcpp","MALTTTRabcpp","SULFACtex","TYRtex","FMNt","PHEMEtiex","COBALT2abcpp","PIuabcpp","FE3tex","CMtpp","GUAtpp","DAMPtex","PEAMNtex","UDPACGALtex","GUAtex","CO2tex","TYRtipp","H2O2tex","23CCMPtex","ADEt2rpp","URIt2pp_copy1","GLYCtpp","QUIN2tpp","ETHAt2pp","DMSOR1pp","MALTTTRtexi","URIt2pp_copy2","URItex","ADEtex","SULabcpp","THRPtex","L_LACt2rpp","L_LACtex","GLCUR1Ptex","PPAtex","PItex","UACGAMtex","DAPabcpp","PTRCORNt7pp","GAMptspp","TMAOtex","DSBAO2","TMAOR2pp","FE2t2pp","TTDCAtexi","CBL1abcpp","XANtex","GALCTNLt2pp","NTRIR4pp","XANt2pp","4ABZGLUtr","4HOXPACDtex","GAMtex","MALDt2_2pp","DMSOtpp","G6Pt6_2pp","PSURItex","DMSOR2pp","SELtex","DMStex","FUMt2_3pp","O16A4COLIPAabctex","23DAPPAt2pp","PYRt2rpp","OCDCAtexi","MAN6Ptex","DTMPtex","FE2tpp","ETHSO3abcpp","DSBAO1","GALTtex","CBL1tonex","GTHRDabcpp","OCDCEAtexi","XTSNt2rpp","ALAtpp","GAL1Ptex","PROGLYabcpp","OCTAtex","ALAt4pp","TUNGSabcpp","GALCTNLtex","GLYt4pp","AGM3Pt2pp","GLYtpp","TTRCYCtpp","ABUTtex","GTHRDtex","ABUTt2pp","NACtex","MALDtex","GLYtex","GAM6Pt6_2pp","TYRPtex","MAN6Pt6_2pp","GAMAN6Ptex","XANtpp","PROGLYtex","DCAtex","FUMt2_2pp","TUNGStex","FUMtex","GALBDtex","TYMtex","FUMt1pp","GLYBabcpp","N2Otpp","ARBTNabcpp","FEOXAMtonex","N2Otex","GALCTNt2pp","G6Ptex","ECAtpp","GALURtex","METSOX1tex","DMSOtex","ARBTNtonex","CH4tex","GLYC3Pt6pp","G3PSabcpp","DSERtex","URAtpp","RMNtpp","PUACGAMtr","Ftex","GALURt2rpp","PItpp","GLYC2Ptex","NO3t7pp","CYTBDpp","FE2t3pp","CYTBD2pp","FRUptspp","SO4t2pp","NADH18pp","URAt2pp","LYSt2pp","LYSabcpp","LIPOt2pp","ALLabcpp","LIPAabctex","GALabcpp","ACMUMtex","LYStex","URAtex","GALtex","SLNTabcpp","MELIBtex","ALLtex","GALCTt2rpp","LALALGLUtex","G3PGabcpp","LALADGLUtpp","SLNTtex","ACMUMptspp","SO2tex","XYLtex","FEOXAMUtex","FRUtex","ASO3t8pp","ASO3tex","XYLUt2pp","NO3tex","GLYC3Ptex","LYSt3pp","12DGR120tipp","PACALDtex","G3PStex","GALTptspp","12DGR181tipp","12DGR140tipp","INOSTt4pp","BTNtex","12PPDRtex","ACMANAtex","GDPtex","LALALGLUtpp","LYXtex","FRULYSt2pp","HYD2pp","PG160abcpp","ACNAMt2pp","TREptspp","METDtex","SO3tex","MALtex","GLYC3Pabcpp","INSt2pp","FUCtex","MELIBt3ipp","FEOXAMabcpp","K2L4Aabctex","12DGR141tipp","METDabcpp","12DGR180tipp","TREtex","CITt7pp","DSERt2pp","FRULYStex","GALCTNtex","PA140abcpp","MELIBt2pp","ISETACabcpp","DURItex","XYLUtex","RMNtex","Ftpp","CHLabcpp","PA120abcpp","FE2tex","23CGMPtex","MEOHtex","PA141abcpp","LYXt2pp","ACNAMtex","G3PGtex","5MTRtex","CYTBO3_4pp","GALt2pp","CELBpts","INSTtex","GLYCAtex","SKMt2pp","PG140abcpp","DHAtex","MPTG2","SKMtex","UDCPPtppi","NTRIR3pp","PG141abcpp","XYLabcpp","3CMPtex","12DGR160tipp","FE3DHBZStonex","GLYCAt2rpp","ISETACtex","GTPtex","HYD1pp","AGM4Pt2pp","12DGR161tipp","FRUURt2rpp","23CUMPtex","GALCTtex","3GMPtex","PG120abcpp","NOVBCNtpp","ACtex","THMDt2pp_copy2","PROt2rpp","DCYTt2pp","LEUabcpp","PPAt4pp","MEOHtrpp","PROabcpp","CPGNUtpp","MEPNabcpp","FACOAL161t2pp","NADH17pp","Kabcpp","G3PIabcpp","THMabcpp","MG2tex","Kt3pp","SQtex","MG2uabcpp","LEUt2rpp","PSCLYSt2pp","METabcpp","MN2tpp","FACOAL120t2pp","Kt2pp","DCMPtex","FUSAtex","ACt2rpp","NOVBCNtex","ARGtex","MN2tipp","SUCCt2_2pp","SQtr","METtex","ACt4pp","ARGabcpp","MNLptspp","MNtex","CPGNabcpp","FACOAL140t2pp","PYDAMtex","FACOAL160t2pp","METSOX2tex","CHLt2pp","SUCCt2_3pp","FADt","DDCAtexi","ARGt3pp","ACSERtpp","CS1tex","G3PItex","PROt4pp","NMNPtpp","PSCLYStex","MINCYCtex","PSERtex","THMtex","CH4t2pp","FE3DCITabcpp","LIPACabcpp","NAt3_1p5pp","MINOHPtexi","SUCCt1pp","LEUtex","THYMtex","NH4tex","34dhpactex","MG2t3_2pp","ACSERtex","Ktex","SUCCtex","BTNt2ipp","MINCYCtpp","FUSAtpp","SUCASPtpp","FADtex","CAt6pp","CITtex","FACOAL141t2pp","CSNt2pp","METSOX1abcpp","PPALtex","NOtex","NMNt7pp","THMDt2pp_copy1","PPALtpp","NO2t2rpp","DCYTtex","MNt2pp","NMNtex","LEUt3pp","R5Ptex","NH4tpp","NO2tex","THMDtex","MEPNtex","DGSNt2pp","CRNt8pp","FORt2pp","BALAtex","BUTSO3tex","DHBSZ3FEabcpp","PPPNtex","MALTHXtexi","TTDCEAtexi","ARBTNtex","LCTStex","FACOAL100t2pp","CRNDabcpp","CITt3pp","FEOXAMUtpp","PPTtex","DGSNtex","PPPNt2rpp","CYSDtex","DOPAtex","HOMt2pp","ARBTNtpp","LCTStpp","CRNDt2rpp","ADNt2pp_copy1","DOXRBCNtpp","DOXRBCNtex","5MTRtpp","CA2t3pp","MALTPTtexi","GTHOXtex","CGLYabcpp","PGP181abcpp","FORtppi","CRNabcpp","AI2tex","CRNt2rpp","ADNt2pp_copy2","PTRCabcpp","D_LACt2pp","G3PEabcpp","GLCDpp","NO3R2pp","CRNtex","HOMtex","AI2tpp","DIMPtex","FEENTERtex","O16AUNDtpp","CRNDtex","GSNt2pp","DINStex","ADNtex","BALAt2pp","TTRCYCtex","PTRCt2pp","CRNt7pp","TSULtex","DINSt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Reactions with Constraints","summary":"Cellular metabolism in any organism usually involves the transport of\nmetabolites across a lipid bi-layer. Hence, this test reports how many\nof these reactions, which transports metabolites from one compartment\nto another, have fixed constraints. This test does not have any mandatory\n'pass' criteria.\n\nImplementation:\nPlease refer to \"Transport Reactions\" for details on how memote identifies\ntransport reactions.\nFrom the pool of transport reactions identify reactions which are\nconstrained to values other than the model's median lower and upper bounds.","message":"A total of 0 (0.00%) transport reactions have fixed\nconstraints in the model:","data":[],"format_type":"count","metric":0.0},"test_transport_reaction_gpr_presence":{"duration":0.003303670999997621,"result":"passed","title":"Fraction of Transport Reactions without GPR","summary":"As it is hard to identify the exact transport processes within a cell,\ntransport reactions are often added purely for modeling purposes.\nHighlighting where assumptions have been made versus where\nthere is proof may help direct the efforts to improve transport and\ntransport energetics of the tested metabolic model.\nHowever, transport reactions without GPR may also be valid:\nDiffusion, or known reactions with yet undiscovered genes likely lack GPR.\n\nImplementation:\nCheck which cobra.Reactions classified as transport reactions have a\nnon-empty \"gene_reaction_rule\" attribute.","message":"There are a total of 53 transport reactions (6.38% of all\ntransport reactions) without GPR:         METSOX2abcpp, PHEMEtiex,\nQUIN2tpp, ETHAt2pp, DAPabcpp, ...","data":["METSOX2abcpp","PHEMEtiex","QUIN2tpp","ETHAt2pp","DAPabcpp","23DAPPAt2pp","PYRt2rpp","XANtpp","ARBTNtonex","CH4tex","URAtpp","LIPOt2pp","FEOXAMUtex","12DGR120tipp","12DGR181tipp","12DGR140tipp","12DGR141tipp","12DGR180tipp","UDCPPtppi","12DGR160tipp","12DGR161tipp","CPGNUtpp","CH4t2pp","MINOHPtexi","MG2t3_2pp","BTNt2ipp","METSOX1abcpp","NMNt7pp","PPALtpp","ARBTNtex","CITt3pp","FEOXAMUtpp","ARBTNtpp","5MTRtpp","PYDXtpp","CYSDabcpp","FE3HOXUtpp","CPGNUtex","12PPDRtpp","12PPDStpp","FECRMUtpp","PYDAMtpp","DXYLONtpp","PYDXNtpp","MALt3pp","FE3HOXUtex","PACALDt2rpp","DHAtpp","NACtpp","THYMt3pp","FE3abcpp","3HPPtpp","FECRMUtex"],"format_type":"percent","metric":0.06377858002406739},"test_find_reversible_oxygen_reactions":{"duration":0.047328750999994895,"result":"passed","title":"Number of Reversible Oxygen-Containing Reactions","summary":"The directionality of oxygen-producing/-consuming reactions affects the\nmodel's ability to grow anaerobically i.e. create faux-anaerobic organisms.\nThis test reports how many of these oxygen-containing reactions are\nreversible. This test does not have any mandatory 'pass' criteria.\n\nImplementation:\nFirst, find the metabolite representing atmospheric oxygen in the model on\nthe basis of an internal mapping table or by specifically looking for the\nformula \"O2\". Then, find all reactions that produce or consume oxygen and\nreport those that are reversible.","message":"There are a total of 5 reversible oxygen-containing reactions\n(9.80% of all oxygen-containing reactions): INOSTO, O2tex, O2tpp,\nEX_o2_e, O2Stex","data":["INOSTO","O2tex","O2tpp","EX_o2_e","O2Stex"],"format_type":"count","metric":0.09803921568627451},"test_find_unique_metabolites":{"duration":0.5761907370000046,"result":"passed","title":"Unique Metabolites","summary":"Metabolites may be transported into different compartments, which means\nthat in a compartimentalized model the number of metabolites may be\nmuch higher than in a model with no compartments. This test counts only\none occurrence of each metabolite and returns this as the number of unique\nmetabolites. The test expects that the model is compartimentalized, and\nthus, that the number of unique metabolites is generally lower than the\ntotal number of metabolites.\n\nImplementation:\nReduce the list of metabolites to a unique set by removing the compartment\ntag. The cobrapy SBML parser adds compartment tags to each metabolite ID.","message":"Not counting the same entities in other compartments, there is a\ntotal of 1169 (62.28%) unique metabolites in the model: unaga, acACP,\ndtdp4d6dg, wco, 3mop, 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Components","summary":"This test checks all boundary reactions in the model that permit flux\ntowards creating a metabolite, and reports those metabolites. This test\ndoes not have any mandatory 'pass' criteria.\n\nImplementation:\nIdentify the metabolite IDs of each reaction in the method\ncobra.Model.medium. Model.medium returns exchange reactions whose bounds\npermit the uptake of metabolites.","message":null,"data":["ca2_e","cl_e","co2_e","cobalt2_e","cu2_e","fe2_e","fe3_e","glc__D_e","h2o_e","h_e","k_e","mg2_e","mn2_e","mobd_e","na1_e","nh4_e","ni2_e","o2_e","pi_e","sel_e","slnt_e","so4_e","tungs_e","zn2_e"],"format_type":"count","metric":1.0},"test_biomass_presence":{"duration":0.0002598370000015393,"result":"passed","title":"Biomass Reactions Identified","summary":"The biomass composition aka biomass formulation aka biomass reaction\nis a common pseudo-reaction accounting for biomass synthesis in\nconstraints-based modelling. It describes the stoichiometry of\nintracellular compounds that are required for cell growth. While this\nreaction may not be relevant to modeling the metabolism of higher\norganisms, it is essential for single-cell modeling.\n\nImplementation:\nIdentifies possible biomass reactions using two principal steps:\n    1. Return reactions that include the SBO annotation \"SBO:0000629\" for\n    biomass.\nIf no reactions can be identifies this way:\n    1. Look for the ``buzzwords`` \"biomass\", \"growth\" and \"bof\" in reaction\n    IDs.\n    2. Look for metabolite IDs or names that contain the ``buzzword``\n    \"biomass\" and obtain the set of reactions they are involved in.\n    3. Remove boundary reactions from this set.\n    4. Return the union of reactions that match the buzzwords and of the\n    reactions that metabolites are involved in that match the buzzword.\nThis test checks if at least one biomass reaction is present.","message":"In this model 2 the following biomass reactions were\nidentified: BIOMASS_Ec_iML1515_WT_75p37M,\nBIOMASS_Ec_iML1515_core_75p37M","data":["BIOMASS_Ec_iML1515_WT_75p37M","BIOMASS_Ec_iML1515_core_75p37M"],"format_type":"count","metric":0.0},"test_biomass_consistency":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0006759239999993838,"BIOMASS_Ec_iML1515_core_75p37M":0.0005263449999972636},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"passed","BIOMASS_Ec_iML1515_core_75p37M":"passed"},"title":"Biomass Consistency","summary":"This test only yields sensible results if all biomass precursor\nmetabolites have chemical formulas assigned to them.\nThe molecular weight of the biomass reaction in metabolic models is\ndefined to be equal to 1 g/mmol. Conforming to this is essential in order\nto be able to reliably calculate growth yields, to cross-compare models,\nand to obtain valid predictions when simulating microbial consortia. A\ndeviation from 1 - 1E-03 to 1 + 1E-06 is accepted.\n\nImplementation:\nMultiplies the coefficient of each metabolite of the biomass reaction with\nits molecular weight calculated from the formula, then divides the overall\nsum of all the products by 1000.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"The component molar mass of the biomass reaction\nBIOMASS_Ec_iML1515_WT_75p37M sums up to 0.9992627956155418\nwhich is outside of the 1e-03 margin from 1 mmol / g[CDW] / h.","BIOMASS_Ec_iML1515_core_75p37M":"The component molar mass of the biomass reaction\nBIOMASS_Ec_iML1515_core_75p37M sums up to 0.9999382297074995\nwhich is outside of the 1e-03 margin from 1 mmol / g[CDW] / h."},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":0.9992627956155418,"BIOMASS_Ec_iML1515_core_75p37M":0.9999382297074995},"format_type":"number","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":1.0,"BIOMASS_Ec_iML1515_core_75p37M":1.0}},"test_biomass_default_production":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":0.1774406380000002,"BIOMASS_Ec_iML1515_core_75p37M":0.02194901499999702},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"failed","BIOMASS_Ec_iML1515_core_75p37M":"passed"},"title":"Biomass Production In Default Medium","summary":"Using flux balance analysis this test optimizes the model for growth in\nthe medium that is set by default. Any non-zero growth rate is accepted to\npass this test.\n\nImplementation:\nCalculate the solution of FBA with the biomass reaction set as objective\nfunction and the model's default constraints.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_WT_75p37M this is the\ngrowth rate (1/h) that         can be achieved when the model is\nsimulated on the provided         default medium: 0.0","BIOMASS_Ec_iML1515_core_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_core_75p37M this is the\ngrowth rate (1/h) that         can be achieved when the model is\nsimulated on the provided         default medium: 0.8769972144269789"},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.8769972144269789},"format_type":"number","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":1.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":1.0}},"test_biomass_open_production":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":0.10477455200000207,"BIOMASS_Ec_iML1515_core_75p37M":0.03737740700000103},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"passed","BIOMASS_Ec_iML1515_core_75p37M":"passed"},"title":"Biomass Production In Complete Medium","summary":"Using flux balance analysis this test optimizes the model for growth using\na complete medium i.e. unconstrained boundary reactions. Any non-zero\ngrowth rate is accepted to pass this test.\n\nImplementation:\nCalculate the solution of FBA with the biomass reaction set as objective\nfunction and after removing any constraints from all boundary reactions.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_WT_75p37M this is the\ngrowth rate that can be         achieved when the model is simulated\non a complete medium i.e.         with all the boundary reactions\nunconstrained: 74.96133508860252","BIOMASS_Ec_iML1515_core_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_core_75p37M this is the\ngrowth rate that can be         achieved when the model is simulated\non a complete medium i.e.         with all the boundary reactions\nunconstrained: 74.89571939472694"},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":74.96133508860252,"BIOMASS_Ec_iML1515_core_75p37M":74.89571939472694},"format_type":"number","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":1.0,"BIOMASS_Ec_iML1515_core_75p37M":1.0}},"test_biomass_precursors_default_production":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":6.831940409999994,"BIOMASS_Ec_iML1515_core_75p37M":4.174682094999994},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"failed","BIOMASS_Ec_iML1515_core_75p37M":"passed"},"title":"Blocked Biomass Precursors In Default Medium","summary":"Using flux balance analysis this test optimizes for the production of each\nmetabolite that is a substrate of the biomass reaction with the exception\nof atp and h2o. Optimizations are carried out using the default\nconditions. This is useful when reconstructing the precursor biosynthesis\npathways of a metabolic model. To pass this test, the model should be able\nto synthesis all the precursors.\n\nImplementation:\nFor each biomass precursor (except ATP and H2O) add a temporary demand\nreaction, then carry out FBA with this reaction as the objective. Collect\nall metabolites for which this optimization is equal to zero or\ninfeasible.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_WT_75p37M and when the\nmodel is simulated on the         provided default medium a total of 1\nprecursors         (1.08% of all precursors except h2o and atp) cannot\nbe produced: ['adocbl_c']","BIOMASS_Ec_iML1515_core_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_core_75p37M and when the\nmodel is simulated on the         provided default medium a total of 0\nprecursors         (0.00% of all precursors except h2o and atp) cannot\nbe produced: []"},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":["adocbl_c"],"BIOMASS_Ec_iML1515_core_75p37M":[]},"format_type":"count","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":0.010752688172043012,"BIOMASS_Ec_iML1515_core_75p37M":0.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":0.989247311827957,"BIOMASS_Ec_iML1515_core_75p37M":1.0}},"test_biomass_precursors_open_production":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":4.187066242,"BIOMASS_Ec_iML1515_core_75p37M":2.7157701000000003},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"passed","BIOMASS_Ec_iML1515_core_75p37M":"passed"},"title":"Blocked Biomass Precursors In Complete Medium","summary":"Using flux balance analysis this test optimizes for the production of each\nmetabolite that is a substrate of the biomass reaction with the exception\nof atp and h2o. Optimizations are carried out using a complete\nmedium i.e. unconstrained boundary reactions. This is useful when\nreconstructing the precursor biosynthesis pathways of a metabolic model.\nTo pass this test, the model should be able to synthesis all the\nprecursors.\n\nImplementation:\nFirst remove any constraints from all boundary reactions, then for each\nbiomass precursor (except ATP and H2O) add a temporary demand\nreaction, then carry out FBA with this reaction as the objective. Collect\nall metabolites for which this optimization is below or equal to zero or is\ninfeasible.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_WT_75p37M and when the\nmodel is simulated in         complete medium a total of 0 precursors\n(0.00% of all precursors except h2o and atp) cannot be produced: []","BIOMASS_Ec_iML1515_core_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_core_75p37M and when the\nmodel is simulated in         complete medium a total of 0 precursors\n(0.00% of all precursors except h2o and atp) cannot be produced: []"},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":[],"BIOMASS_Ec_iML1515_core_75p37M":[]},"format_type":"count","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":1.0,"BIOMASS_Ec_iML1515_core_75p37M":1.0}},"test_gam_in_biomass":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":0.20160550100000307,"BIOMASS_Ec_iML1515_core_75p37M":0.21041515599999627},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"passed","BIOMASS_Ec_iML1515_core_75p37M":"passed"},"title":"Growth-associated Maintenance in Biomass Reaction","summary":"The growth-associated maintenance (GAM) term accounts for the energy in\nthe form of ATP that is required to synthesize macromolecules such as\nProteins, DNA and RNA, and other processes during growth. A GAM term is\ntherefore a requirement for any well-defined biomass reaction. There are\ndifferent ways to implement this term depending on\nwhat kind of experimental data is available and the preferred\nway of implementing the biomass reaction:\n- Chemostat growth experiments yield a single GAM value representing the\n  required energy per gram of biomass (Figure 6 of [1]_). This can be\n  implemented in a lumped biomass reaction or in the final term of a split\n  biomass reaction.\n- Experimentally delineating or estimating the GAM requirements\n  for each macromolecule separately is possible, yet requires either\n  data from multi-omics experiments [2]_ or detailed resources [1]_ ,\n  respectively. Individual energy requirements can either be implemented\n  in a split biomass equation on the term for each macromolecule, or, on\n  the basis of the biomass composition, they can be summed into a single\n  GAM value for growth and treated as mentioned above.\n\nThis test is only able to detect if a lumped biomass reaction or the final\nterm of a split biomass reaction contains this term. Hence, it will\nonly detect the use of a single GAM value as opposed to individual energy\nrequirements of each macromolecule. Both approaches, however, have\nits merits.\n\nImplementation:\nDetermines the metabolite identifiers of ATP, ADP, H2O, HO4P and H+ based\non an internal mapping table. Checks if ATP and H2O are a subset of the\nreactants and ADP, HO4P and H+ a subset of the products of the biomass\nreaction.\n\nReferences:\n.. [1] Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for\n       generating a high-quality genome-scale metabolic reconstruction.\n       Nature protocols. Nature Publishing Group.\n       http://doi.org/10.1038/nprot.2009.203\n.. [2] Hackett, S. R., Zanotelli, V. R. T., Xu, W., Goya, J., Park, J. O.,\n       Perlman, D. H., Gibney, P. A., Botstein, D., Storey, J. D.,\n       Rabinowitz, J. D.  (2010, January). Systems-level analysis of\n       mechanisms regulating yeast metabolic flux\n       Science\n       http://doi.org/10.1126/science.aaf2786","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"Yes, BIOMASS_Ec_iML1515_WT_75p37M contains a term for growth-\nassociated maintenance.","BIOMASS_Ec_iML1515_core_75p37M":"Yes, BIOMASS_Ec_iML1515_core_75p37M contains a term for growth-\nassociated maintenance."},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":true,"BIOMASS_Ec_iML1515_core_75p37M":true},"format_type":"raw","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":1.0,"BIOMASS_Ec_iML1515_core_75p37M":1.0}},"test_fast_growth_default":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":0.07652988099999902,"BIOMASS_Ec_iML1515_core_75p37M":0.01497243600000786},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"failed","BIOMASS_Ec_iML1515_core_75p37M":"failed"},"title":"Unrealistic Growth Rate In Default Medium","summary":"The growth rate of a metabolic model should not be faster than that of the\nfastest growing organism. This is based on a doubling time of Vibrio\nnatriegens which was reported to be 14.8 minutes by: Henry H. Lee, Nili\nOstrov, Brandon G. Wong, Michaela A. Gold, Ahmad S. Khalil,\nGeorge M. Church\nin https://www.biorxiv.org/content/biorxiv/early/2016/06/12/058487.full.pdf\n\nThe calculation ln(2)/(14.8/60) ~ 2.81 yields the corresponding growth\nrate.\n\nImplementation:\nCalculate the solution of FBA with the biomass reaction set as objective\nfunction and a model's default constraints. Then check if the objective\nvalue is higher than 2.81.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_WT_75p37M and when the\nmodel is simulated on             the provided default medium the\ngrowth rate is *lower* than that             of the fastest bacteria.\nThis is to be expected for             a majority of organisms.","BIOMASS_Ec_iML1515_core_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_core_75p37M and when the\nmodel is simulated on             the provided default medium the\ngrowth rate is *lower* than that             of the fastest bacteria.\nThis is to be expected for             a majority of organisms."},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":false,"BIOMASS_Ec_iML1515_core_75p37M":false},"format_type":"raw","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":1.0,"BIOMASS_Ec_iML1515_core_75p37M":1.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0}},"test_direct_metabolites_in_biomass":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":0.18995351799999582,"BIOMASS_Ec_iML1515_core_75p37M":0.1876929879999949},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"passed","BIOMASS_Ec_iML1515_core_75p37M":"passed"},"title":"Ratio of Direct Metabolites in Biomass Reaction","summary":"Some biomass precursors are taken from the media and directly consumed by\nthe biomass reaction. It might not be a problem for ions or\nmetabolites for which the organism in question is auxotrophic. However,\ntoo many of these metabolites may be artifacts of automated gap-filling\nprocedures. Many gap-filling algorithms attempt to minimise the number of\nadded reactions. This can lead to many biomass precursors being\n\"direct metabolites\".\n\nThis test reports the ratio of direct metabolites to the total amount of\nprecursors to a given biomass reaction. It specifically looks for\nmetabolites that are only in either exchange, transport or biomass\nreactions. Bear in mind that this may lead to false positives in heavily\ncompartimentalized models.\n\nTo pass this test, the ratio of direct metabolites should be less than 50%\nof all biomass precursors. This is an arbitrary threshold but it takes\ninto account that while certain ions do not serve a relevant metabolic\nfunction, it may still be important to include them in the biomass\nreaction to account for the impact of their uptake energy costs.\n\nThis threshold is subject to change in the future.\n\nImplementation:\nIdentify biomass precursors (excluding ATP and H+), identify cytosol\nand extracellular compartment from an internal mapping table. Then,\ndetermine which precursors is only involved in transport, boundary and\nbiomass reactions. Using FBA with the biomass function as the objective\nthen determine whether the metabolite is taken up only to be consumed by\nthe biomass reaction.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"BIOMASS_Ec_iML1515_WT_75p37M contains a total of 8 direct metabolites\n(8.60%).         Specifically these are: ['k_c', 'cl_c', 'ni2_c',\n'mg2_c', 'cobalt2_c', 'mn2_c', 'zn2_c', 'ca2_c'].","BIOMASS_Ec_iML1515_core_75p37M":"BIOMASS_Ec_iML1515_core_75p37M contains a total of 8 direct\nmetabolites (12.50%).         Specifically these are: ['k_c', 'cl_c',\n'ni2_c', 'mg2_c', 'cobalt2_c', 'mn2_c', 'zn2_c', 'ca2_c']."},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":["k_c","cl_c","ni2_c","mg2_c","cobalt2_c","mn2_c","zn2_c","ca2_c"],"BIOMASS_Ec_iML1515_core_75p37M":["k_c","cl_c","ni2_c","mg2_c","cobalt2_c","mn2_c","zn2_c","ca2_c"]},"format_type":"percent","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":0.08602150537634409,"BIOMASS_Ec_iML1515_core_75p37M":0.125},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":0.9139784946236559,"BIOMASS_Ec_iML1515_core_75p37M":0.875}},"test_essential_precursors_not_in_biomass":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":1.609216903999993,"BIOMASS_Ec_iML1515_core_75p37M":1.5340833439999955},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"failed","BIOMASS_Ec_iML1515_core_75p37M":"failed"},"title":"Number of Missing Essential Biomass Precursors","summary":"There are universal components of life that make up the biomass of all\nknown organisms. These include all proteinogenic amino acids, deoxy- and\nribonucleotides, water and a range of metabolic cofactors.\n\nThis test reports the amount of biomass precursors that have been reported\nto be essential constituents of the biomass equation. All of the following\nprecursors need to be included in the biomass reaction to pass the test:\n\nAminoacids:\ntrp__L, cys__L, his__L, tyr__L, met__L, phe__L, ser__L, pro__L, asp__L,\nthr__L, gln__L, glu__L, ile__L, arg__L, lys__L, val__L, leu__L, ala__L,\ngly, asn__L\nDNA: datp, dctp, dttp, dgtp\nRNA: atp, ctp, utp, gtp\nCofactors: nad, nadp, amet, fad, pydx5p, coa, thmpp, fmn and h2o\n\nThese metabolites were selected based on the results presented by\nDOI:10.1016/j.ymben.2016.12.002\n\nPlease note, that the authors also suggest to count C1 carriers\n(derivatives of tetrahydrofolate(B9) or tetrahydromethanopterin) as\nuniversal cofactors. We have omitted these from this check because there\nare many individual compounds that classify as C1 carriers, and it is not\nclear a priori which one should be preferred. In a future update, we may\nconsider identifying these using a chemical ontology.\n\nImplementation:\nDetermine whether the model employs a lumped or split biomass reaction.\nThen, using an internal mapping table, try to identify the above list of\nessential precursors in list of precursor metabolites of either type of\nbiomass reaction. List IDs in the models namespace if the metabolite\nexists, else use the MetaNetX namespace if the metabolite does not exist\nin the model. Identifies the cytosol from an internal mapping\ntable, and assumes that all precursors exist in that compartment.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"BIOMASS_Ec_iML1515_WT_75p37M lacks a total of 1 essential metabolites\n(1.08% of all biomass precursors). Specifically         these are:\n['fmn_c'].","BIOMASS_Ec_iML1515_core_75p37M":"BIOMASS_Ec_iML1515_core_75p37M lacks a total of 1 essential\nmetabolites         (1.56% of all biomass precursors). Specifically\nthese are: ['fmn_c']."},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":["fmn_c"],"BIOMASS_Ec_iML1515_core_75p37M":["fmn_c"]},"format_type":"count","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":0.010752688172043012,"BIOMASS_Ec_iML1515_core_75p37M":0.015625},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":0.989247311827957,"BIOMASS_Ec_iML1515_core_75p37M":0.984375}},"test_stoichiometric_consistency":{"duration":2.9894777800000014,"result":"passed","title":"Stoichiometric Consistency","summary":"Stoichiometric inconsistency violates universal constraints:\n1. Molecular masses are always positive, and\n2. On each side of a reaction the mass is conserved.\nA single incorrectly defined reaction can lead to stoichiometric\ninconsistency in the model, and consequently to unconserved metabolites.\nSimilar to insufficient constraints, this may give rise to cycles which\neither produce mass from nothing or consume mass from the model.\n\nImplementation:\nThis test uses an implementation of the algorithm presented in\nsection 3.1 by Gevorgyan, A., M. G Poolman, and D. A Fell.\n\"Detection of Stoichiometric Inconsistencies in Biomolecular Models.\"\nBioinformatics 24, no. 19 (2008): 2245.\ndoi: 10.1093/bioinformatics/btn425","message":"This model's stoichiometry consistent","data":true,"format_type":"percent","metric":0.0},"test_unconserved_metabolites":{"duration":3.278004987999992,"result":"passed","title":"Uncoserved Metabolites","summary":"The list of unconserved metabolites is computed using the algorithm described\nin section 3.2 of\n\"Detection of Stoichiometric Inconsistencies in Biomolecular Models.\"\nBioinformatics 24, no. 19 (2008): 2245.\ndoi: 10.1093/bioinformatics/btn425.","message":"This model contains 0 unconserved metabolites:","data":[],"format_type":"count","metric":0},"test_inconsistent_min_stoichiometry":{"duration":2.990533685999992,"result":"passed","title":"Minimal Inconsistent Net Stoichiometries","summary":"Only 10 unconserved metabolites are reported and considered to\navoid computing for too long.\n\nImplementation:\nAlgorithm described in section 3.3 of\n\"Detection of Stoichiometric Inconsistencies in Biomolecular Models.\"\nBioinformatics 24, no. 19 (2008): 2245.\ndoi: 10.1093/bioinformatics/btn425.","message":"This model contains more than 10 minimal unconservable sets:","data":[],"format_type":"count","metric":0},"test_detect_energy_generating_cycles":{"duration":{"MNXM3":0.00017881499999816697,"MNXM63":0.0001482470000127023,"MNXM51":0.00016643099999669175,"MNXM121":0.0001699479999928144,"MNXM423":0.00015735399999528,"MNXM6":0.00015839600000333576,"MNXM10":0.0013965240000004542,"MNXM38":0.00015116299999817784,"MNXM208":0.00014839700000379707,"MNXM191":0.000144660999993107,"MNXM223":0.00014661499999135685,"MNXM7517":0.00014416999999866675,"MNXM12233":0.00016756299999087787,"MNXM558":0.00016888700000095014,"MNXM21":0.00014898899999593596,"MNXM89557":0.00014482100000634546},"result":{"MNXM3":"skipped","MNXM63":"skipped","MNXM51":"skipped","MNXM121":"skipped","MNXM423":"skipped","MNXM6":"skipped","MNXM10":"skipped","MNXM38":"skipped","MNXM208":"skipped","MNXM191":"skipped","MNXM223":"skipped","MNXM7517":"skipped","MNXM12233":"skipped","MNXM558":"skipped","MNXM21":"skipped","MNXM89557":"skipped"},"title":"Erroneous Energy-generating Cycles","summary":"When a model is not sufficiently constrained to account for the\nthermodynamics of reactions, flux cycles may form which provide reduced\nmetabolites to the model without requiring nutrient uptake. These cycles\nare referred to as erroneous energy-generating cycles. Their effect on the\npredicted growth rate in FBA may account for an increase of up to 25%,\nwhich makes studies involving the growth rates predicted from such models\nunreliable.\n\nImplementation:\nThis test uses an implementation of the algorithm presented by:\nFritzemeier, C. J., Hartleb, D., Szappanos, B., Papp, B., & Lercher,\nM. J. (2017). Erroneous energy-generating cycles in published genome scale\nmetabolic networks: Identification and removal. PLoS Computational\nBiology, 13(4), 1–14. http://doi.org/10.1371/journal.pcbi.1005494\n\nFirst attempt to identify the main compartment (cytosol), then attempt to\nidentify each metabolite of the referenced list of energy couples via an\ninternal mapping table. Construct a dissipation reaction for each couple.\nCarry out FBA with each dissipation reaction as the objective and report\nthose reactions that non-zero carry flux.","message":{},"data":{},"format_type":"count","metric":{},"score":{}},"test_reaction_charge_balance":{"duration":0.005664420999991648,"result":"passed","title":"Charge Balance","summary":"This will exclude biomass, exchange and demand reactions as they are\nunbalanced by definition. It will also fail all reactions where at\nleast one metabolite does not have a charge defined.\n\nIn steady state, for each metabolite the sum of influx equals the sum\nof efflux. Hence the net charges of both sides of any model reaction have\nto be equal. Reactions where at least one metabolite does not have a\ncharge are not considered to be balanced, even though the remaining\nmetabolites participating in the reaction might be.\n\nImplementation:\nFor each reaction that isn't a boundary or biomass reaction check if each\nmetabolite has a non-zero charge attribute and if so calculate if the\noverall sum of charges of reactants and products is equal to zero.","message":"A total of 0 (0.00%) reactions are charge unbalanced with at\nleast one of the metabolites not having a charge or the overall\ncharge not equal to 0:","data":[],"format_type":"count","metric":0.0},"test_reaction_mass_balance":{"duration":0.0897508259999995,"result":"failed","title":"Mass Balance","summary":"This will exclude biomass, exchange and demand reactions as they are\nunbalanced by definition. It will also fail all reactions where at\nleast one metabolite does not have a formula defined.\n\nIn steady state, for each metabolite the sum of influx equals the sum\nof efflux. Hence the net masses of both sides of any model reaction have\nto be equal. Reactions where at least one metabolite does not have a\nformula are not considered to be balanced, even though the remaining\nmetabolites participating in the reaction might be.\n\nImplementation:\nFor each reaction that isn't a boundary or biomass reaction check if each\nmetabolite has a non-zero elements attribute and if so calculate if the\noverall element balance of reactants and products is equal to zero.","message":"A total of 1 (0.04%) reactions are mass unbalanced with at least\none of the metabolites not having a formula or the overall mass not\nequal to 0: PUACGAMS","data":["PUACGAMS"],"format_type":"count","metric":0.00042140750105351877},"test_blocked_reactions":{"duration":34.866435648999996,"result":"failed","title":"Universally Blocked Reactions","summary":"Universally blocked reactions are reactions that during Flux Variability\nAnalysis cannot carry any flux while all model boundaries are open.\nGenerally blocked reactions are caused by network gaps, which can be\nattributed to scope or knowledge gaps.\n\nImplementation:\nUse flux variability analysis (FVA) implemented in\ncobra.flux_analysis.find_blocked_reactions with open_exchanges=True.\nPlease refer to the cobrapy documentation for more information:\nhttps://cobrapy.readthedocs.io/en/stable/autoapi/cobra/flux_analysis/\nvariability/index.html#cobra.flux_analysis.variability.\nfind_blocked_reactions","message":"There are 260 (9.59%) blocked reactions in         the model: 13PPDH2,\n23DOGULNt4pp, 2DGLCptspp, 2DGLCtex, 2DGULRGx, ...","data":["13PPDH2","23DOGULNt4pp","2DGLCptspp","2DGLCtex","2DGULRGx","2DGULRGy","2DGULRx","2DGULRy","2DOXG6PP","2HESR","2HPTCOAT","3HBZCT","3HPADHi","3KGK","4HBZt3pp","AB6PGH","ACANTHAT","ACBIPGT","ACOLIPAabctex","ACONIs","ACONMT","ACOXT","ACP1p","ACPS1","ADOCBIK","ADOCBLS","AGt3","ALPATE160pp","ALPATG160pp","AMPNTAT","AP5AH","APCS","APPLDHr","ARABDI","ARBTptspp","ARBTtex","ARHGDx","ASO3t8pp","ASO3tex","ASR","BMOCOS","BMOGDS1","BMOGDS2","BSORx","BSORy","BWCOGDS1","BWCOGDS2","BWCOS","CBIAT","CBItonex","CBIuabcpp","CCGS","CD2tex","CDGR","CDGS","CFAS160E","CFAS160G","CFAS180E","CFAS180G","CHOLATEtpp","CHOLID","CHTBSptspp","CHTBStex","CINNDO","CLBtex","CLIPAabctex","COLIPAKpp","COLIPAPabctex","CPH4S","CRNBTCT","CRNCAL2","CRNCAR","CRNCBCT","CRNCDH","CRNDCAL2","CRNDtex","CRNt7pp","CRNtex","CS1tex","CTBTCAL2","CU1abcpp","CURR","CUt2pp","CUt3","CXSAMS","CYANST","CYSItex","CYSItpp","CYSSADS","CYSTA","DC6PDA","DHBSZ3FEabcpp","DHCIND","DHCURR","DHMPTR","DHNPTE","DHPTDNR","DHPTDNRN","DHPTPE","DKGLCNR1","DKGLCNR2x","DKGLCNR2y","DMSOR1","DMSOR2","DMSOtpp","DOGULNR","DSBAO1","DSBAO2","DSBCGT","DSBDR","DSBGGT","DURADx","DXYLK","E4PP","EDTXS3","EDTXS4","EX_2dglc_e","EX_ag_e","EX_arbt_e","EX_aso3_e","EX_cbi_e","EX_cd2_e","EX_chtbs_e","EX_cm_e","EX_crn__D_e","EX_crn_e","EX_cs1_e","EX_doxrbcn_e","EX_fe3dhbzs_e","EX_fusa_e","EX_gbbtn_e","EX_gthox_e","EX_hg2_e","EX_met__D_e","EX_mincyc_e","EX_na1_e","EX_novbcn_e","EX_rfamp_e","EX_sel_e","EX_slnt_e","EX_so2_e","EX_sucr_e","EX_ttrcyc_e","EX_tungs_e","FE3DCITR5","FE3DHBZS3R","FE3DHBZStonex","FEENTERES","FHL","FORCT","Ftex","Ftpp","GBBTNtex","GDMANE","GHBDHx","GLCATr","GMAND","GOFUCR","GP4GH","GTHOXtex","HETZK","HG2abcpp","HG2t3pp","HG2tex","HMPK1","HPACOAT","KDUI","LA4NTpp","LIPACabcpp","LKDRA","LPLIPAL2ATE120","LPLIPAL2ATE140","LPLIPAL2ATE141","LPLIPAL2ATE160","LPLIPAL2ATE161","LPLIPAL2ATE180","LPLIPAL2ATE181","LPLIPAL2ATG120","LPLIPAL2ATG140","LPLIPAL2ATG141","LPLIPAL2ATG160","LPLIPAL2ATG161","LPLIPAL2ATG180","LPLIPAL2ATG181","LYSAM","MALTATr","MALTptspp","MC6PH","MCPST","METDabcpp","METDtex","METNA","MI1PP","MTRPOX","NAtex","NNDMBRT","NTP11","NTP12","O16A4COLIPAabctex","O16A4Lpp","O16AP1pp","O16AP2pp","O16AP3pp","O16AT","O16AUNDtpp","O16GALFT","O16GLCT1","O16GLCT2","OXCDC","PCNO","PGLYCP","PHDA","PNSPA","PSURIK","PSURItex","PSURItpp","PUACGAMS","PUACGAMtr","RHMND","RU5PP","RZ5PP","SARCOX","SELGTHR","SELGTHR2","SELGTHR3","SELNPS","SELR","SELabcpp","SELtex","SLNTabcpp","SLNTtex","SO2tex","SO2tpp","SPMDAT1","SPMDAT2","SQGH","SUCRtex","SUCptspp","TDSR1","TDSR2","TEO2M","TMAOR1","TMAOR2","TPRDCOAS","TSULabcpp","TUNGSabcpp","TUNGStex","ThDPAT","UDPGALM","UDPGD","UDPGDC","UDPGPT","UDPKAAT","ULA4NFT","ULA4Ntppi","UPLA4FNF","UPLA4FNT","WCOS","XYHDL","YUMPS"],"format_type":"count","metric":0.09587020648967552},"test_find_stoichiometrically_balanced_cycles":{"duration":26.335889277000007,"result":"failed","title":"Stoichiometrically Balanced Cycles","summary":"Stoichiometrically Balanced Cycles are artifacts of insufficiently\nconstrained networks resulting in reactions that can carry flux when\nall the boundaries have been closed.\n\nImplementation:\nClose all model boundary reactions and then use flux variability analysis\n(FVA) to identify reactions that carry flux.","message":"There are 61 (2.25%) reactions         which participate in SBC in the\nmodel: ABUTt2pp, ACCOAL, ACOAD1f, ACOAD1fr, ACt2rpp, ...","data":["ABUTt2pp","ACCOAL","ACOAD1f","ACOAD1fr","ACt2rpp","ACt4pp","ADK1","ADK3","ADNt2pp_copy1","ADNt2pp_copy2","ALATA_L","ASPtpp","CA2t3pp","CAt6pp","CRNDt2rpp","CRNt2rpp","CRNt8pp","CYTDt2pp_copy1","CYTDt2pp_copy2","FOMETRi","FUMt1pp","GLBRAN2","GLCtex_copy1","GLCtex_copy2","GLDBRAN2","GLUABUTt7pp","GLUt2rpp","GLUt4pp","GLYCLTt2rpp","GLYCLTt4pp","HPYRI","HPYRRx","ICHORS_copy1","ICHORS_copy2","INDOLEt2pp","INDOLEt2rpp","MN2tipp","MN2tpp","NAt3pp","NDPK1","PPAKr","PPCSCT","PPM","PROt2rpp","PROt4pp","PRPPS","PTA2","R15BPK","R1PK","SUCASPtpp","SUCCt1pp","SUCFUMtpp","SUCOAS","THFAT","THMDt2pp_copy1","THMDt2pp_copy2","TRSARr","URIt2pp_copy1","URIt2pp_copy2","VALTA","VPAMTr"],"format_type":"count","metric":0.022492625368731565},"test_find_orphans":{"duration":0.020557494000001952,"result":"failed","title":"Orphan Metabolites","summary":"Orphans are metabolites that are only consumed but not produced by\nreactions in the model. They may indicate the presence of network and\nknowledge gaps.\n\nImplementation:\nFind orphan metabolites structurally by considering only reaction\nequations and bounds. FBA is not carried out.","message":"A total of 45 (2.40%) metabolites are not produced by any reaction\nof the model: 23doguln_p, 25dkglcn_c, 2hptcoa_c, 2pglyc_c,\n34dphacoa_c, ...","data":["23doguln_p","25dkglcn_c","2hptcoa_c","2pglyc_c","34dphacoa_c","3hbzcoa_c","3sala_c","4ahmmp_c","4mhetz_c","5phdt_c","Nmtrp_c","ag_c","alpp_p","ampnt_c","ap5a_c","apoACP_c","aso4_c","btnso_c","cholate_c","cinnm_c","cu_c","cur_c","cyan_c","cysi__L_c","dhptdn_c","dmbzid_c","dsbard_p","dsbcox_p","dsbgox_p","dt5hsu_c","dtgcl_c","dxyl_c","f_c","fe3dcit_c","fe3dhbzs3_p","gmplys_c","gp4g_c","hg2_c","iprimv_c","mi1p__D_c","ragund_c","sarcs_c","sqg_c","teo2_c","tmao_c"],"format_type":"count","metric":0.02397442727757059},"test_find_deadends":{"duration":0.01743447000001197,"result":"failed","title":"Dead-end Metabolites","summary":"Dead-ends are metabolites that can only be produced but not consumed by\nreactions in the model. They may indicate the presence of network and\nknowledge gaps.\n\nImplementation:\nFind dead-end metabolites structurally by considering only reaction\nequations and bounds. FBA is not carried out.","message":"A total of 63 (3.36%) metabolites are not consumed by any reaction\nof the model: 23dhbzs3_c, 2dglc_c, 2hptcl_c, 2tpr3dpcoa_c, 34dhpha_c,\n...","data":["23dhbzs3_c","2dglc_c","2hptcl_c","2tpr3dpcoa_c","34dhpha_c","3hbz_c","4hbz_p","5phua_c","N1aspmd_c","acampnt_c","acanth_c","acolipa_e","aconm_c","apg120_c","apg140_c","apg141_c","apg160_c","apg161_c","apg180_c","apg181_c","athtp_c","bmocogdp_c","bwcogdp_c","cholate_p","colipap_e","cpe160_c","cpe180_c","cpg160_c","cpg180_c","cxsam_c","dhcholn_c","didp_c","dkdglcn_c","dms_c","dsbaox_p","dsbcrd_p","dsbgrd_p","erthrs_c","fe3dhbzs_p","gam_c","gdpfuc_c","hqn_c","lipa_cold_e","lpp_p","malt6p_c","mercpeth_c","met__D_c","mteo2_c","n8aspmd_c","na15dap_c","nalme_c","o16a4colipa_e","preq1_c","puacgam_p","ribflv_p","selnp_c","suc6p_c","tcynt_c","thcur_c","thmnp_c","thptdn_c","tma_c","xdp_c"],"format_type":"count","metric":0.03356419818859883},"test_find_disconnected":{"duration":0.0009365429999945718,"result":"passed","title":"Metabolite Connectivity","summary":"Disconnected metabolites are not part of any reaction in the model. They\nare most likely left-over from the reconstruction process, but may also\npoint to network and knowledge gaps.\n\nImplementation:\nCheck for any metabolites of the cobra.Model object with emtpy reaction\nattribute.","message":"A total of 0 (0.00%) metabolites are not associated with any\nreaction of the model:","data":[],"format_type":"count","metric":0.0},"test_find_metabolites_not_produced_with_open_bounds":{"duration":54.856292352,"result":"failed","title":"Metabolite Production In Complete Medium","summary":"In complete medium, a model should be able to divert flux to every\nmetabolite. This test opens all the boundary reactions i.e. simulates a\ncomplete medium and checks if any metabolite cannot be produced\nindividually using flux balance analysis. Metabolites that cannot be\nproduced this way are likely orphan metabolites, downstream of reactions\nwith fixed constraints, or blocked by a cofactor imbalance. To pass this\ntest all metabolites should be producible.\n\nImplementation:\nOpen all model boundary reactions, then for each metabolite in the model\nadd a boundary reaction and maximize it with FBA.","message":"A total of 181 (9.64%) metabolites cannot be produced in complete\nmedium: 13ppd_c, 23doguln_c, 23doguln_p, 25dkglcn_c, 2dhguln_c, ...","data":["13ppd_c","23doguln_c","23doguln_p","25dkglcn_c","2dhguln_c","2hptcl_c","2hptcoa_c","2pglyc_c","34dhpha_c","34dphacoa_c","3dhguln_c","3haACP_c","3hbz_c","3hbzcoa_c","3hcddec5eACP_c","3hcmrs7eACP_c","3hcpalm9eACP_c","3hcvac11eACP_c","3hddecACP_c","3hdecACP_c","3hhexACP_c","3hmrsACP_c","3hoctACP_c","3hoctaACP_c","3hpalmACP_c","3hppnl_c","3ocddec5eACP_c","3ocmrs7eACP_c","3ocpalm9eACP_c","3ocvac11eACP_c","3oddecACP_c","3odecACP_c","3ohexACP_c","3omrsACP_c","3ooctACP_c","3ooctdACP_c","3opalmACP_c","3sala_c","4ahmmp_c","4mhetz_c","5phdt_c","5phua_c","5prdmbz_c","ACP_c","Nmtrp_c","acACP_c","acampnt_c","actACP_c","ag_c","alpp_p","ampnt_c","ap5a_c","apoACP_c","aragund_c","aso3_c","aso4_c","bbtcoa_c","btnso_c","but2eACP_c","butACP_c","cddec5eACP_c","cdec3eACP_c","cenchddd_c","cholate_c","cholate_p","cinnm_c","cu_c","cur_c","cyan_c","cysi__L_c","cysi__L_e","cysi__L_p","dcaACP_c","ddcaACP_c","dhcholn_c","dhcur_c","dhptdn_c","dkdglcn_c","dmbzid_c","dsbaox_p","dsbard_p","dsbcox_p","dsbcrd_p","dsbdox_c","dsbdrd_c","dsbgox_p","dsbgrd_p","dt5hsu_c","dtgcl_c","dxyl_c","egmeACP_c","epmeACP_c","f_c","f_e","f_p","fe3dcit_c","fe3dhbzs3_p","flxr_c","flxso_c","garagund_c","gbbtn_c","gfgaragund_c","glutrna_c","gmeACP_c","gmplys_c","gp4g_c","grxox_c","grxrd_c","hdeACP_c","hexACP_c","hg2_c","hgmeACP_c","hpmeACP_c","iprimv_c","iscs_c","iscssh_c","iscu_2fe2s2_c","iscu_2fe2s_c","iscu_4fe4s_c","iscu_c","lpp_p","malACP_c","mercpeth_c","mi1p__D_c","moadamp_c","moadcoo_c","moadcosh_c","mteo2_c","myrsACP_c","nalme_c","o16a2und_p","o16a3und_p","o16a4colipa_e","o16a4colipa_p","o16a4und_p","o16aund_c","o16aund_p","ocACP_c","ocdcaACP_c","octeACP_c","ogmeACP_c","opmeACP_c","oxa_c","oxalcoa_c","palmACP_c","pimACP_c","pmeACP_c","psuri_c","psuri_e","psuri_p","ragund_c","rdmbzi_c","sarcs_c","sqg_c","sufbcd_2fe2s2_c","sufbcd_2fe2s_c","sufbcd_4fe4s_c","sufbcd_c","sufse_c","sufsesh_c","t3c11vaceACP_c","t3c5ddeceACP_c","t3c7mrseACP_c","t3c9palmeACP_c","tcynt_c","tddec2eACP_c","tdeACP_c","tdec2eACP_c","teo2_c","thcur_c","thex2eACP_c","thptdn_c","tma_c","tmao_c","tmrs2eACP_c","toct2eACP_c","toctd2eACP_c","tpalm2eACP_c","trdox_c","trdrd_c","trnaglu_c"],"format_type":"count","metric":0.09643047416089505},"test_find_metabolites_not_consumed_with_open_bounds":{"duration":68.639176383,"result":"failed","title":"Metabolite Consumption In Complete Medium","summary":"In complete medium, a model should be able to divert flux from every\nmetabolite. This test opens all the boundary reactions i.e. simulates a\ncomplete medium and checks if any metabolite cannot be consumed\nindividually using flux balance analysis. Metabolites that cannot be\nconsumed this way are likely dead-end metabolites or upstream of reactions\nwith fixed constraints. To pass this test all metabolites should be\nconsumable.\n\nImplementation:\nOpen all model boundary reactions, then for each metabolite in the model\nadd a boundary reaction and minimize it with FBA.","message":"A total of 234 (12.47%) metabolites cannot be consumed in complete\nmedium: 23dhbzs3_c, 2dglc_c, 2doxg6p_c, 2hptcl_c, 2hptcoa_c, ...","data":["23dhbzs3_c","2dglc_c","2doxg6p_c","2hptcl_c","2hptcoa_c","2tpr3dpcoa_c","34dhpha_c","34dphacoa_c","3haACP_c","3hbz_c","3hbzcoa_c","3hcddec5eACP_c","3hcmrs7eACP_c","3hcpalm9eACP_c","3hcvac11eACP_c","3hddecACP_c","3hdecACP_c","3hhexACP_c","3hmrsACP_c","3hoctACP_c","3hoctaACP_c","3hpalmACP_c","3ocddec5eACP_c","3ocmrs7eACP_c","3ocpalm9eACP_c","3ocvac11eACP_c","3oddecACP_c","3odecACP_c","3ohexACP_c","3omrsACP_c","3ooctACP_c","3ooctdACP_c","3opalmACP_c","4hbz_p","5phdt_c","5phua_c","ACP_c","N1aspmd_c","acACP_c","acampnt_c","acanth_c","acolipa_e","acolipa_p","aconm_c","actACP_c","adocbi_c","adocbip_c","agdpcbi_c","alpp_p","ampnt_c","apg120_c","apg140_c","apg141_c","apg160_c","apg161_c","apg180_c","apg181_c","apoACP_c","arab__D_c","aragund_c","arbt6p_c","arbt_p","athtp_c","bbtcoa_c","bmoco1gdp_c","bmoco_c","bmocogdp_c","but2eACP_c","butACP_c","bwco1gdp_c","bwco_c","bwcogdp_c","cbi_c","cbi_p","cddec5eACP_c","cdec3eACP_c","cdg_c","cholate_c","cholate_p","chtbs6p_c","colipap_e","colipap_p","cpe160_c","cpe180_c","cpg160_c","cpg180_c","cph4_c","crnDcoa_c","crncoa_c","ctbtcoa_c","cur_c","cxsam_c","cyan_c","cysi__L_c","cysi__L_e","cysi__L_p","dcaACP_c","ddcaACP_c","dgslnt_c","dhcholn_c","dhcur_c","dhptdn_c","didp_c","dkdglcn_c","dms_c","dsbaox_p","dsbard_p","dsbcox_p","dsbcrd_p","dsbdox_c","dsbdrd_c","dsbgox_p","dsbgrd_p","dt5hsu_c","dtgcl_c","egmeACP_c","epmeACP_c","erthrs_c","f_c","f_e","f_p","fe3dhbzs3_c","fe3dhbzs3_p","fe3dhbzs_p","flxr_c","flxso_c","gam_c","garagund_c","gdpddman_c","gdpfuc_c","gdpofuc_c","gfgaragund_c","glutrna_c","gmeACP_c","gmplys_c","grxox_c","grxrd_c","gslnt_c","hdeACP_c","hexACP_c","hgmeACP_c","hpmeACP_c","hqn_c","iscs_c","iscssh_c","iscu_2fe2s2_c","iscu_2fe2s_c","iscu_4fe4s_c","iscu_c","kdo2lipid4p_c","lipa_cold_c","lipa_cold_e","lipa_cold_p","lpp_p","malACP_c","malt6p_c","mchtbs6p_c","mercpeth_c","mercppyr_c","met__D_c","moadamp_c","moadcoo_c","moadcosh_c","mteo2_c","myrsACP_c","n8aspmd_c","na15dap_c","nalme_c","o16a2und_p","o16a3und_p","o16a4colipa_e","o16a4colipa_p","o16a4und_p","o16aund_c","o16aund_p","ocACP_c","ocdcaACP_c","octeACP_c","ogmeACP_c","opmeACP_c","palmACP_c","pimACP_c","pmeACP_c","preq0_c","preq1_c","puacgam_p","ragund_c","rbl__D_c","ribflv_p","sel_c","seln_c","selnp_c","slnt_c","suc6p_c","sufbcd_2fe2s2_c","sufbcd_2fe2s_c","sufbcd_4fe4s_c","sufbcd_c","sufse_c","sufsesh_c","t3c11vaceACP_c","t3c5ddeceACP_c","t3c7mrseACP_c","t3c9palmeACP_c","tcynt_c","tddec2eACP_c","tdeACP_c","tdec2eACP_c","teo2_c","thcur_c","thex2eACP_c","thmnp_c","thptdn_c","tma_c","tmao_c","tmrs2eACP_c","toct2eACP_c","toctd2eACP_c","tpalm2eACP_c","trdox_c","trdrd_c","trnaglu_c","tsul_c","tungs_c","uLa4fn_c","uLa4n_c","uLa4n_p","udpLa4fn_c","udpLa4n_c","udpLa4o_c","udpgalfur_c","udpglcur_c","wco_c","xdp_c"],"format_type":"count","metric":0.12466702184336707},"test_find_reactions_unbounded_flux_default_condition":{"duration":23.860448443999985,"result":"failed","title":"Unbounded Flux In Default Medium","summary":"A large fraction of model reactions able to carry unlimited flux under\ndefault conditions indicates problems with reaction directionality,\nmissing cofactors, incorrectly defined transport reactions and more.\n\nImplementation:\nWithout changing the default constraints run flux variability analysis.\nFrom the FVA results identify those reactions that carry flux equal to the\nmodel's maximal or minimal flux.","message":" A fraction of 11.13% of the non-blocked reactions (in total 58\nreactions) can carry unbounded flux in the default model\ncondition. Unbounded reactions may be involved in\nthermodynamically infeasible cycles: ABUTt2pp, ACCOAL, ACOAD1fr,\nACt2rpp, ACt4pp, ...","data":["ABUTt2pp","ACCOAL","ACOAD1fr","ACt2rpp","ACt4pp","ADK1","ADK3","ADNt2pp_copy1","ADNt2pp_copy2","ALATA_L","ASPtpp","CA2t3pp","CAt6pp","CRNDt2rpp","CRNt2rpp","CRNt8pp","CYTDt2pp_copy1","CYTDt2pp_copy2","EX_fe2_e","FE2tex","FOMETRi","FUMt1pp","GLBRAN2","GLCtex_copy1","GLDBRAN2","GLUABUTt7pp","GLUt2rpp","GLUt4pp","GLYCLTt2rpp","GLYCLTt4pp","HPYRI","HPYRRx","ICHORS_copy1","ICHORS_copy2","INDOLEt2pp","INDOLEt2rpp","MN2tipp","MN2tpp","NAt3pp","NDPK1","PPAKr","PPM","PROt2rpp","PROt4pp","PTA2","R15BPK","R1PK","SUCASPtpp","SUCCt1pp","SUCFUMtpp","SUCOAS","THFAT","THMDt2pp_copy1","THMDt2pp_copy2","TRSARr","URIt2pp_copy1","URIt2pp_copy2","VALTA"],"format_type":"percent","metric":0.11132437619961612},"test_gene_essentiality_from_data_qualitative":{"duration":{"experiment0":0.00021556399997280096},"result":{"experiment0":"skipped"},"title":"Gene Essentiality Prediction","summary":"The in-silico gene essentiality is compared with experimental\ndata and the accuracy is expected to be better than 0.95.\nIn principal, Matthews' correlation coefficient is a more comprehensive\nmetric but is a little fragile to not having any false negatives or false\npositives in the output.\n\nImplementation:\nRead and validate experimental config file and data tables. Constrain the\nmodel with the parameters provided by a user's definition of the medium,\nthen compute a confusion matrix based on the predicted essential, expected\nessential, predicted nonessential and expected nonessential genes.\nThe individual values of the confusion matrix are calculated as described\nin https://en.wikipedia.org/wiki/Confusion_matrix","message":{},"data":{},"format_type":"percent","metric":{},"score":{}},"test_growth_from_data_qualitative":{"duration":{"experiment0":0.00021004299998139686},"result":{"experiment0":"skipped"},"title":"Growth Prediction","summary":"The in-silico growth prediction is compared with experimental\ndata and the accuracy is expected to be better than 0.95.\nIn principal, Matthews' correlation coefficient is a more comprehensive\nmetric but is a little fragile to not having any false negatives or false\npositives in the output.\n\nImplementation:\nRead and validate experimental config file and data tables. Constrain the\nmodel with the parameters provided by a user's definition of the medium,\nthen compute a confusion matrix based on the predicted true, expected\ntrue, predicted false and expected false growth.\nThe individual values of the confusion matrix are calculated as described\nin https://en.wikipedia.org/wiki/Confusion_matrix","message":{},"data":{},"format_type":"percent","metric":{},"score":{}},"test_absolute_extreme_coefficient_ratio":{"duration":0.019572754999956032,"result":"passed","title":"Ratio Min/Max Non-Zero Coefficients","summary":"This test will return the absolute largest and smallest, non-zero\ncoefficients of the stoichiometric matrix. A large ratio of these values\nmay point to potential numerical issues when trying to solve different\nmathematical optimization problems such as flux-balance analysis.\n\nTo pass this test the ratio should not exceed 10^9. This threshold has\nbeen selected based on experience, and is likely to be adapted when more\ndata on solver performance becomes available.\n\nImplementation:\nCompose the stoichiometric matrix, then calculate absolute coefficients and\nlastly use the maximal value and minimal non-zero value to calculate the\nratio.","message":"The ratio of the absolute values of the largest coefficient 75.55223\nand         the lowest, non-zero coefficient 2e-06 is: 3.78E+07.","data":37776115.0,"format_type":"percent","metric":0.0},"test_number_independent_conservation_relations":{"duration":3.640959247000012,"result":"passed","title":"Independent Conservation Relations","summary":"This test will return the number of conservation relations, i.e.,\nconservation pools through the left null space of the stoichiometric\nmatrix. This test is not scored, as the dimension of the left null space\nis system-specific.\n\nImplementation:\nCalculate the left null space, i.e., the null space of the transposed\nstoichiometric matrix, using an algorithm based on the singular value\ndecomposition adapted from\nhttps://scipy.github.io/old-wiki/pages/Cookbook/RankNullspace.html\nThen, return the estimated dimension of that null space.","message":"The number of independent conservation relations is 31.","data":31,"format_type":"raw","metric":0.016515716568993075},"test_matrix_rank":{"duration":1.9210226089999765,"result":"passed","title":"Rank","summary":"The rank of the stoichiometric matrix is system specific. It is\ncalculated using singular value decomposition (SVD).\n\nImplementation:\nCompose the stoichiometric matrix, then estimate the rank, i.e. the\ndimension of the column space, of a matrix. The algorithm used by this\nfunction is based on the singular value decomposition of the matrix.","message":"The rank of the S-Matrix is 1845.","data":1845,"format_type":"raw","metric":0.6803097345132744},"test_degrees_of_freedom":{"duration":1.9177652299999863,"result":"passed","title":"Degrees Of Freedom","summary":"The degrees of freedom of the stoichiometric matrix, i.e., the number\nof 'free variables' is system specific and corresponds to the dimension\nof the (right) null space of the matrix.\n\nImplementation:\nCompose the stoichiometric matrix, then calculate the dimensionality of the\nnull space using the rank-nullity theorem outlined by\nAlama, J. The Rank+Nullity Theorem. Formalized Mathematics 15, (2007).","message":"The degrees of freedom of the S-Matrix are 867.","data":867,"format_type":"raw","metric":0.3196902654867257},"test_sbml_level":{"duration":0.00021625499999800013,"result":"failed","title":"SBML Level and Version","summary":"This test reports if the model file is represented in the latest edition\n(level) of the Systems Biology Markup Language (SBML) which is Level 3,\nand at least version 1.\n\nImplementation:\nThe level and version are parsed directly from the SBML document.","message":null,"data":null,"format_type":"raw","metric":1.0},"test_fbc_presence":{"duration":0.00020195799999100927,"result":"failed","title":"FBC enabled","summary":"The Flux Balance Constraints (FBC) Package extends SBML with structured\nand semantic descriptions for domain-specific model components such as\nflux bounds, multiple linear objective functions, gene-protein-reaction\nassociations, metabolite chemical formulas, charge and related annotations\nwhich are relevant for parameterized GEMs and FBA models. The SBML and\nconstraint-based modeling communities collaboratively develop this package\nand update it based on user input.\n\nImplementation:\nParse the state of the FBC plugin from the SBML document.","message":null,"data":null,"format_type":"raw","metric":1.0},"test_metabolite_sbo_presence":{"duration":0.0037648740000122416,"result":"failed","title":"Metabolite General SBO Presence","summary":"    The Systems Biology Ontology (SBO) allows researchers to annotate a model\n    with terms which indicate the intended function of its individual\n    components. The available terms are controlled and relational and can be\n    viewed here http://www.ebi.ac.uk/sbo/main/tree.\n\n    Implementation:\n    Check if each cobra.Metabolite has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\".","message":"A total of 0 metabolites (0.00%) lack annotation with any type\nof SBO term:","data":[],"format_type":"count","metric":0.0},"test_reaction_sbo_presence":{"duration":0.003793408999968051,"result":"failed","title":"Reaction General SBO Presence","summary":"    The Systems Biology Ontology (SBO) allows researchers to annotate a model\n    with terms which indicate the intended function of its individual\n    components. The available terms are controlled and relational and can be\n    viewed here http://www.ebi.ac.uk/sbo/main/tree.\n\n    Implementation:\n    Check if each cobra.Reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\".","message":"A total of 0 reactions (0.00%) lack annotation with any type\nof SBO term:","data":[],"format_type":"count","metric":0.0},"test_gene_sbo_presence":{"duration":0.0019806160000257478,"result":"failed","title":"Gene General SBO Presence","summary":"    The Systems Biology Ontology (SBO) allows researchers to annotate a model\n    with terms which indicate the intended function of its individual\n    components. The available terms are controlled and relational and can be\n    viewed here http://www.ebi.ac.uk/sbo/main/tree.\n\n    Check if each cobra.Gene has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\".","message":"A total of 0 genes (0.00%) lack annotation with any type of\nSBO term:","data":[],"format_type":"count","metric":0.0},"test_metabolic_reaction_specific_sbo_presence":{"duration":0.0014474390000032145,"result":"failed","title":"Metabolic Reaction SBO:0000176 Presence","summary":"    SBO:0000176 represents the term 'biochemical reaction'. Every metabolic\n    reaction that is not a transport or boundary reaction should be annotated\n    with this. The results shown are relative to the total amount of pure\n    metabolic reactions.\n\n    Implementation:\n    Check if each pure metabolic reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being the SBO term above.","message":"A total of 0 metabolic reactions (0.00% of all purely\nmetabolic reactions) lack annotation with the SBO term\n\"SBO:0000176\" for 'biochemical reaction':","data":[],"format_type":"count","metric":0.0},"test_transport_reaction_specific_sbo_presence":{"duration":0.0013586129999794139,"result":"failed","title":"Transport Reaction SBO:0000185 Presence","summary":"    'SBO:0000185', 'SBO:0000588', 'SBO:0000587', 'SBO:0000655', 'SBO:0000654',\n    'SBO:0000660', 'SBO:0000659', 'SBO:0000657', and 'SBO:0000658' represent\n    the terms 'transport reaction' and 'translocation reaction', in addition\n    to their children (more specific transport reaction labels). Every\n    transport reaction that is not a pure metabolic or boundary reaction should\n    be annotated with one of these terms. The results shown are relative to the\n    total of all transport reactions.\n\n    Implementation:\n    Check if each transport reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"A total of 10 metabolic reactions (1.20% of all transport\nreactions) lack annotation with one of the SBO terms: ['SBO:0000185',\n'SBO:0000588', 'SBO:0000587', 'SBO:0000655', 'SBO:0000654',\n'SBO:0000660', 'SBO:0000659', 'SBO:0000657', 'SBO:0000658'] for\n'biochemical reaction': URIt2pp_copy1, URIt2pp_copy2, THMDt2pp_copy2,\nTHMDt2pp_copy1, ADNt2pp_copy1, ...","data":["URIt2pp_copy1","URIt2pp_copy2","THMDt2pp_copy2","THMDt2pp_copy1","ADNt2pp_copy1","ADNt2pp_copy2","CYTDt2pp_copy2","GLCtex_copy1","GLCtex_copy2","CYTDt2pp_copy1"],"format_type":"count","metric":0.012033694344163659},"test_metabolite_specific_sbo_presence":{"duration":0.0023728900000037356,"result":"failed","title":"Metabolite SBO:0000247 Presence","summary":"    SBO:0000247 represents the term 'simple chemical'. Every metabolite should\n    be annotated with this.\n\n    Implementation:\n    Check if each cobra.Metabolite has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"A total of 0 transport reactions (0.00% of all metabolites)\nlack annotation with the SBO term \"SBO:0000247\" for\n'simple chemical':","data":[],"format_type":"count","metric":0.0},"test_gene_specific_sbo_presence":{"duration":0.0020906919999674756,"result":"failed","title":"Gene SBO:0000243 Presence","summary":"    SBO:0000243 represents the term 'gene'. Every gene should\n    be annotated with this.\n\n    Implementation:\n    Check if each cobra.Gene has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"A total of 0 genes (0.00% of all genes) lack             annotation\nwith the SBO term \"SBO:0000243\" for             'gene':","data":[],"format_type":"count","metric":0.0},"test_exchange_specific_sbo_presence":{"duration":0.009925241999951595,"result":"failed","title":"Exchange Reaction SBO:0000627 Presence","summary":"    SBO:0000627 represents the term 'exchange reaction'. The Systems Biology\n    Ontology defines an exchange reaction as follows: 'A modeling process to\n    provide matter influx or efflux to a model, for example to replenish a\n    metabolic network with raw materials (eg carbon / energy sources). Such\n    reactions are conceptual, created solely for modeling purposes, and do not\n    have a  physical correspondence. Exchange reactions, often represented as\n    'R_EX_', can operate in the negative (uptake) direction or positive\n    (secretion) direction. By convention, a negative flux through an exchange\n    reaction represents uptake of the corresponding metabolite, and a positive\n    flux represent discharge.' Every exchange reaction should be annotated with\n    this. Exchange reactions differ from demand reactions in that the\n    metabolites are removed from or added to the extracellular\n    environment only.\n\n    Implementation:\n    Check if each exchange reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"A total of 0 exchange reactions (0.00% of all exchange\nreactions) lack annotation with the SBO term \"SBO:0000627\" for\n'exchange reaction':","data":[],"format_type":"count","metric":0.0},"test_demand_specific_sbo_presence":{"duration":0.009335157999998955,"result":"failed","title":"Demand Reaction SBO:0000628 Presence","summary":"    SBO:0000628 represents the term 'demand reaction'. The Systems Biology\n    Ontology defines a demand reaction as follows: 'A modeling process\n    analogous to exchange reaction, but which operates upon \"internal\"\n    metabolites. Metabolites that are consumed by these reactions are assumed\n    to be used in intra-cellular processes that are not part of the model.\n    Demand reactions, often represented 'R_DM_', can also deliver metabolites\n    (from intra-cellular processes that are not considered in the model).'\n    Every demand reaction should be annotated with\n    this. Demand reactions differ from exchange reactions in that the\n    metabolites are not removed from the extracellular environment, but from\n    any of the organism's compartments. Demand reactions differ from sink\n    reactions in that they are designated as irreversible.\n\n    Implementation:\n    Check if each demand reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"A total of 0 genes (0.00% of all demand reactions) lack\nannotation with the SBO term \"SBO:0000628\" for             'demand\nreaction':","data":[],"format_type":"count","metric":0.0},"test_sink_specific_sbo_presence":{"duration":0.009012673999961862,"result":"skipped","title":"Sink Reactions SBO:0000632 Presence","summary":"    SBO:0000632 represents the term 'sink reaction'. The Systems Biology\n    Ontology defines a sink reaction as follows: 'A modeling process to\n    provide matter influx or efflux to a model, for example to replenish a\n    metabolic network with raw materials (eg carbon / energy sources). Such\n    reactions are conceptual, created solely for modeling purposes, and do not\n    have a physical correspondence. Unlike the analogous demand (SBO:....)\n    reactions, which are usually designated as irreversible, sink reactions\n    always represent a reversible uptake/secretion processes, and act as a\n    metabolite source with no cost to the cell. Sink reactions, also referred\n    to as R_SINK_, are generally used for compounds that are metabolized by\n    the cell but are produced by non-metabolic, un-modeled cellular processes.'\n    Every sink reaction should be annotated with\n    this. Sink reactions differ from exchange reactions in that the metabolites\n    are not removed from the extracellular environment, but from any of the\n    organism's compartments.\n\n    Implementation:\n    Check if each sink reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"No sink reactions found.","data":[],"format_type":"count","metric":1.0},"test_biomass_specific_sbo_presence":{"duration":0.0002040819999820087,"result":"passed","title":"Biomass Reactions SBO:0000629 Presence","summary":"    SBO:0000629 represents the term 'biomass production'. The Systems Biology\n    Ontology defines an exchange reaction as follows: 'Biomass production,\n    often represented 'R_BIOMASS_', is usually the optimization target reaction\n    of constraint-based models, and can consume multiple reactants to produce\n    multiple products. It is also assumed that parts of the reactants are also\n    consumed in unrepresented processes and hence products do not have to\n    reflect all the atom composition of the reactants. Formulation of a\n    biomass production process entails definition of the macromolecular\n    content (eg. cellular protein fraction), metabolic constitution of\n    each fraction (eg. amino acids), and subsequently the atomic composition\n    (eg. nitrogen atoms). More complex biomass functions can additionally\n    incorporate details of essential vitamins and cofactors required for\n    growth.'\n    Every reaction representing the biomass production should be annotated with\n    this.\n\n    Implementation:\n    Check if each biomass reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"A total of 0 biomass reactions (0.00% of all biomass reactions)\nlack annotation with the SBO term \"SBO:0000629\" for         'biomass\nproduction':","data":[],"format_type":"count","metric":0.0}},"score":{"sections":[{"section":"consistency","score":0.98403631661419},{"section":"annotation_met","score":0.7878142102968955},{"section":"annotation_rxn","score":0.8085975909537857},{"section":"annotation_gene","score":0.633245382585752},{"section":"annotation_sbo","score":0.9079969368778034}],"total_score":0.9060384928327713},"cards":{"scored":{"title":"Core Tests","sections":{"consistency":{"title":"Consistency","weight":3.0,"cases":["test_stoichiometric_consistency","test_reaction_mass_balance","test_reaction_charge_balance","test_find_disconnected","test_find_reactions_unbounded_flux_default_condition"]},"annotation_met":{"title":"Annotation - Metabolites","weight":1.0,"cases":["test_metabolite_annotation_presence","test_metabolite_annotation_overview","test_metabolite_annotation_wrong_ids","test_metabolite_id_namespace_consistency"]},"annotation_rxn":{"title":"Annotation - Reactions","weight":1.0,"cases":["test_reaction_annotation_presence","test_reaction_annotation_overview","test_reaction_annotation_wrong_ids","test_reaction_id_namespace_consistency"]},"annotation_gene":{"title":"Annotation - Genes","weight":1.0,"cases":["test_gene_product_annotation_presence","test_gene_product_annotation_overview","test_gene_product_annotation_wrong_ids"]},"annotation_sbo":{"title":"Annotation - SBO Terms","weight":2.0,"cases":["test_metabolite_sbo_presence","test_metabolite_specific_sbo_presence","test_reaction_sbo_presence","test_metabolic_reaction_specific_sbo_presence","test_transport_reaction_specific_sbo_presence","test_exchange_specific_sbo_presence","test_demand_specific_sbo_presence","test_sink_specific_sbo_presence","test_gene_sbo_presence","test_gene_specific_sbo_presence","test_biomass_specific_sbo_presence"]}}},"sbml_format":{"title":"SBML","cases":["test_sbml_level","test_fbc_presence"]},"basic_info":{"title":"Basic Information","cases":["test_model_id_presence","test_metabolites_presence","test_reactions_presence","test_genes_presence","test_compartments_presence","test_metabolic_coverage","test_unconserved_metabolites","test_inconsistent_min_stoichiometry"]},"basic_met":{"title":"Metabolite Information","cases":["test_find_unique_metabolites","test_find_duplicate_metabolites_in_compartments","test_metabolites_charge_presence","test_metabolites_formula_presence","test_find_medium_metabolites"]},"basic_rxn":{"title":"Reaction Information","cases":["test_find_pure_metabolic_reactions","test_find_constrained_pure_metabolic_reactions","test_find_transport_reactions","test_find_constrained_transport_reactions","test_find_candidate_irreversible_reactions","test_find_reactions_with_partially_identical_annotations","test_find_duplicate_reactions","test_find_reactions_with_identical_genes"]},"gpr_calculations":{"title":"Gene-Protein-Reaction (GPR) Associations","cases":["test_gene_protein_reaction_rule_presence","test_transport_reaction_gpr_presence","test_protein_complex_presence"]},"test_biomass":{"title":"Biomass","cases":["test_biomass_presence","test_biomass_consistency","test_biomass_default_production","test_fast_growth_default","test_biomass_open_production","test_biomass_precursors_default_production","test_biomass_precursors_open_production","test_direct_metabolites_in_biomass","test_essential_precursors_not_in_biomass"]},"energy_metabolism":{"title":"Energy Metabolism","cases":["test_ngam_presence","test_gam_in_biomass","test_find_reversible_oxygen_reactions","test_detect_energy_generating_cycles"]},"gap_finding":{"title":"Network Topology","cases":["test_blocked_reactions","test_find_orphans","test_find_deadends","test_find_stoichiometrically_balanced_cycles","test_find_metabolites_not_produced_with_open_bounds","test_find_metabolites_not_consumed_with_open_bounds"]},"matrix":{"title":"Matrix Conditioning","cases":["test_absolute_extreme_coefficient_ratio","test_number_independent_conservation_relations","test_matrix_rank","test_degrees_of_freedom"]},"experimental":{"title":"Experimental Data Comparison","cases":["test_growth_from_data_qualitative","test_gene_essentiality_from_data_qualitative"]},"misc":{"title":"Misc. Tests","cases":[]}},"weights":{"test_reaction_mass_balance":1.0,"test_find_disconnected":1.0,"test_stoichiometric_consistency":3.0,"test_reaction_charge_balance":1.0,"test_metabolite_annotation_presence":1.0,"test_reaction_annotation_presence":1.0,"test_metabolite_annotation_overview":1.0,"test_reaction_annotation_overview":1.0,"test_metabolite_annotation_wrong_ids":1.0,"test_reaction_annotation_wrong_ids":1.0,"test_metabolite_id_namespace_consistency":1.0,"test_reaction_id_namespace_consistency":1.0}};
+    window.data = {"meta":{"timestamp":"2025-09-08 06:26:10.179197","platform":"Linux","release":"6.11.0-1018-azure","python":"3.9.16","packages":{"memote":"0.13.0","click":"8.1.3","click-configfile":"0.2.3","click-log":"0.4.0","six":"1.16.0","future":"0.18.3","pytest":"7.2.2","gitpython":"3.1.31","pandas":"1.5.3","Jinja2":"3.1.2","cookiecutter":"2.1.1","cobra":"0.26.2","ruamel.yaml":"0.17.21","travis-encrypt":"1.1.2","sympy":"1.11.1","sqlalchemy":"2.0.5.post1","requests":"2.28.2","importlib-resources":"5.12.0","numpydoc":"1.5.0","pylru":"1.2.1","goodtables":"2.5.4","depinfo":"1.7.0","black ; extra == 'development'":"not installed","isort ; extra == 'development'":"not installed","tox ; extra == 'development'":"not installed","pip":"23.0.1","setuptools":"67.6.0","wheel":"0.38.4"}},"tests":{"test_metabolite_annotation_presence":{"duration":0.0010170220000134123,"result":"passed","title":"Presence of Metabolite Annotation","summary":"This test checks if any annotations at all are present in the SBML\nannotations field for each metabolite, irrespective of the type of\nannotation i.e. specific database  cross-references, ontology terms,\nadditional information. For this test to pass the model is expected to\nhave metabolites and each of them should have some form of annotation.\n\nImplementation:\nCheck if the annotation attribute of each cobra.Metabolite object of the\nmodel is unset or empty.","message":"A total of 0 metabolites (0.00%) lack any form of annotation:","data":[],"format_type":"count","metric":0.0},"test_reaction_annotation_presence":{"duration":0.0014797930000156612,"result":"passed","title":"Presence of Reaction Annotation","summary":"This test checks if any annotations at all are present in the SBML\nannotations field for each reaction, irrespective of the type of\nannotation i.e. specific database  cross-references, ontology terms,\nadditional information. For this test to pass the model is expected to\nhave reactions and each of them should have some form of annotation.\n\nImplementation:\nCheck if the annotation attribute of each cobra.Reaction object of the\nmodel is unset or empty.","message":"A total of 0 reactions (0.00%) lack any form of annotation:","data":[],"format_type":"count","metric":0.0},"test_gene_product_annotation_presence":{"duration":0.0008415759999991224,"result":"passed","title":"Presence of Gene Annotation","summary":"This test checks if any annotations at all are present in the SBML\nannotations field (extended by FBC package) for each gene product,\nirrespective of the type of annotation i.e. specific database,\ncross-references, ontology terms, additional information. For this test to\npass the model is expected to have genes and each of them should have some\nform of annotation.\n\nImplementation:\nCheck if the annotation attribute of each cobra.Gene object of the\nmodel is unset or empty.","message":"A total of 0 genes (0.00%) lack any form of         annotation:","data":[],"format_type":"count","metric":0.0},"test_metabolite_annotation_overview":{"duration":{"pubchem.compound":0.001271526000010681,"kegg.compound":0.0009316630000171244,"seed.compound":0.0009041419999959999,"inchikey":0.000941581999995833,"inchi":0.0009407400000043253,"chebi":0.0007999480000080439,"hmdb":0.0008903659999930369,"reactome":0.0008739060000095833,"metanetx.chemical":0.00063973000001738,"bigg.metabolite":0.0005861709999805953,"biocyc":0.0008109689999855618},"result":{"pubchem.compound":"failed","kegg.compound":"failed","seed.compound":"failed","inchikey":"failed","inchi":"failed","chebi":"failed","hmdb":"failed","reactome":"failed","metanetx.chemical":"failed","bigg.metabolite":"passed","biocyc":"failed"},"title":"Metabolite Annotations Per Database","summary":"Specific database cross-references are paramount to mapping information.\nTo provide references to as many databases as possible helps to make the\nmetabolic model more accessible to other researchers. This does not only\nfacilitate the use of a model in a broad array of computational pipelines,\nit also promotes the metabolic model itself to become an organism-specific\nknowledge base.\n\nFor this test to pass, each metabolite annotation should contain\ncross-references to a number of databases. The currently selection is\nlisted in `annotation.py`, but an ongoing discussion can be found at\nhttps://github.com/opencobra/memote/issues/332. For each database this\ntest checks for the presence of its corresponding namespace ID to comply\nwith the MIRIAM guidelines i.e. they have to match those defined on\nhttps://identifiers.org/.\n\nSince each database is quite different and some potentially incomplete, it\nmay not be feasible to achieve 100% coverage for each of them. Generally\nit should be possible, however, to obtain cross-references to at least\none of the databases for all metabolites consistently.\n\nImplementation:\nCheck if the keys of the annotation attribute of each cobra.Metabolite of\nthe model match with a selection of common biochemical databases. The\nannotation  attribute of cobrapy components is a dictionary of\nkey:value pairs.","message":{"pubchem.compound":"The following 1877 metabolites (100.00%) lack annotation for\npubchem.compound:         10fthf_c, 12dgr120_c, 12dgr120_p,\n12dgr140_c, 12dgr140_p, ...","kegg.compound":"The following 527 metabolites (28.08%) lack annotation for\nkegg.compound:         12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p,\n12dgr141_c, ...","seed.compound":"The following 275 metabolites (14.65%) lack annotation for\nseed.compound:         12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p,\n12dgr141_c, ...","inchikey":"The following 1877 metabolites (100.00%) lack annotation for inchikey:\n10fthf_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...","inchi":"The following 1877 metabolites (100.00%) lack annotation for inchi:\n10fthf_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...","chebi":"The following 438 metabolites (23.34%) lack annotation for chebi:\n12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, 12dgr141_c, ...","hmdb":"The following 817 metabolites (43.53%) lack annotation for hmdb:\n12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, 12dgr141_c, ...","reactome":"The following 1877 metabolites (100.00%) lack annotation for reactome:\n10fthf_c, 12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, ...","metanetx.chemical":"The following 73 metabolites (3.89%) lack annotation for\nmetanetx.chemical:         2ddara_c, 2hptcl_c, 2hptcoa_c, 34dphacoa_c,\n3hbz_c, ...","bigg.metabolite":"The following 0 metabolites (0.00%) lack annotation for\nbigg.metabolite:","biocyc":"The following 378 metabolites (20.14%) lack annotation for biocyc:\n12dgr120_c, 12dgr120_p, 12dgr140_c, 12dgr140_p, 12dgr141_c, 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Annotations Per Database","summary":"Specific database cross-references are paramount to mapping information.\nTo provide references to as many databases as possible helps to make the\nmetabolic model more accessible to other researchers. This does not only\nfacilitate the use of a model in a broad array of computational pipelines,\nit also promotes the metabolic model itself to become an organism-specific\nknowledge base.\n\nFor this test to pass, each reaction annotation should contain\ncross-references to a number of databases. The currently selection is\nlisted in `annotation.py`, but an ongoing discussion can be found at\nhttps://github.com/opencobra/memote/issues/332. For each database this\ntest checks for the presence of its corresponding namespace ID to comply\nwith the MIRIAM guidelines i.e. they have to match those defined on\nhttps://identifiers.org/.\n\nSince each database is quite different and some potentially incomplete, it\nmay not be feasible to achieve 100% coverage for each of them. Generally\nit should be possible, however, to obtain cross-references to at least\none of the databases for all reactions consistently.\n\nImplementation:\nCheck if the keys of the annotation attribute of each cobra.Reaction of\nthe model match with a selection of common biochemical databases. The\nannotation  attribute of cobrapy components is a dictionary of\nkey:value pairs.","message":{"rhea":"The following 1535 reactions (56.64%) lack annotation for rhea:\n12DGR120tipp, 12DGR140tipp, 12DGR141tipp, 12DGR160tipp, 12DGR161tipp,\n...","kegg.reaction":"The following 1966 reactions (72.55%) lack annotation for\nkegg.reaction:         12DGR120tipp, 12DGR140tipp, 12DGR141tipp,\n12DGR160tipp, 12DGR161tipp, ...","seed.reaction":"The following 846 reactions (31.22%) lack annotation for\nseed.reaction:         12DGR120tipp, 12DGR140tipp, 12DGR141tipp,\n12DGR160tipp, 12DGR161tipp, ...","metanetx.reaction":"The following 151 reactions (5.57%) lack annotation for\nmetanetx.reaction:         13PPDH2, 23DOGULNt4pp, 2DDARAA, 2DGLCptspp,\n2DGLCtex, ...","bigg.reaction":"The following 0 reactions (0.00%) lack annotation for bigg.reaction:","reactome":"The following 2710 reactions (100.00%) lack annotation for reactome:\n12DGR120tipp, 12DGR140tipp, 12DGR141tipp, 12DGR160tipp, 12DGR161tipp,\n...","ec-code":"The following 1616 reactions (59.63%) lack annotation for ec-code:\n12DGR120tipp, 12DGR140tipp, 12DGR141tipp, 12DGR160tipp, 12DGR161tipp,\n...","brenda":"The following 2710 reactions (100.00%) lack annotation for brenda:\n12DGR120tipp, 12DGR140tipp, 12DGR141tipp, 12DGR160tipp, 12DGR161tipp,\n...","biocyc":"The following 1621 reactions (59.82%) lack annotation for biocyc:\n12DGR120tipp, 12DGR140tipp, 12DGR141tipp, 12DGR160tipp, 12DGR161tipp,\n..."},"data":{"rhea":["12DGR120tipp","12DGR140tipp","12DGR141tipp","12DGR160tipp","12DGR161tipp","12DGR180tipp","12DGR181tipp","12PPDRtex","12PPDRtpp","12PPDStex","12PPDStpp","13PPDH2","14GLUCANabcpp","14GLUCANtexi","23CAMPtex","23CCMPtex","23CGMPtex","23CUMPtex","23DAPPAt2pp","23DAPPAtex","23DOGULNt4pp","26DAHtex","2AGPA120tipp","2AGPA140tipp","2AGPA141tipp","2AGPA160tipp","2AGPA161tipp","2AGPA180tipp","2AGPA181tipp","2AGPE120tipp","2AGPE140tipp","2AGPE141tipp","2AGPE160tipp","2AGPE161tipp","2AGPE180tipp","2AGPE181tipp","2AGPEAT120","2AGPEAT140","2AGPEAT141","2AGPEAT160","2AGPEAT161","2AGPEAT180","2AGPEAT181","2AGPG120tipp","2AGPG140tipp","2AGPG141tipp","2AGPG160tipp","2AGPG161tipp","2AGPG180tipp","2AGPG181tipp","2AGPGAT120","2AGPGAT140","2AGPGAT141","2AGPGAT160","2AGPGAT161","2AGPGAT180","2AGPGAT181","2DDARAA","2DGLCptspp","2DGLCtex","2DGULRGx","2DGULRGy","2DGULRx","2DGULRy","2HESR","2HPTCOAT","2MAHMP","34dhpactex","3AMPtex","3CMPtex","3GMPtex","3HAD100","3HAD120","3HAD121","3HAD140","3HAD141","3HAD160","3HAD161","3HAD180","3HAD181","3HAD40","3HAD60","3HAD80","3HBZCT","3HPADHi","3HPPtpp","3OAR100","3OAR120","3OAR121","3OAR140","3OAR141","3OAR160","3OAR161","3OAR180","3OAR181","3OAR40","3OAR60","3OAR80","3OAS100","3OAS120","3OAS121","3OAS140","3OAS141","3OAS160","3OAS161","3OAS180","3OAS181","3OAS60","3OAS80","3PEPTabcpp","3PEPTtex","3SLAR","3UMPtex","4ABZGLUH","4ABZGLUtex","4ABZGLUtr","4HBZt3pp","4HOXPACDtex","4HTHRA","4PCP","4PCPpp","4PEPTabcpp","4PEPTtex","5DGLCNtex","5DKGR","5MTRtpp","6D6SFK","6D6SPA","AACPS1","AACPS2","AACPS3","AACPS4","AACPS5","AACPS6","AACPS7","AACPS8","AACPS9","AADDGT","AAMYL","AAMYLpp","AB6PGH","ACACT3r","ACACT5r","ACACt2pp","ACALDtex","ACALDtpp","ACCOAL","ACGAL1PPpp","ACGAL1Ptex","ACGALtex","ACGAM1PPpp","ACGAM1Ptex","ACGAMT","ACGAptspp","ACGAtex","ACMANAptspp","ACMANAtex","ACMUMptspp","ACMUMtex","ACOAD1fr","ACOAD2f","ACOAD4f","ACOATA","ACOLIPAabctex","ACOXT","ACP1p","ACPPAT120","ACPPAT140","ACPPAT141","ACPPAT160","ACPPAT161","ACPPAT180","ACPPAT181","ACPS1","ACt2rpp","ACt4pp","ADEtex","ADNtex","ADOCBIK","ADOCBLS","ADOCBLabcpp","ADOCBLtonex","ADPRDP","AGM3PA","AGM3PApp","AGM3PH","AGM3Pt2pp","AGM4PA","AGM4PApp","AGM4PCP","AGM4PCPpp","AGM4PH","AGM4Pt2pp","AGMH","AGMt2pp","AGMtex","AGPAT120","AGPAT140","AGPAT141","AGPAT160","AGPAT161","AGPAT180","AGPAT181","AGt3","AHGDx","AI2K","AI2abcpp","AI2tex","AI2tpp","AKGtex","ALAALAabcpp","ALAALAtex","ALAabcpp","ALAtex","ALAtpp","ALDD3y","ALDD4","ALLK","ALLTAMH2","ALLTNt2rpp","ALLTNtex","ALLULPE","ALLabcpp","ALLtex","ALPATE160pp","ALPATG160pp","ALR2x","ALR4x","AM3PA","AM4PA","AM4PCP","AMALT1","AMALT2","AMALT3","AMALT4","AMPMS2","AMPN","AMPNTAT","AMPtex","ANHGMtex","ANHMK","AOXSr2","APG3PAT120","APG3PAT140","APG3PAT141","APG3PAT160","APG3PAT161","APG3PAT180","APG3PAT181","APH120","APH140","APH141","APH160","APH161","APH180","APH181","ARAI","ARBTNR1","ARBTNR2","ARBTNR3","ARBTNabcpp","ARBTNexs","ARBTNtex","ARBTNtonex","ARBTNtpp","ARBabcpp","ARBt2rpp","ARBt3ipp","ARBtex","ARGt3pp","ARHGDx","ARMEPNS","ASCBptspp","ASCBtex","ASNt2rpp","ASNtex","ASO3tex","ASPt2_3pp","ASPt2pp","ASPtex","ASPtpp","ASR","ATPS4rpp","BALAtex","BGLA1","BIOMASS_Ec_iML1515_WT_75p37M","BIOMASS_Ec_iML1515_core_75p37M","BMOCOS","BMOGDS1","BMOGDS2","BTNt2ipp","BTS5","BUTCT","BUTSO3abcpp","BUTSO3tex","BUTt2rpp","BUTtex","BWCOGDS1","BWCOGDS2","BWCOS","CA2t3pp","CADVtpp","CBIAT","CBItonex","CBIuabcpp","CBL1abcpp","CBL1tonex","CBLAT","CDAPPA120","CDAPPA140","CDAPPA141","CDAPPA160","CDAPPA161","CDAPPA180","CDAPPA181","CDGUNPD","CDPPH","CELBpts","CFAS160E","CFAS160G","CFAS180E","CFAS180G","CGLYabcpp","CGLYtex","CH4t2pp","CH4tex","CHLt3pp","CHOLATEtpp","CHOLID","CHTBSptspp","CHTBStex","CITt3pp","CLBtex","CLIPAabctex","CLPNH120pp","CLPNH140pp","CLPNH141pp","CLPNH160pp","CLPNH161pp","CLPNH180pp","CLPNH181pp","CLPNS120pp","CLPNS140pp","CLPNS141pp","CLPNS160pp","CLPNS161pp","CLPNS180pp","CLPNS181pp","CLtipp","CMPN","CMPtex","CMtpp","CO2tex","CO2tpp","COBALT2t3pp","COLIPAKpp","COLIPAPabctex","COLIPAabcpp","COLIPAabctex","CPGNR1","CPGNR2","CPGNR3","CPGNUtex","CPGNUtpp","CPGNabcpp","CPGNexs","CPGNtonex","CPL","CPMPS","CRNCAL2","CRNDabcpp","CRNDt2rpp","CRNt2rpp","CRNt8pp","CS1tex","CSNtex","CTBTabcpp","CTBTt2rpp","CTECOAI6","CTECOAI7","CTECOAI8","CURR","CUt2pp","CUt3","CUtex","CXSAMS","CYANtex","CYNTtex","CYSDabcpp","CYSDtex","CYSItex","CYSItpp","CYSSADS","CYTBD2pp","CYTBDpp","CYTBO3_4pp","CYTDtex","DAAD","DADNtex","DAGK120","DAGK140","DAGK141","DAGK160","DAGK161","DAGK180","DAGK181","DALAtex","DAMPtex","DAPabcpp","DAPtex","DASYN120","DASYN140","DASYN141","DASYN160","DASYN161","DASYN180","DASYN181","DATPHs","DB4PS","DC6PDA","DCAtex","DCMPtex","DCYTtex","DDCAtexi","DDGLCNtex","DGMPtex","DGSNt2pp","DGSNtex","DGUNC","DHAtex","DHAtpp","DHBSH","DHBSZ3FEabcpp","DHCINDO","DHCURR","DHDPRy","DHGLYH","DHMPTR","DHNCOAS","DHNCOAT","DHNPTE","DHPStex","DHPStr","DHPTPE","DIMPtex","DINStex","DKGLCNR1","DMPPS","DMSOR1pp","DMSOR2pp","DMStex","DM_5drib_c","DM_aacald_c","DM_amob_c","DM_oxam_c","DOPAte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Annotations Per Database","summary":"Specific database cross-references are paramount to mapping information.\nTo provide references to as many databases as possible helps to make the\nmetabolic model more accessible to other researchers. This does not only\nfacilitate the use of a model in a broad array of computational pipelines,\nit also promotes the metabolic model itself to become an organism-specific\nknowledge base.\n\nFor this test to pass, each gene annotation should contain\ncross-references to a number of databases. The currently selection is\nlisted in `annotation.py`, but an ongoing discussion can be found at\nhttps://github.com/opencobra/memote/issues/332. For each database this\ntest checks for the presence of its corresponding namespace ID to comply\nwith the MIRIAM guidelines i.e. they have to match those defined on\nhttps://identifiers.org/.\n\nSince each database is quite different and some potentially incomplete, it\nmay not be feasible to achieve 100% coverage for each of them. Generally\nit should be possible, however, to obtain cross-references to at least\none of the databases for all gene products consistently.\n\nImplementation:\nCheck if the keys of the annotation attribute of each cobra.Gene of\nthe model match with a selection of common genome databases. The\nannotation  attribute of cobrapy components is a dictionary of\nkey:value pairs.","message":{"refseq":"The following 1516 genes (100.00%) lack annotation for refseq:\nb0002, b0003, b0004, b0007, b0008, ...","uniprot":"The following 1 genes (0.07%) lack annotation for uniprot:\ns0001","ecogene":"The following 1 genes (0.07%) lack annotation for ecogene:\ns0001","kegg.genes":"The following 1516 genes (100.00%) lack annotation for kegg.genes:\nb0002, b0003, b0004, b0007, b0008, ...","ncbigi":"The following 3 genes (0.20%) lack annotation for ncbigi:\nb2092, b4104, s0001","ncbigene":"The following 1 genes (0.07%) lack annotation for ncbigene:\ns0001","ncbiprotein":"The following 1516 genes (100.00%) lack annotation for ncbiprotein:\nb0002, b0003, b0004, b0007, b0008, ...","ccds":"The following 1516 genes (100.00%) lack annotation for ccds:\nb0002, b0003, b0004, b0007, b0008, ...","hprd":"The following 1516 genes (100.00%) lack annotation for hprd:\nb0002, b0003, b0004, b0007, b0008, ...","asap":"The following 1 genes (0.07%) lack annotation for asap:         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Annotation Conformity Per Database","summary":"To identify databases and the identifiers belonging to them, computational\ntools rely on the presence of specific patterns. Only when these patterns\ncan be identified consistently is an ID truly machine-readable. This test\nchecks if the database cross-references in metabolite annotations conform\nto patterns defined according to the MIRIAM guidelines, i.e. matching\nthose that are defined at https://identifiers.org/.\n\nThe required formats, i.e., regex patterns are further outlined in\n`annotation.py`. This test does not carry out a web query for the composed\nURI, it merely controls that the regex patterns match the identifiers.\n\nImplementation:\nFor those metabolites whose annotation keys match any of the tested\ndatabases, check if the corresponding values match the identifier pattern\nof each database.","message":{"pubchem.compound":"There are no metabolite annotations for the pubchem.compound database.","kegg.compound":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nkegg.compound         database:","seed.compound":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nseed.compound         database:","inchikey":"There are no metabolite annotations for the inchikey database.","inchi":"There are no metabolite annotations for the inchi database.","chebi":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the chebi\ndatabase:","hmdb":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the hmdb\ndatabase:","reactome":"There are no metabolite annotations for the reactome database.","metanetx.chemical":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nmetanetx.chemical         database:","bigg.metabolite":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nbigg.metabolite         database:","biocyc":"A total of 0 metabolite annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the biocyc\ndatabase:"},"data":{"pubchem.compound":[],"kegg.compound":[],"seed.compound":[],"inchikey":[],"inchi":[],"chebi":[],"hmdb":[],"reactome":[],"metanetx.chemical":[],"bigg.metabolite":[],"biocyc":[]},"format_type":"percent","metric":{"pubchem.compound":1.0,"kegg.compound":0.0,"seed.compound":0.0,"inchikey":1.0,"inchi":1.0,"chebi":0.0,"hmdb":0.0,"reactome":1.0,"metanetx.chemical":0.0,"bigg.metabolite":0.0,"biocyc":0.0},"score":{"pubchem.compound":0.0,"kegg.compound":1.0,"seed.compound":1.0,"inchikey":0.0,"inchi":0.0,"chebi":1.0,"hmdb":1.0,"reactome":0.0,"metanetx.chemical":1.0,"bigg.metabolite":1.0,"biocyc":1.0}},"test_reaction_annotation_wrong_ids":{"duration":{"rhea":0.005897432000011804,"kegg.reaction":0.0025003920000017388,"seed.reaction":0.003815578999990521,"metanetx.reaction":0.003737323000024162,"bigg.reaction":0.0034034419999784404,"reactome":0.0009678400000154852,"ec-code":0.0033048689999759517,"brenda":0.0010623370000075738,"biocyc":0.0027501969999832454},"result":{"rhea":"failed","kegg.reaction":"passed","seed.reaction":"passed","metanetx.reaction":"passed","bigg.reaction":"passed","reactome":"failed","ec-code":"failed","brenda":"failed","biocyc":"passed"},"title":"Reaction Annotation Conformity Per Database","summary":"To identify databases and the identifiers belonging to them, computational\ntools rely on the presence of specific patterns. Only when these patterns\ncan be identified consistently is an ID truly machine-readable. This test\nchecks if the database cross-references in reaction annotations conform\nto patterns defined according to the MIRIAM guidelines, i.e. matching\nthose that are defined at https://identifiers.org/.\n\nThe required formats, i.e., regex patterns are further outlined in\n`annotation.py`. This test does not carry out a web query for the composed\nURI, it merely controls that the regex patterns match the identifiers.\n\nImplementation:\nFor those reaction whose annotation keys match any of the tested\ndatabases, check if the corresponding values match the identifier pattern\nof each database.","message":{"rhea":"A total of 51 reaction annotations (1.88%) do not match the\nregular expression patterns defined on identifiers.org for the rhea\ndatabase: ARGabcpp, ASO3t8pp, ASPabcpp, CD2abcpp, CHLabcpp, ...","kegg.reaction":"A total of 0 reaction annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nkegg.reaction         database:","seed.reaction":"A total of 0 reaction annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nseed.reaction         database:","metanetx.reaction":"A total of 0 reaction annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nmetanetx.reaction         database:","bigg.reaction":"A total of 0 reaction annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the\nbigg.reaction         database:","reactome":"There are no reaction annotations for the reactome database.","ec-code":"A total of 53 reaction annotations (1.96%) do not match the\nregular expression patterns defined on identifiers.org for the ec-code\ndatabase: 4HTHRK, 5DGLCNR, AACPS7, AACPS9, AHGDx, ...","brenda":"There are no reaction annotations for the brenda database.","biocyc":"A total of 0 reaction annotations (0.00%) do not match the\nregular expression patterns defined on identifiers.org for the biocyc\ndatabase:"},"data":{"rhea":["ARGabcpp","ASO3t8pp","ASPabcpp","CD2abcpp","CHLabcpp","COBALT2abcpp","CRNabcpp","CU1abcpp","CU2abcpp","CYSabc2pp","CYSabcpp","FDH4pp","FE3abcpp","GLNabcpp","GLUabcpp","GLYBabcpp","GLYC2Pabcpp","GLYC3Pabcpp","GTHRDabc2pp","GTHRDabcpp","HISabcpp","HYD1pp","HYD2pp","ILEabcpp","K2L4Aabcpp","Kabcpp","LEUabcpp","LIPAabcpp","LYSabcpp","MALTabcpp","METDabcpp","METabcpp","MG2uabcpp","MOBDabcpp","NI2abcpp","NI2uabcpp","NO3R1pp","NO3R2pp","ORNabcpp","PHEMEabcpp","PIuabcpp","PROabcpp","PTRCabcpp","RIBabcpp","SPMDabcpp","SULabcpp","TAURabcpp","TSULabcpp","TUNGSabcpp","VALabcpp","XYLabcpp"],"kegg.reaction":[],"seed.reaction":[],"metanetx.reaction":[],"bigg.reaction":[],"reactome":[],"ec-code":["4HTHRK","5DGLCNR","AACPS7","AACPS9","AHGDx","ALKP","ALLULPE","ALR2","AP4AS","APCS","ASCBPL","ASPO5","CHOLD","CRNCAR","CU1Opp","CU2abcpp","DHPTPE","DKGLCNR2y","DNMPPA","DXYLK","ENTERES","F6PA","FALDH2","FBA3","FDMO2","GALCTLO","GART","GDMANE","GLTPD","GLUTRS","GTHRDHpp","HCYSMT","HEPT1","HEPT2","HOPNTAL","HPYRRy","IDONt2rpp","IG3PS","MACPD","MALTTRabcpp","MALTTTRabcpp","NTP10","NTP12","OBTFL","PDH","PFK_3","PPDOy","PPM","PTHRpp","TDP","TRSARr","ThDPAT","UDCPDPS"],"brenda":[],"biocyc":[]},"format_type":"percent","metric":{"rhea":0.018819188191881917,"kegg.reaction":0.0,"seed.reaction":0.0,"metanetx.reaction":0.0,"bigg.reaction":0.0,"reactome":1.0,"ec-code":0.01955719557195572,"brenda":1.0,"biocyc":0.0},"score":{"rhea":0.9811808118081181,"kegg.reaction":1.0,"seed.reaction":1.0,"metanetx.reaction":1.0,"bigg.reaction":1.0,"reactome":0.0,"ec-code":0.9804428044280443,"brenda":0.0,"biocyc":1.0}},"test_gene_product_annotation_wrong_ids":{"duration":{"refseq":0.0009239390000175263,"uniprot":0.002300831000013659,"ecogene":0.0017720660000009048,"kegg.genes":0.0005685680000055982,"ncbigi":0.0019207940000001145,"ncbigene":0.0017566790000103083,"ncbiprotein":0.0005628570000055788,"ccds":0.0005631470000082572,"hprd":0.0006156659999874137,"asap":0.0016857169999866528},"result":{"refseq":"failed","uniprot":"passed","ecogene":"passed","kegg.genes":"failed","ncbigi":"failed","ncbigene":"passed","ncbiprotein":"failed","ccds":"failed","hprd":"failed","asap":"passed"},"title":"Gene Annotation Conformity Per Database","summary":"To identify databases and the identifiers belonging to them, computational\ntools rely on the presence of specific patterns. Only when these patterns\ncan be identified consistently is an ID truly machine-readable. This test\nchecks if the database cross-references in reaction annotations conform\nto patterns defined according to the MIRIAM guidelines, i.e. matching\nthose that are defined at https://identifiers.org/.\n\nThe required formats, i.e., regex patterns are further outlined in\n`annotation.py`. This test does not carry out a web query for the composed\nURI, it merely controls that the regex patterns match the identifiers.\n\nImplementation:\nFor those genes whose annotation keys match any of the tested\ndatabases, check if the corresponding values match the identifier pattern\nof each database.","message":{"refseq":"There are no gene annotations for the refseq database.","uniprot":"A total of 0 gene annotations (0.00%) do not match the         regular\nexpression patterns defined on identifiers.org for the uniprot\ndatabase:","ecogene":"A total of 0 gene annotations (0.00%) do not match the         regular\nexpression patterns defined on identifiers.org for the ecogene\ndatabase:","kegg.genes":"There are no gene annotations for the kegg.genes database.","ncbigi":"A total of 1513 gene annotations (99.80%) do not match the\nregular expression patterns defined on identifiers.org for the ncbigi\ndatabase: b0002, b0003, b0004, b0007, b0008, ...","ncbigene":"A total of 0 gene annotations (0.00%) do not match the         regular\nexpression patterns defined on identifiers.org for the ncbigene\ndatabase:","ncbiprotein":"There are no gene annotations for the ncbiprotein database.","ccds":"There are no gene annotations for the ccds database.","hprd":"There are no gene annotations for the hprd database.","asap":"A total of 0 gene annotations (0.00%) do not match the         regular\nexpression patterns defined on identifiers.org for the 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Metabolite Identifier Namespace","summary":"In well-annotated models it is no problem if the pool of main identifiers\nfor metabolites consists of identifiers from several databases. However,\nin models that lack appropriate annotations, it may hamper the ability of\nother researchers to use it. Running the model through a computational\npipeline may be difficult without first consolidating the namespace.\n\nHence, this test checks if the main metabolite identifiers can be\nattributed to one single namespace based on the regex patterns defined at\nhttps://identifiers.org/\n\nImplementation:\nGenerate a table with each column corresponding to one\ndatabase from the selection and each row to a metabolite identifier. A\nBoolean entry indicates whether the identifier matches the regular\nexpression of the corresponding database. Since the Biocyc pattern matches\nbroadly, we assume that any instance of an identifier matching to Biocyc\nAND any other database pattern is a false positive match for Biocyc and\nthus set it to ``false``. Sum the positive matches for each database and\nassume that the largest set is the 'main' identifier namespace.","message":"0 metabolite identifiers (0.00%) deviate from the largest found\nnamespace (bigg.metabolite):","data":[],"format_type":"count","metric":0.0},"test_reaction_id_namespace_consistency":{"duration":0.01818585399999506,"result":"passed","title":"Uniform Reaction Identifier Namespace","summary":"In well-annotated models it is no problem if the pool of main identifiers\nfor reactions consists of identifiers from several databases. However,\nin models that lack appropriate annotations, it may hamper the ability of\nother researchers to use it. Running the model through a computational\npipeline may be difficult without first consolidating the namespace.\n\nHence, this test checks if the main reaction identifiers can be\nattributed to one single namespace based on the regex patterns defined at\nhttps://identifiers.org/\n\nImplementation:\nGenerate a pandas.DataFrame with each column corresponding to one\ndatabase from the selection and each row to the reaction ID. A boolean\nentry indicates whether the metabolite ID matches the regex pattern\nof the corresponding database. Since the Biocyc pattern matches quite,\nassume that any instance of an identifier matching to Biocyc\nAND any other DB pattern is a false positive match for Biocyc and then set\nthe boolean to ``false``. Sum the positive matches for each database and\nassume that the largest set is the 'main' identifier namespace.","message":"0 reaction identifiers (0.00%) deviate from the largest found\nnamespace (bigg.reaction):","data":[],"format_type":"count","metric":0.0},"test_model_id_presence":{"duration":0.00022828400000207694,"result":"failed","title":"Model Identifier","summary":"The MIRIAM guidelines require a model to be identified via an ID.\nFurther, the ID will be displayed on the memote snapshot\nreport, which helps to distinguish the output clearly.\n\nImplementation:\nCheck if the cobra.Model object has a non-empty \"id\"\nattribute, this value is parsed from the \"id\" attribute of the <model> tag\nin the SBML file e.g. <model fbc:strict=\"true\" id=\"iJO1366\">.","message":"The model ID is ","data":"","format_type":"raw","metric":1.0},"test_genes_presence":{"duration":0.0005121429999803695,"result":"passed","title":"Total Genes","summary":"A metabolic model can still be a useful tool without any\ngenes, however there are certain methods which rely on the presence of\ngenes and, more importantly, the corresponding gene-protein-reaction\nrules. 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without Formula","summary":"To be able to ensure that reactions are mass-balanced, all model\nmetabolites ought to be provided with a chemical formula. Since it may be\ndifficult to obtain formulas for certain metabolites this test serves as a\nmere report. Models can still be stoichiometrically consistent even\nwhen chemical formulas are not defined for each metabolite.\n\nImplementation:\nCheck if each cobra.Metabolite has a non-empty \"formula\"\nattribute. This attribute is set by the parser if there is an\nfbc:chemicalFormula attribute for the corresponding species in the\nSBML.","message":"There are a total of 0         metabolites (0.00%) without a formula:","data":[],"format_type":"count","metric":0.0},"test_metabolites_charge_presence":{"duration":0.00034431100002052517,"result":"passed","title":"Metabolites without Charge","summary":"To be able to ensure that reactions are charge-balanced, all model\nmetabolites ought to be provided with a charge. Since it may be\ndifficult to obtain charges for certain metabolites this test serves as a\nmere report. Models can still be stoichiometrically consistent even\nwhen charge information is not defined for each metabolite.\n\nImplementation:\nCheck if each cobra.Metabolite has a non-empty \"charge\"\nattribute. This attribute is set by the parser if there is an\nfbc:charge attribute for the corresponding species in the\nSBML.","message":"There are a total of 0         metabolites (0.00%) without a charge:","data":[],"format_type":"count","metric":0.0},"test_gene_protein_reaction_rule_presence":{"duration":0.009269445999990467,"result":"failed","title":"Reactions without GPR","summary":"Gene-Protein-Reaction rules express which gene has what function.\nThe presence of this annotation is important to justify the existence\nof reactions in the model, and is required to conduct in silico gene\ndeletion studies. However, reactions without GPR may also be valid:\nSpontaneous reactions, or known reactions with yet undiscovered genes\nlikely lack GPR.\n\nImplementation:\nCheck if each cobra.Reaction has a non-empty\n\"gene_reaction_rule\" attribute, which is set by the parser if there is an\nfbc:geneProductAssociation defined for the corresponding reaction in the\nSBML.","message":"There are a total of 109 reactions (4.02%) without GPR:\nTHYMt3pp, ARBTNtex, ARBTNR2, PYRt2rpp, CMPN, ...","data":["THYMt3pp","ARBTNtex","ARBTNR2","PYRt2rpp","CMPN","DXYLONtpp","URAtpp","PYDXtpp","CLPNH140pp","ALDD4","URIC","GUR1PPpp","ARBTNR1","23DAPPAt2pp","SELGTHR2","FE3HOXR1","CPGNUtex","12DGR120tipp","12DGR181tipp","ARBTNR3","12DGR140tipp","FE3HOXUtpp","CPGNUtpp","OMMBLHX3","FE3HOXR3","CPGNR1","DHORDfum","ACGAL1PPpp","ACGAM1PPpp","12DGR141tipp","H2SO","12DGR180tipp","BIOMASS_Ec_iML1515_core_75p37M","FTHFLi","NMNN","FECRMUtex","FEENTERR1","NADPPPS","PYDAMtpp","LIPOt2pp","FE3HOXUtex","ThDPAT","FE3HOXR2","ARBTNtpp","NMNt7pp","CDGS","12DGR160tipp","SELGTHR3","CPGNR3","XANtpp","12DGR161tipp","PYDXNtpp","QUIN2tpp","UDCPPtppi","PACALDt2rpp","3HPPtpp","CH4tex","FECRMR3","DNMPPA","MINOHPtexi","BIOMASS_Ec_iML1515_WT_75p37M","CITt3pp","CH4t2pp","CYSDabcpp","METSOX1abcpp","NACtpp","CPGNR2","MOX","SELGTHR","HEX4","CLPNH181pp","MALt3pp","GUACYC","OPHHX3","12PPDRtpp","ETHAt2pp","5MTRtpp","FECRMUtpp","CLPNH180pp","FEENTERR2","O16GLCT2","12PPDStpp","NADN","FECRMR2","FE3abcpp","AACTOOR","BTNt2ipp","PDX5PO2","PPALtpp","HYPOE","R1PK","LALDO3","DHAtpp","FEENTERR3","FEOXAMUtpp","FEOXAMUtex","MG2t3_2pp","CLPNH161pp","ATPM","PHEMEtiex","CLPNH120pp","CLPNH141pp","FECRMR1","ARBTNtonex","OXAMTC","METSOX2abcpp","DAPabcpp","CLPNH160pp","DHBSH"],"format_type":"count","metric":0.040221402214022144},"test_ngam_presence":{"duration":0.29057128200000193,"result":"passed","title":"Non-Growth Associated Maintenance Reaction","summary":"The Non-Growth Associated Maintenance reaction (NGAM) is an\nATP-hydrolysis reaction added to metabolic models to represent energy\nexpenses that the cell invests in continuous processes independent of\nthe growth rate. Memote tries to infer this reaction from a list of\nbuzzwords, and the stoichiometry and components of a simple ATP-hydrolysis\nreaction.\n\nImplementation:\nFrom the list of all reactions that convert ATP to ADP select the reactions\nthat match the irreversible reaction \"ATP + H2O -> ADP + HO4P + H+\",\nwhose metabolites are situated within the main model compartment.\nThe main model compartment is assumed to be the cytosol, yet, if that\ncannot be identified, it is assumed to be the compartment with the most\nmetabolites. The resulting list of reactions is then filtered further by\nattempting to match the reaction name with any of the following buzzwords\n('maintenance', 'atpm', 'requirement', 'ngam', 'non-growth', 'associated').\nIf this is possible only the filtered reactions are returned, if not the\nlist is returned as is.","message":"A total of 1 NGAM reactions could be identified:         ATPM","data":["ATPM"],"format_type":"count","metric":0.0},"test_metabolic_coverage":{"duration":0.00019396100000790284,"result":"passed","title":"Metabolic Coverage","summary":"The degree of metabolic coverage indicates the modeling detail of a\ngiven reconstruction calculated by dividing the total amount of\nreactions by the amount of genes. Models with a 'high level of modeling\ndetail have ratios >1, and models with a low level of detail have\nratios <1. This difference arises as models with basic or intermediate\nlevels of detail are assumed to include many reactions in which several\ngene products and their enzymatic transformations are ‘lumped’.\n\nImplementation:\nDivides the amount reactions by the amount of genes. Raises an error\nif the model does not contain either reactions or genes.","message":"The degree of metabolic coverage is 1.8.","data":[2710,1516],"format_type":"percent","metric":1.787598944591029},"test_compartments_presence":{"duration":0.0009046429999841621,"result":"passed","title":"Total Compartments","summary":"While simplified metabolic models may be perfectly viable, generally\nacross the tree of life organisms contain at least one distinct\ncompartment: the cytosol or cytoplasm. In the case of prokaryotes there is\nusually a periplasm, and eurkaryotes are more complex. In addition to the\ninternal compartment, a metabolic model also reflects the extracellular\nenvironment i.e. the medium/ metabolic context in which the modelled cells\ngrow. Hence, in total, at least two compartments can be expected from a\nmetabolic model.\n\nImplementation:\nCheck if the cobra.Model object has a non-empty \"compartments\"\nattribute, this list is populated from the list of sbml:listOfCompartments\nwhich should contain at least two sbml:compartment elements.","message":"A total of 3 compartments are defined in the model: c, p, e","data":["c","p","e"],"format_type":"count","metric":0.0},"test_protein_complex_presence":{"duration":0.058782032999999956,"result":"passed","title":"Enzyme Complexes","summary":"Based on the gene-protein-reaction (GPR) rules, it is possible to infer\nwhether a reaction is catalyzed by a single gene product, isozymes or by a\nheteromeric protein complex. This test checks that at least one\nsuch heteromeric protein complex is defined in any GPR of the model. For\nS. cerevisiae it could be shown that \"essential proteins tend to [cluster]\ntogether in essential complexes\"\n(https://doi.org/10.1074%2Fmcp.M800490-MCP200).\n\nThis might also be a relevant metric for other organisms.\n\nImplementation:\nIdentify GPRs which contain at least one logical AND that combines two\ndifferent gene products.","message":"A total of 305 reactions are catalyzed by complexes defined\nthrough GPR rules in the model.","data":["14GLUCANabcpp","23DOGULNt4pp","2DGLCptspp","3PEPTabcpp","4ABZGLUH","4HBZt3pp","4PEPTabcpp","AACPS1","AACPS2","AACPS3","AACPS4","AACPS5","AACPS6","AACPS7","AACPS8","AACPS9","ACACCT","ACCOAC","ACGAptspp","ACHBS","ACLS","ACMANAptspp","ACMUMptspp","ACOATA","ACOLIPAabctex","ACPPAT120","ACPPAT140","ACPPAT141","ACPPAT160","ACPPAT161","ACPPAT180","ACPPAT181","ADCS","ADOCBLabcpp","ADOCBLtonex","AGt3","AI2abcpp","AKGDH","ALAALAabcpp","ALAabcpp","ALLabcpp","ALPATE160pp","ALPATG160pp","ANS","ARBTNabcpp","ARBTptspp","ARBabcpp","ARGabcpp","ARMEPNS","ASCBptspp","ASPCT","ASPabcpp","ASR","ATPS4rpp","BUTCT","BUTSO3abcpp","CBItonex","CBIuabcpp","CBL1abcpp","CBL1tonex","CBPS","CELBpts","CGLYabcpp","CHLabcpp","CHTBSptspp","CINNDO","CITL","CLIPAabctex","CMtpp","COLIPAPabctex","COLIPAabctex","CPGNabcpp","CPGNtonex","CPMPS","CRNDabcpp","CRNabcpp","CTBTabcpp","CUt3","CYSabc2pp","CYSabcpp","CYTBD2pp","CYTBDpp","CYTBO3_4pp","DHAPT","DHBSZ3FEabcpp","DMSOR1","DMSOR1pp","DMSOR2","DMSOR2pp","DOXRBCNtpp","DSBAO1","DSBAO2","DSBDR","DURADx","ECA4COLIPAabctex","ECAP1pp","ECAP2pp","ECAP3pp","ENLIPAabctex","ETHAAL","ETHSO3abcpp","FDH4pp","FDH5pp","FE3DCITabcpp","FE3DCITtonex","FE3DHBZStonex","FE3HOXabcpp","FE3HOXtonex","FECRMabcpp","FECRMtonex","FEENTERabcpp","FEENTERtonex","FEOXAMabcpp","FEOXAMtonex","FHL","FLDR2","FLVR","FRD2","FRD3","FRUpts2pp","FRUptspp","FUSAtpp","G3PAT120","G3PAT140","G3PAT141","G3PAT160","G3PAT161","G3PAT180","G3PAT181","G3PCabcpp","G3PD5","G3PD6","G3PD7","G3PEabcpp","G3PGabcpp","G3PIabcpp","G3PSabcpp","GALTptspp","GALabcpp","GAMptspp","GLCabcpp","GLCptspp","GLNabcpp","GLUSy","GLUabcpp","GLYBabcpp","GLYC2Pabcpp","GLYC3Pabcpp","GLYCL","GLYCTO2","GLYCTO3","GLYCTO4","GTHRDabc2pp","GTHRDabcpp","HISabcpp","HXAND","HXCT","HYD1pp","HYD2pp","HYD3pp","I2FE2SR","I2FE2SS","I2FE2SS2","I2FE2ST","I4FE4ST","IG3PS","ILEabcpp","INDOLEt2pp","IPPMIa","IPPMIb","ISETACabcpp","K2L4Aabctex","Kabcpp","Kt2pp","LEUabcpp","LIPAabctex","LYSabcpp","L_LACD2","L_LACD3","MALTHXabcpp","MALTPTabcpp","MALTTRabcpp","MALTTTRabcpp","MALTabcpp","MALTptspp","MANGLYCptspp","MANptspp","MCOATA","MCTP1App","MCTP2App","MECDPDH5","MEPNabcpp","METDabcpp","METSOXR1","METSOXR2","METabcpp","MINCYCtpp","MNLptspp","MOADSUx","MOBDabcpp","MPTG","MPTG2","MPTS","MSO3abcpp","NADH16pp","NADH17pp","NADH18pp","NADHPO","NHFRBO","NI2uabcpp","NO3R1bpp","NO3R1pp","NO3R2bpp","NO3R2pp","NOVBCNtpp","NTRIR2x","NTRIR3pp","NTRIR4pp","O16A4COLIPAabctex","O16AP1pp","O16AP2pp","O16AP3pp","OBTFL","ORNabcpp","OXDHCOAT","PACCOAE","PAPSR","PAPSR2","PDH","PDX5PS","PFL","PHEMEabcpp","PIuabcpp","POR5","PPPNDO","PROGLYabcpp","PROabcpp","PTRCabcpp","PUACGAMS","PUACGAMtr","PYROX","RFAMPtpp","RIBabcpp","RNDR1","RNDR1b","RNDR2","RNDR2b","RNDR3","RNDR3b","RNDR4","RNDR4b","RNTR1c2","RNTR2c2","RNTR3c2","RNTR4c2","S2FE2SR","S2FE2SS","S2FE2SS2","S2FE2ST","S4FE4SR","S4FE4ST","SADT2","SBTptspp","SCYSDS","SELR","SELabcpp","SLNTabcpp","SPMDabcpp","SPMDt3pp","SUCDi","SUCOAS","SUCptspp","SULFACabcpp","SULR","SULabcpp","TARTD","TAURabcpp","TDSR1","TDSR2","TGBPA","THD2pp","THIORDXi","THMabcpp","THRabcpp","THZPSN3","TMAOR1","TMAOR1pp","TMAOR2","TMAOR2pp","TRDR","TREptspp","TRPS1","TRPS2","TRPS3","TSULabcpp","TTRCYCtpp","TUNGSabcpp","UAGAAT","ULA4Ntppi","VALabcpp","VALt3pp","XAND","XYLUt2pp","XYLabcpp","ZNabcpp"],"format_type":"count","metric":0.11254612546125461},"test_find_pure_metabolic_reactions":{"duration":0.03072391199998492,"result":"passed","title":"Purely Metabolic Reactions","summary":"If a reaction is neither a transport reaction, a biomass reaction nor a\nboundary reaction, it is counted as a purely metabolic reaction. This test\nrequires the presence of metabolite formula to be able to identify\ntransport reactions. This test is passed when the model contains at least\none purely metabolic reaction i.e. a conversion of one metabolite into\nanother.\n\nImplementation:\nFrom the list of all reactions, those that are boundary, transport and\nbiomass reactions are removed and the remainder assumed to be pure\nmetabolic reactions. Boundary reactions are identified using the attribute\ncobra.Model.boundary. Please read the description of \"Transport Reactions\"\nand \"Biomass Reaction Identified\" to learn how they are identified.","message":"A total of 1540 (56.83%) purely metabolic reactions are defined in\nthe model, this excludes transporters, exchanges, or pseudo-reactions:\nRPE, TRPAS2, EDD, TGBPA, GUI1, 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Metabolic Reactions with Constraints","summary":"If a reaction is neither a transport reaction, a biomass reaction nor a\nboundary reaction, it is counted as a purely metabolic reaction. This test\nrequires the presence of metabolite formula to be able to identify\ntransport reactions. This test simply reports the number of purely\nmetabolic reactions that have fixed constraints and does not have any\nmandatory 'pass' criteria.\n\nImplementation: From the pool of pure metabolic reactions identify\nreactions which are constrained to values other than the model's minimal or\nmaximal possible bounds.","message":"A total of 2 (0.13%) purely metabolic reactions have fixed\nconstraints in the model, this excludes transporters, exchanges, or\npseudo-reactions: 0.0 <= FHL <= 0.0, 6.86 <= ATPM <= 1000.0","data":["0.0 <= FHL <= 0.0","6.86 <= ATPM <= 1000.0"],"format_type":"count","metric":0.0012987012987012987},"test_find_transport_reactions":{"duration":0.00048440099999425,"result":"passed","title":"Transport Reactions","summary":"Cellular metabolism in any organism usually involves the transport of\nmetabolites across a lipid bi-layer. This test reports how many\nof these reactions, which transports metabolites from one compartment\nto another, are present in the model, as at least one transport reaction\nmust be present for cells to take up nutrients and/or excrete waste.\n\nImplementation:\nA transport reaction is defined as follows:\n1. It contains metabolites from at least 2 compartments and\n2. at least 1 metabolite undergoes no chemical reaction, i.e.,\nthe formula and/or annotation stays the same on both sides of the equation.\n\nA notable exception is transport via PTS, which also contains the following\nrestriction:\n3. The transported metabolite(s) are transported into a compartment through\nthe exchange of a phosphate.\n\nAn example of transport via PTS would be\npep(c) + glucose(e) -> glucose-6-phosphate(c) + pyr(c)\n\nReactions similar to transport via PTS (referred to as \"modified transport\nreactions\") follow a similar pattern:\nA(x) + B-R(y) -> A-R(y) + B(y)\n\nSuch modified transport reactions can be detected, but only when the\nformula is defined for all metabolites in a particular reaction. If this\nis not the case, transport reactions are identified through annotations,\nwhich cannot detect modified transport reactions.","message":"A total of 831 (30.66%) transport reactions are defined in the\nmodel, this excludes purely metabolic reactions, exchanges, or\npseudo-reactions: XANtex, FRUtex, CLtipp, HDCAtexi, NADH17pp, 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Reactions with Constraints","summary":"Cellular metabolism in any organism usually involves the transport of\nmetabolites across a lipid bi-layer. Hence, this test reports how many\nof these reactions, which transports metabolites from one compartment\nto another, have fixed constraints. This test does not have any mandatory\n'pass' criteria.\n\nImplementation:\nPlease refer to \"Transport Reactions\" for details on how memote identifies\ntransport reactions.\nFrom the pool of transport reactions identify reactions which are\nconstrained to values other than the model's median lower and upper bounds.","message":"A total of 0 (0.00%) transport reactions have fixed\nconstraints in the model:","data":[],"format_type":"count","metric":0.0},"test_transport_reaction_gpr_presence":{"duration":0.0031420960000048126,"result":"passed","title":"Fraction of Transport Reactions without GPR","summary":"As it is hard to identify the exact transport processes within a cell,\ntransport reactions are often added purely for modeling purposes.\nHighlighting where assumptions have been made versus where\nthere is proof may help direct the efforts to improve transport and\ntransport energetics of the tested metabolic model.\nHowever, transport reactions without GPR may also be valid:\nDiffusion, or known reactions with yet undiscovered genes likely lack GPR.\n\nImplementation:\nCheck which cobra.Reactions classified as transport reactions have a\nnon-empty \"gene_reaction_rule\" attribute.","message":"There are a total of 53 transport reactions (6.38% of all\ntransport reactions) without GPR:         DXYLONtpp, URAtpp, CPGNUtpp,\nLIPOt2pp, XANtpp, ...","data":["DXYLONtpp","URAtpp","CPGNUtpp","LIPOt2pp","XANtpp","PACALDt2rpp","MALt3pp","5MTRtpp","ARBTNtex","CPGNUtex","ARBTNtpp","UDCPPtppi","CH4t2pp","CITt3pp","METSOX1abcpp","12PPDRtpp","FECRMUtpp","12PPDStpp","FE3abcpp","BTNt2ipp","DHAtpp","DAPabcpp","THYMt3pp","PYDXtpp","FE3HOXUtpp","FE3HOXUtex","NMNt7pp","3HPPtpp","MINOHPtexi","CYSDabcpp","NACtpp","FEOXAMUtpp","FEOXAMUtex","ARBTNtonex","PYRt2rpp","23DAPPAt2pp","12DGR120tipp","12DGR181tipp","12DGR140tipp","12DGR141tipp","12DGR180tipp","FECRMUtex","PYDAMtpp","12DGR160tipp","PYDXNtpp","12DGR161tipp","QUIN2tpp","CH4tex","ETHAt2pp","PPALtpp","MG2t3_2pp","PHEMEtiex","METSOX2abcpp"],"format_type":"percent","metric":0.06377858002406739},"test_find_reversible_oxygen_reactions":{"duration":0.047667224000008446,"result":"passed","title":"Number of Reversible Oxygen-Containing Reactions","summary":"The directionality of oxygen-producing/-consuming reactions affects the\nmodel's ability to grow anaerobically i.e. create faux-anaerobic organisms.\nThis test reports how many of these oxygen-containing reactions are\nreversible. This test does not have any mandatory 'pass' criteria.\n\nImplementation:\nFirst, find the metabolite representing atmospheric oxygen in the model on\nthe basis of an internal mapping table or by specifically looking for the\nformula \"O2\". Then, find all reactions that produce or consume oxygen and\nreport those that are reversible.","message":"There are a total of 5 reversible oxygen-containing reactions\n(9.80% of all oxygen-containing reactions): O2tex, INOSTO, O2tpp,\nO2Stex, EX_o2_e","data":["O2tex","INOSTO","O2tpp","O2Stex","EX_o2_e"],"format_type":"count","metric":0.09803921568627451},"test_find_unique_metabolites":{"duration":0.600933064000003,"result":"passed","title":"Unique Metabolites","summary":"Metabolites may be transported into different compartments, which means\nthat in a compartimentalized model the number of metabolites may be\nmuch higher than in a model with no compartments. This test counts only\none occurrence of each metabolite and returns this as the number of unique\nmetabolites. The test expects that the model is compartimentalized, and\nthus, that the number of unique metabolites is generally lower than the\ntotal number of metabolites.\n\nImplementation:\nReduce the list of metabolites to a unique set by removing the compartment\ntag. The cobrapy SBML parser adds compartment tags to each metabolite ID.","message":"Not counting the same entities in other compartments, there is a\ntotal of 1169 (62.28%) unique metabolites in the model: dgmp, allul6p,\nara5p, 1hdec9eg3p, crncoa, 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The heuristic looks at annotations with the keys\n\"metanetx.reaction\", \"kegg.reaction\", \"brenda\", \"rhea\", \"biocyc\",\n\"bigg.reaction\" only.","message":"Based on annotations there are 355 different groups of overlapping\nannotation which corresponds to a total of 750 duplicated reactions in\nthe 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Components","summary":"This test checks all boundary reactions in the model that permit flux\ntowards creating a metabolite, and reports those metabolites. This test\ndoes not have any mandatory 'pass' criteria.\n\nImplementation:\nIdentify the metabolite IDs of each reaction in the method\ncobra.Model.medium. Model.medium returns exchange reactions whose bounds\npermit the uptake of metabolites.","message":null,"data":["ca2_e","cl_e","co2_e","cobalt2_e","cu2_e","fe2_e","fe3_e","glc__D_e","h2o_e","h_e","k_e","mg2_e","mn2_e","mobd_e","na1_e","nh4_e","ni2_e","o2_e","pi_e","sel_e","slnt_e","so4_e","tungs_e","zn2_e"],"format_type":"count","metric":1.0},"test_biomass_presence":{"duration":0.0002262710000024981,"result":"passed","title":"Biomass Reactions Identified","summary":"The biomass composition aka biomass formulation aka biomass reaction\nis a common pseudo-reaction accounting for biomass synthesis in\nconstraints-based modelling. It describes the stoichiometry of\nintracellular compounds that are required for cell growth. While this\nreaction may not be relevant to modeling the metabolism of higher\norganisms, it is essential for single-cell modeling.\n\nImplementation:\nIdentifies possible biomass reactions using two principal steps:\n    1. Return reactions that include the SBO annotation \"SBO:0000629\" for\n    biomass.\nIf no reactions can be identifies this way:\n    1. Look for the ``buzzwords`` \"biomass\", \"growth\" and \"bof\" in reaction\n    IDs.\n    2. Look for metabolite IDs or names that contain the ``buzzword``\n    \"biomass\" and obtain the set of reactions they are involved in.\n    3. Remove boundary reactions from this set.\n    4. Return the union of reactions that match the buzzwords and of the\n    reactions that metabolites are involved in that match the buzzword.\nThis test checks if at least one biomass reaction is present.","message":"In this model 2 the following biomass reactions were\nidentified: BIOMASS_Ec_iML1515_WT_75p37M,\nBIOMASS_Ec_iML1515_core_75p37M","data":["BIOMASS_Ec_iML1515_WT_75p37M","BIOMASS_Ec_iML1515_core_75p37M"],"format_type":"count","metric":0.0},"test_biomass_consistency":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0006302710000056777,"BIOMASS_Ec_iML1515_core_75p37M":0.0005327000000079352},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"passed","BIOMASS_Ec_iML1515_core_75p37M":"passed"},"title":"Biomass Consistency","summary":"This test only yields sensible results if all biomass precursor\nmetabolites have chemical formulas assigned to them.\nThe molecular weight of the biomass reaction in metabolic models is\ndefined to be equal to 1 g/mmol. Conforming to this is essential in order\nto be able to reliably calculate growth yields, to cross-compare models,\nand to obtain valid predictions when simulating microbial consortia. A\ndeviation from 1 - 1E-03 to 1 + 1E-06 is accepted.\n\nImplementation:\nMultiplies the coefficient of each metabolite of the biomass reaction with\nits molecular weight calculated from the formula, then divides the overall\nsum of all the products by 1000.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"The component molar mass of the biomass reaction\nBIOMASS_Ec_iML1515_WT_75p37M sums up to 0.9992627956155418\nwhich is outside of the 1e-03 margin from 1 mmol / g[CDW] / h.","BIOMASS_Ec_iML1515_core_75p37M":"The component molar mass of the biomass reaction\nBIOMASS_Ec_iML1515_core_75p37M sums up to 0.9999382297074995\nwhich is outside of the 1e-03 margin from 1 mmol / g[CDW] / h."},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":0.9992627956155418,"BIOMASS_Ec_iML1515_core_75p37M":0.9999382297074995},"format_type":"number","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":1.0,"BIOMASS_Ec_iML1515_core_75p37M":1.0}},"test_biomass_default_production":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":0.11482716399999049,"BIOMASS_Ec_iML1515_core_75p37M":0.004851975999997649},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"failed","BIOMASS_Ec_iML1515_core_75p37M":"failed"},"title":"Biomass Production In Default Medium","summary":"Using flux balance analysis this test optimizes the model for growth in\nthe medium that is set by default. Any non-zero growth rate is accepted to\npass this test.\n\nImplementation:\nCalculate the solution of FBA with the biomass reaction set as objective\nfunction and the model's default constraints.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_WT_75p37M this is the\ngrowth rate (1/h) that         can be achieved when the model is\nsimulated on the provided         default medium: 0.0","BIOMASS_Ec_iML1515_core_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_core_75p37M this is the\ngrowth rate (1/h) that         can be achieved when the model is\nsimulated on the provided         default medium: 0.0"},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0},"format_type":"number","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":1.0,"BIOMASS_Ec_iML1515_core_75p37M":1.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0}},"test_biomass_open_production":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":0.10167868099998145,"BIOMASS_Ec_iML1515_core_75p37M":0.01374945099999536},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"passed","BIOMASS_Ec_iML1515_core_75p37M":"passed"},"title":"Biomass Production In Complete Medium","summary":"Using flux balance analysis this test optimizes the model for growth using\na complete medium i.e. unconstrained boundary reactions. Any non-zero\ngrowth rate is accepted to pass this test.\n\nImplementation:\nCalculate the solution of FBA with the biomass reaction set as objective\nfunction and after removing any constraints from all boundary reactions.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_WT_75p37M this is the\ngrowth rate that can be         achieved when the model is simulated\non a complete medium i.e.         with all the boundary reactions\nunconstrained: 74.96133508860257","BIOMASS_Ec_iML1515_core_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_core_75p37M this is the\ngrowth rate that can be         achieved when the model is simulated\non a complete medium i.e.         with all the boundary reactions\nunconstrained: 74.89571939472715"},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":74.96133508860257,"BIOMASS_Ec_iML1515_core_75p37M":74.89571939472715},"format_type":"number","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":1.0,"BIOMASS_Ec_iML1515_core_75p37M":1.0}},"test_biomass_precursors_default_production":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":5.937776439999993,"BIOMASS_Ec_iML1515_core_75p37M":3.9922349219999944},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"failed","BIOMASS_Ec_iML1515_core_75p37M":"failed"},"title":"Blocked Biomass Precursors In Default Medium","summary":"Using flux balance analysis this test optimizes for the production of each\nmetabolite that is a substrate of the biomass reaction with the exception\nof atp and h2o. Optimizations are carried out using the default\nconditions. This is useful when reconstructing the precursor biosynthesis\npathways of a metabolic model. To pass this test, the model should be able\nto synthesis all the precursors.\n\nImplementation:\nFor each biomass precursor (except ATP and H2O) add a temporary demand\nreaction, then carry out FBA with this reaction as the objective. Collect\nall metabolites for which this optimization is equal to zero or\ninfeasible.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_WT_75p37M and when the\nmodel is simulated on the         provided default medium a total of 8\nprecursors         (8.60% of all precursors except h2o and atp) cannot\nbe produced: ['ile__L_c', 'thr__L_c', 'adocbl_c', 'spmd_c',\n'met__L_c', 'btn_c', 'lipopb_c', 'amet_c']","BIOMASS_Ec_iML1515_core_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_core_75p37M and when the\nmodel is simulated on the         provided default medium a total of 5\nprecursors         (7.81% of all precursors except h2o and atp) cannot\nbe produced: ['ile__L_c', 'thr__L_c', 'met__L_c', 'btn_c', 'amet_c']"},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":["ile__L_c","thr__L_c","adocbl_c","spmd_c","met__L_c","btn_c","lipopb_c","amet_c"],"BIOMASS_Ec_iML1515_core_75p37M":["ile__L_c","thr__L_c","met__L_c","btn_c","amet_c"]},"format_type":"count","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":0.08602150537634409,"BIOMASS_Ec_iML1515_core_75p37M":0.078125},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":0.9139784946236559,"BIOMASS_Ec_iML1515_core_75p37M":0.921875}},"test_biomass_precursors_open_production":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":4.167378616000008,"BIOMASS_Ec_iML1515_core_75p37M":2.622545752999997},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"passed","BIOMASS_Ec_iML1515_core_75p37M":"passed"},"title":"Blocked Biomass Precursors In Complete Medium","summary":"Using flux balance analysis this test optimizes for the production of each\nmetabolite that is a substrate of the biomass reaction with the exception\nof atp and h2o. Optimizations are carried out using a complete\nmedium i.e. unconstrained boundary reactions. This is useful when\nreconstructing the precursor biosynthesis pathways of a metabolic model.\nTo pass this test, the model should be able to synthesis all the\nprecursors.\n\nImplementation:\nFirst remove any constraints from all boundary reactions, then for each\nbiomass precursor (except ATP and H2O) add a temporary demand\nreaction, then carry out FBA with this reaction as the objective. Collect\nall metabolites for which this optimization is below or equal to zero or is\ninfeasible.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_WT_75p37M and when the\nmodel is simulated in         complete medium a total of 0 precursors\n(0.00% of all precursors except h2o and atp) cannot be produced: []","BIOMASS_Ec_iML1515_core_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_core_75p37M and when the\nmodel is simulated in         complete medium a total of 0 precursors\n(0.00% of all precursors except h2o and atp) cannot be produced: []"},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":[],"BIOMASS_Ec_iML1515_core_75p37M":[]},"format_type":"count","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":1.0,"BIOMASS_Ec_iML1515_core_75p37M":1.0}},"test_gam_in_biomass":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":0.2011301610000089,"BIOMASS_Ec_iML1515_core_75p37M":0.2022138659999939},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"passed","BIOMASS_Ec_iML1515_core_75p37M":"passed"},"title":"Growth-associated Maintenance in Biomass Reaction","summary":"The growth-associated maintenance (GAM) term accounts for the energy in\nthe form of ATP that is required to synthesize macromolecules such as\nProteins, DNA and RNA, and other processes during growth. A GAM term is\ntherefore a requirement for any well-defined biomass reaction. There are\ndifferent ways to implement this term depending on\nwhat kind of experimental data is available and the preferred\nway of implementing the biomass reaction:\n- Chemostat growth experiments yield a single GAM value representing the\n  required energy per gram of biomass (Figure 6 of [1]_). This can be\n  implemented in a lumped biomass reaction or in the final term of a split\n  biomass reaction.\n- Experimentally delineating or estimating the GAM requirements\n  for each macromolecule separately is possible, yet requires either\n  data from multi-omics experiments [2]_ or detailed resources [1]_ ,\n  respectively. Individual energy requirements can either be implemented\n  in a split biomass equation on the term for each macromolecule, or, on\n  the basis of the biomass composition, they can be summed into a single\n  GAM value for growth and treated as mentioned above.\n\nThis test is only able to detect if a lumped biomass reaction or the final\nterm of a split biomass reaction contains this term. Hence, it will\nonly detect the use of a single GAM value as opposed to individual energy\nrequirements of each macromolecule. Both approaches, however, have\nits merits.\n\nImplementation:\nDetermines the metabolite identifiers of ATP, ADP, H2O, HO4P and H+ based\non an internal mapping table. Checks if ATP and H2O are a subset of the\nreactants and ADP, HO4P and H+ a subset of the products of the biomass\nreaction.\n\nReferences:\n.. [1] Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for\n       generating a high-quality genome-scale metabolic reconstruction.\n       Nature protocols. Nature Publishing Group.\n       http://doi.org/10.1038/nprot.2009.203\n.. [2] Hackett, S. R., Zanotelli, V. R. T., Xu, W., Goya, J., Park, J. O.,\n       Perlman, D. H., Gibney, P. A., Botstein, D., Storey, J. D.,\n       Rabinowitz, J. D.  (2010, January). Systems-level analysis of\n       mechanisms regulating yeast metabolic flux\n       Science\n       http://doi.org/10.1126/science.aaf2786","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"Yes, BIOMASS_Ec_iML1515_WT_75p37M contains a term for growth-\nassociated maintenance.","BIOMASS_Ec_iML1515_core_75p37M":"Yes, BIOMASS_Ec_iML1515_core_75p37M contains a term for growth-\nassociated maintenance."},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":true,"BIOMASS_Ec_iML1515_core_75p37M":true},"format_type":"raw","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":1.0,"BIOMASS_Ec_iML1515_core_75p37M":1.0}},"test_fast_growth_default":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":0.05814315599999986,"BIOMASS_Ec_iML1515_core_75p37M":0.006166548999999577},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"failed","BIOMASS_Ec_iML1515_core_75p37M":"failed"},"title":"Unrealistic Growth Rate In Default Medium","summary":"The growth rate of a metabolic model should not be faster than that of the\nfastest growing organism. This is based on a doubling time of Vibrio\nnatriegens which was reported to be 14.8 minutes by: Henry H. Lee, Nili\nOstrov, Brandon G. Wong, Michaela A. Gold, Ahmad S. Khalil,\nGeorge M. Church\nin https://www.biorxiv.org/content/biorxiv/early/2016/06/12/058487.full.pdf\n\nThe calculation ln(2)/(14.8/60) ~ 2.81 yields the corresponding growth\nrate.\n\nImplementation:\nCalculate the solution of FBA with the biomass reaction set as objective\nfunction and a model's default constraints. Then check if the objective\nvalue is higher than 2.81.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_WT_75p37M and when the\nmodel is simulated on             the provided default medium the\ngrowth rate is *lower* than that             of the fastest bacteria.\nThis is to be expected for             a majority of organisms.","BIOMASS_Ec_iML1515_core_75p37M":"Using the biomass reaction BIOMASS_Ec_iML1515_core_75p37M and when the\nmodel is simulated on             the provided default medium the\ngrowth rate is *lower* than that             of the fastest bacteria.\nThis is to be expected for             a majority of organisms."},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":false,"BIOMASS_Ec_iML1515_core_75p37M":false},"format_type":"raw","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":1.0,"BIOMASS_Ec_iML1515_core_75p37M":1.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0}},"test_direct_metabolites_in_biomass":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":0.10630725099997562,"BIOMASS_Ec_iML1515_core_75p37M":0.10727116399999659},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"failed","BIOMASS_Ec_iML1515_core_75p37M":"failed"},"title":"Ratio of Direct Metabolites in Biomass Reaction","summary":"Some biomass precursors are taken from the media and directly consumed by\nthe biomass reaction. It might not be a problem for ions or\nmetabolites for which the organism in question is auxotrophic. However,\ntoo many of these metabolites may be artifacts of automated gap-filling\nprocedures. Many gap-filling algorithms attempt to minimise the number of\nadded reactions. This can lead to many biomass precursors being\n\"direct metabolites\".\n\nThis test reports the ratio of direct metabolites to the total amount of\nprecursors to a given biomass reaction. It specifically looks for\nmetabolites that are only in either exchange, transport or biomass\nreactions. Bear in mind that this may lead to false positives in heavily\ncompartimentalized models.\n\nTo pass this test, the ratio of direct metabolites should be less than 50%\nof all biomass precursors. This is an arbitrary threshold but it takes\ninto account that while certain ions do not serve a relevant metabolic\nfunction, it may still be important to include them in the biomass\nreaction to account for the impact of their uptake energy costs.\n\nThis threshold is subject to change in the future.\n\nImplementation:\nIdentify biomass precursors (excluding ATP and H+), identify cytosol\nand extracellular compartment from an internal mapping table. Then,\ndetermine which precursors is only involved in transport, boundary and\nbiomass reactions. Using FBA with the biomass function as the objective\nthen determine whether the metabolite is taken up only to be consumed by\nthe biomass reaction.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"This model does not grow.","BIOMASS_Ec_iML1515_core_75p37M":"This model does not grow."},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":[],"BIOMASS_Ec_iML1515_core_75p37M":[]},"format_type":"percent","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":1.0,"BIOMASS_Ec_iML1515_core_75p37M":1.0},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":0.0,"BIOMASS_Ec_iML1515_core_75p37M":0.0}},"test_essential_precursors_not_in_biomass":{"duration":{"BIOMASS_Ec_iML1515_WT_75p37M":1.60028029099999,"BIOMASS_Ec_iML1515_core_75p37M":1.5613021849999882},"result":{"BIOMASS_Ec_iML1515_WT_75p37M":"failed","BIOMASS_Ec_iML1515_core_75p37M":"failed"},"title":"Number of Missing Essential Biomass Precursors","summary":"There are universal components of life that make up the biomass of all\nknown organisms. These include all proteinogenic amino acids, deoxy- and\nribonucleotides, water and a range of metabolic cofactors.\n\nThis test reports the amount of biomass precursors that have been reported\nto be essential constituents of the biomass equation. All of the following\nprecursors need to be included in the biomass reaction to pass the test:\n\nAminoacids:\ntrp__L, cys__L, his__L, tyr__L, met__L, phe__L, ser__L, pro__L, asp__L,\nthr__L, gln__L, glu__L, ile__L, arg__L, lys__L, val__L, leu__L, ala__L,\ngly, asn__L\nDNA: datp, dctp, dttp, dgtp\nRNA: atp, ctp, utp, gtp\nCofactors: nad, nadp, amet, fad, pydx5p, coa, thmpp, fmn and h2o\n\nThese metabolites were selected based on the results presented by\nDOI:10.1016/j.ymben.2016.12.002\n\nPlease note, that the authors also suggest to count C1 carriers\n(derivatives of tetrahydrofolate(B9) or tetrahydromethanopterin) as\nuniversal cofactors. We have omitted these from this check because there\nare many individual compounds that classify as C1 carriers, and it is not\nclear a priori which one should be preferred. In a future update, we may\nconsider identifying these using a chemical ontology.\n\nImplementation:\nDetermine whether the model employs a lumped or split biomass reaction.\nThen, using an internal mapping table, try to identify the above list of\nessential precursors in list of precursor metabolites of either type of\nbiomass reaction. List IDs in the models namespace if the metabolite\nexists, else use the MetaNetX namespace if the metabolite does not exist\nin the model. Identifies the cytosol from an internal mapping\ntable, and assumes that all precursors exist in that compartment.","message":{"BIOMASS_Ec_iML1515_WT_75p37M":"BIOMASS_Ec_iML1515_WT_75p37M lacks a total of 1 essential metabolites\n(1.08% of all biomass precursors). Specifically         these are:\n['fmn_c'].","BIOMASS_Ec_iML1515_core_75p37M":"BIOMASS_Ec_iML1515_core_75p37M lacks a total of 1 essential\nmetabolites         (1.56% of all biomass precursors). Specifically\nthese are: ['fmn_c']."},"data":{"BIOMASS_Ec_iML1515_WT_75p37M":["fmn_c"],"BIOMASS_Ec_iML1515_core_75p37M":["fmn_c"]},"format_type":"count","metric":{"BIOMASS_Ec_iML1515_WT_75p37M":0.010752688172043012,"BIOMASS_Ec_iML1515_core_75p37M":0.015625},"score":{"BIOMASS_Ec_iML1515_WT_75p37M":0.989247311827957,"BIOMASS_Ec_iML1515_core_75p37M":0.984375}},"test_stoichiometric_consistency":{"duration":3.038482786000003,"result":"passed","title":"Stoichiometric Consistency","summary":"Stoichiometric inconsistency violates universal constraints:\n1. Molecular masses are always positive, and\n2. On each side of a reaction the mass is conserved.\nA single incorrectly defined reaction can lead to stoichiometric\ninconsistency in the model, and consequently to unconserved metabolites.\nSimilar to insufficient constraints, this may give rise to cycles which\neither produce mass from nothing or consume mass from the model.\n\nImplementation:\nThis test uses an implementation of the algorithm presented in\nsection 3.1 by Gevorgyan, A., M. G Poolman, and D. A Fell.\n\"Detection of Stoichiometric Inconsistencies in Biomolecular Models.\"\nBioinformatics 24, no. 19 (2008): 2245.\ndoi: 10.1093/bioinformatics/btn425","message":"This model's stoichiometry consistent","data":true,"format_type":"percent","metric":0.0},"test_unconserved_metabolites":{"duration":3.1762363569999934,"result":"passed","title":"Uncoserved Metabolites","summary":"The list of unconserved metabolites is computed using the algorithm described\nin section 3.2 of\n\"Detection of Stoichiometric Inconsistencies in Biomolecular Models.\"\nBioinformatics 24, no. 19 (2008): 2245.\ndoi: 10.1093/bioinformatics/btn425.","message":"This model contains 0 unconserved metabolites:","data":[],"format_type":"count","metric":0},"test_inconsistent_min_stoichiometry":{"duration":3.0371992139999975,"result":"passed","title":"Minimal Inconsistent Net Stoichiometries","summary":"Only 10 unconserved metabolites are reported and considered to\navoid computing for too long.\n\nImplementation:\nAlgorithm described in section 3.3 of\n\"Detection of Stoichiometric Inconsistencies in Biomolecular Models.\"\nBioinformatics 24, no. 19 (2008): 2245.\ndoi: 10.1093/bioinformatics/btn425.","message":"This model contains more than 10 minimal unconservable sets:","data":[],"format_type":"count","metric":0},"test_detect_energy_generating_cycles":{"duration":{"MNXM3":0.00019942199998013166,"MNXM63":0.0001745650000088972,"MNXM51":0.00018688800000177253,"MNXM121":0.00017305200000805598,"MNXM423":0.00016112000000134685,"MNXM6":0.00015773300000887502,"MNXM10":0.0022041720000061105,"MNXM38":0.00015077000000474072,"MNXM208":0.00014965799999799856,"MNXM191":0.00014564100001734914,"MNXM223":0.00014621200000419776,"MNXM7517":0.00014599200000020573,"MNXM12233":0.00015091100001995983,"MNXM558":0.0001510410000093998,"MNXM21":0.00014715399998976864,"MNXM89557":0.0001435570000012376},"result":{"MNXM3":"skipped","MNXM63":"skipped","MNXM51":"skipped","MNXM121":"skipped","MNXM423":"skipped","MNXM6":"skipped","MNXM10":"skipped","MNXM38":"skipped","MNXM208":"skipped","MNXM191":"skipped","MNXM223":"skipped","MNXM7517":"skipped","MNXM12233":"skipped","MNXM558":"skipped","MNXM21":"skipped","MNXM89557":"skipped"},"title":"Erroneous Energy-generating Cycles","summary":"When a model is not sufficiently constrained to account for the\nthermodynamics of reactions, flux cycles may form which provide reduced\nmetabolites to the model without requiring nutrient uptake. These cycles\nare referred to as erroneous energy-generating cycles. Their effect on the\npredicted growth rate in FBA may account for an increase of up to 25%,\nwhich makes studies involving the growth rates predicted from such models\nunreliable.\n\nImplementation:\nThis test uses an implementation of the algorithm presented by:\nFritzemeier, C. J., Hartleb, D., Szappanos, B., Papp, B., & Lercher,\nM. J. (2017). Erroneous energy-generating cycles in published genome scale\nmetabolic networks: Identification and removal. PLoS Computational\nBiology, 13(4), 1–14. http://doi.org/10.1371/journal.pcbi.1005494\n\nFirst attempt to identify the main compartment (cytosol), then attempt to\nidentify each metabolite of the referenced list of energy couples via an\ninternal mapping table. Construct a dissipation reaction for each couple.\nCarry out FBA with each dissipation reaction as the objective and report\nthose reactions that non-zero carry flux.","message":{},"data":{},"format_type":"count","metric":{},"score":{}},"test_reaction_charge_balance":{"duration":0.00565537500000346,"result":"passed","title":"Charge Balance","summary":"This will exclude biomass, exchange and demand reactions as they are\nunbalanced by definition. It will also fail all reactions where at\nleast one metabolite does not have a charge defined.\n\nIn steady state, for each metabolite the sum of influx equals the sum\nof efflux. Hence the net charges of both sides of any model reaction have\nto be equal. Reactions where at least one metabolite does not have a\ncharge are not considered to be balanced, even though the remaining\nmetabolites participating in the reaction might be.\n\nImplementation:\nFor each reaction that isn't a boundary or biomass reaction check if each\nmetabolite has a non-zero charge attribute and if so calculate if the\noverall sum of charges of reactants and products is equal to zero.","message":"A total of 0 (0.00%) reactions are charge unbalanced with at\nleast one of the metabolites not having a charge or the overall\ncharge not equal to 0:","data":[],"format_type":"count","metric":0.0},"test_reaction_mass_balance":{"duration":0.08978269900001123,"result":"failed","title":"Mass Balance","summary":"This will exclude biomass, exchange and demand reactions as they are\nunbalanced by definition. It will also fail all reactions where at\nleast one metabolite does not have a formula defined.\n\nIn steady state, for each metabolite the sum of influx equals the sum\nof efflux. Hence the net masses of both sides of any model reaction have\nto be equal. Reactions where at least one metabolite does not have a\nformula are not considered to be balanced, even though the remaining\nmetabolites participating in the reaction might be.\n\nImplementation:\nFor each reaction that isn't a boundary or biomass reaction check if each\nmetabolite has a non-zero elements attribute and if so calculate if the\noverall element balance of reactants and products is equal to zero.","message":"A total of 1 (0.04%) reactions are mass unbalanced with at least\none of the metabolites not having a formula or the overall mass not\nequal to 0: PUACGAMS","data":["PUACGAMS"],"format_type":"count","metric":0.00042176296921130323},"test_blocked_reactions":{"duration":16.873528298999986,"result":"failed","title":"Universally Blocked Reactions","summary":"Universally blocked reactions are reactions that during Flux Variability\nAnalysis cannot carry any flux while all model boundaries are open.\nGenerally blocked reactions are caused by network gaps, which can be\nattributed to scope or knowledge gaps.\n\nImplementation:\nUse flux variability analysis (FVA) implemented in\ncobra.flux_analysis.find_blocked_reactions with open_exchanges=True.\nPlease refer to the cobrapy documentation for more information:\nhttps://cobrapy.readthedocs.io/en/stable/autoapi/cobra/flux_analysis/\nvariability/index.html#cobra.flux_analysis.variability.\nfind_blocked_reactions","message":"There are 269 (9.93%) blocked reactions in         the model: 13PPDH2,\n23DOGULNt4pp, 2DGLCptspp, 2DGLCtex, 2DGULRGx, ...","data":["13PPDH2","23DOGULNt4pp","2DGLCptspp","2DGLCtex","2DGULRGx","2DGULRGy","2DGULRx","2DGULRy","2DOXG6PP","2HESR","2HPTCOAT","3HBZCT","3HPADHi","3KGK","4HBZt3pp","AB6PGH","ACANTHAT","ACBIPGT","ACOLIPAabctex","ACONIs","ACONMT","ACOXT","ACP1p","ACPS1","ADOCBIK","ADOCBLS","AGt3","ALPATE160pp","ALPATG160pp","AMPNTAT","AP5AH","APCS","APPLDHr","ARABDI","ARBTptspp","ARBTtex","ARHGDx","ASO3t8pp","ASO3tex","ASR","BMOCOS","BMOGDS1","BMOGDS2","BSORx","BSORy","BWCOGDS1","BWCOGDS2","BWCOS","CBIAT","CBItonex","CBIuabcpp","CCGS","CD2tex","CDGR","CDGS","CFAS160E","CFAS160G","CFAS180E","CFAS180G","CHOLATEtpp","CHOLID","CHTBSptspp","CHTBStex","CINNDO","CLBtex","CLIPAabctex","COLIPAKpp","COLIPAPabctex","CPH4S","CRNBTCT","CRNCAL2","CRNCAR","CRNCBCT","CRNCDH","CRNDCAL2","CRNDtex","CRNt7pp","CRNtex","CS1tex","CTBTCAL2","CU1abcpp","CURR","CUt2pp","CUt3","CXSAMS","CYANST","CYSItex","CYSItpp","CYSSADS","CYSTA","CYSTL","DC6PDA","DHBSZ3FEabcpp","DHCIND","DHCURR","DHMPTR","DHNPTE","DHPTDNR","DHPTDNRN","DHPTPE","DKGLCNR1","DKGLCNR2x","DKGLCNR2y","DMSOR1","DMSOR2","DMSOtpp","DOGULNR","DSBAO1","DSBAO2","DSBCGT","DSBDR","DSBGGT","DURADx","DXYLK","E4PP","EDTXS3","EDTXS4","EX_2dglc_e","EX_ag_e","EX_arbt_e","EX_aso3_e","EX_cbi_e","EX_cd2_e","EX_chtbs_e","EX_cm_e","EX_crn__D_e","EX_crn_e","EX_cs1_e","EX_doxrbcn_e","EX_fe3dhbzs_e","EX_fusa_e","EX_gbbtn_e","EX_gthox_e","EX_hg2_e","EX_hom__L_e","EX_met__D_e","EX_mincyc_e","EX_na1_e","EX_novbcn_e","EX_rfamp_e","EX_sel_e","EX_slnt_e","EX_so2_e","EX_sucr_e","EX_ttrcyc_e","EX_tungs_e","FE3DCITR5","FE3DHBZS3R","FE3DHBZStonex","FEENTERES","FHL","FORCT","Ftex","Ftpp","GBBTNtex","GDMANE","GHBDHx","GLCATr","GMAND","GOFUCR","GP4GH","GTHOXtex","HETZK","HG2abcpp","HG2t3pp","HG2tex","HMPK1","HOMt2pp","HOMtex","HPACOAT","HSDy","HSK","HSST","KDUI","LA4NTpp","LIPACabcpp","LKDRA","LPLIPAL2ATE120","LPLIPAL2ATE140","LPLIPAL2ATE141","LPLIPAL2ATE160","LPLIPAL2ATE161","LPLIPAL2ATE180","LPLIPAL2ATE181","LPLIPAL2ATG120","LPLIPAL2ATG140","LPLIPAL2ATG141","LPLIPAL2ATG160","LPLIPAL2ATG161","LPLIPAL2ATG180","LPLIPAL2ATG181","LYSAM","MALTATr","MALTptspp","MC6PH","MCPST","METDabcpp","METDtex","METNA","MI1PP","MTRPOX","NAtex","NNDMBRT","NTP11","NTP12","O16A4COLIPAabctex","O16A4Lpp","O16AP1pp","O16AP2pp","O16AP3pp","O16AT","O16AUNDtpp","O16GALFT","O16GLCT1","O16GLCT2","OXCDC","PCNO","PGLYCP","PHDA","PNSPA","PSURIK","PSURItex","PSURItpp","PUACGAMS","PUACGAMtr","RHMND","RU5PP","RZ5PP","SARCOX","SELGTHR","SELGTHR2","SELGTHR3","SELNPS","SELR","SELabcpp","SELtex","SHSL1","SLNTabcpp","SLNTtex","SO2tex","SO2tpp","SPMDAT1","SPMDAT2","SQGH","SUCRtex","SUCptspp","TDSR1","TDSR2","TEO2M","THRS","TMAOR1","TMAOR2","TPRDCOAS","TSULabcpp","TUNGSabcpp","TUNGStex","ThDPAT","UDPGALM","UDPGD","UDPGDC","UDPGPT","UDPKAAT","ULA4NFT","ULA4Ntppi","UPLA4FNF","UPLA4FNT","WCOS","XYHDL","YUMPS"],"format_type":"count","metric":0.0992619926199262},"test_find_stoichiometrically_balanced_cycles":{"duration":12.314585924999989,"result":"failed","title":"Stoichiometrically Balanced Cycles","summary":"Stoichiometrically Balanced Cycles are artifacts of insufficiently\nconstrained networks resulting in reactions that can carry flux when\nall the boundaries have been closed.\n\nImplementation:\nClose all model boundary reactions and then use flux variability analysis\n(FVA) to identify reactions that carry flux.","message":"There are 61 (2.25%) reactions         which participate in SBC in the\nmodel: ABUTt2pp, ACCOAL, ACOAD1f, ACOAD1fr, ACt2rpp, ...","data":["ABUTt2pp","ACCOAL","ACOAD1f","ACOAD1fr","ACt2rpp","ACt4pp","ADK1","ADK3","ADNt2pp_copy1","ADNt2pp_copy2","ALATA_L","ASPtpp","CA2t3pp","CAt6pp","CRNDt2rpp","CRNt2rpp","CRNt8pp","CYTDt2pp_copy1","CYTDt2pp_copy2","FOMETRi","FUMt1pp","GLBRAN2","GLCtex_copy1","GLCtex_copy2","GLDBRAN2","GLUABUTt7pp","GLUt2rpp","GLUt4pp","GLYCLTt2rpp","GLYCLTt4pp","HPYRI","HPYRRx","ICHORS_copy1","ICHORS_copy2","INDOLEt2pp","INDOLEt2rpp","MN2tipp","MN2tpp","NAt3pp","NDPK1","PPAKr","PPCSCT","PPM","PROt2rpp","PROt4pp","PRPPS","PTA2","R15BPK","R1PK","SUCASPtpp","SUCCt1pp","SUCFUMtpp","SUCOAS","THFAT","THMDt2pp_copy1","THMDt2pp_copy2","TRSARr","URIt2pp_copy1","URIt2pp_copy2","VALTA","VPAMTr"],"format_type":"count","metric":0.022509225092250923},"test_find_orphans":{"duration":0.01996384399998874,"result":"failed","title":"Orphan Metabolites","summary":"Orphans are metabolites that are only consumed but not produced by\nreactions in the model. They may indicate the presence of network and\nknowledge gaps.\n\nImplementation:\nFind orphan metabolites structurally by considering only reaction\nequations and bounds. FBA is not carried out.","message":"A total of 46 (2.45%) metabolites are not produced by any reaction\nof the model: 23doguln_p, 25dkglcn_c, 2hptcoa_c, 2pglyc_c,\n34dphacoa_c, ...","data":["23doguln_p","25dkglcn_c","2hptcoa_c","2pglyc_c","34dphacoa_c","3hbzcoa_c","3sala_c","4ahmmp_c","4mhetz_c","5phdt_c","Nmtrp_c","ag_c","alpp_p","ampnt_c","ap5a_c","apoACP_c","aso4_c","btnso_c","cholate_c","cinnm_c","cu_c","cur_c","cyan_c","cysi__L_c","dhptdn_c","dmbzid_c","dsbard_p","dsbcox_p","dsbgox_p","dt5hsu_c","dtgcl_c","dxyl_c","f_c","fe3dcit_c","fe3dhbzs3_p","gmplys_c","gp4g_c","hg2_c","hom__L_c","iprimv_c","mi1p__D_c","ragund_c","sarcs_c","sqg_c","teo2_c","tmao_c"],"format_type":"count","metric":0.024507192328183273},"test_find_deadends":{"duration":0.01761224300000208,"result":"failed","title":"Dead-end Metabolites","summary":"Dead-ends are metabolites that can only be produced but not consumed by\nreactions in the model. They may indicate the presence of network and\nknowledge gaps.\n\nImplementation:\nFind dead-end metabolites structurally by considering only reaction\nequations and bounds. FBA is not carried out.","message":"A total of 63 (3.36%) metabolites are not consumed by any reaction\nof the model: 23dhbzs3_c, 2dglc_c, 2hptcl_c, 2tpr3dpcoa_c, 34dhpha_c,\n...","data":["23dhbzs3_c","2dglc_c","2hptcl_c","2tpr3dpcoa_c","34dhpha_c","3hbz_c","4hbz_p","5phua_c","N1aspmd_c","acampnt_c","acanth_c","acolipa_e","aconm_c","apg120_c","apg140_c","apg141_c","apg160_c","apg161_c","apg180_c","apg181_c","athtp_c","bmocogdp_c","bwcogdp_c","cholate_p","colipap_e","cpe160_c","cpe180_c","cpg160_c","cpg180_c","cxsam_c","dhcholn_c","didp_c","dkdglcn_c","dms_c","dsbaox_p","dsbcrd_p","dsbgrd_p","erthrs_c","fe3dhbzs_p","gam_c","gdpfuc_c","hqn_c","lipa_cold_e","lpp_p","malt6p_c","mercpeth_c","met__D_c","mteo2_c","n8aspmd_c","na15dap_c","nalme_c","o16a4colipa_e","preq1_c","puacgam_p","ribflv_p","selnp_c","suc6p_c","tcynt_c","thcur_c","thmnp_c","thptdn_c","tma_c","xdp_c"],"format_type":"count","metric":0.03356419818859883},"test_find_disconnected":{"duration":0.001007425000011608,"result":"passed","title":"Metabolite Connectivity","summary":"Disconnected metabolites are not part of any reaction in the model. They\nare most likely left-over from the reconstruction process, but may also\npoint to network and knowledge gaps.\n\nImplementation:\nCheck for any metabolites of the cobra.Model object with emtpy reaction\nattribute.","message":"A total of 0 (0.00%) metabolites are not associated with any\nreaction of the model:","data":[],"format_type":"count","metric":0.0},"test_find_metabolites_not_produced_with_open_bounds":{"duration":26.61117283400003,"result":"failed","title":"Metabolite Production In Complete Medium","summary":"In complete medium, a model should be able to divert flux to every\nmetabolite. This test opens all the boundary reactions i.e. simulates a\ncomplete medium and checks if any metabolite cannot be produced\nindividually using flux balance analysis. Metabolites that cannot be\nproduced this way are likely orphan metabolites, downstream of reactions\nwith fixed constraints, or blocked by a cofactor imbalance. To pass this\ntest all metabolites should be producible.\n\nImplementation:\nOpen all model boundary reactions, then for each metabolite in the model\nadd a boundary reaction and maximize it with FBA.","message":"A total of 185 (9.86%) metabolites cannot be produced in complete\nmedium: 13ppd_c, 23doguln_c, 23doguln_p, 25dkglcn_c, 2dhguln_c, ...","data":["13ppd_c","23doguln_c","23doguln_p","25dkglcn_c","2dhguln_c","2hptcl_c","2hptcoa_c","2pglyc_c","34dhpha_c","34dphacoa_c","3dhguln_c","3haACP_c","3hbz_c","3hbzcoa_c","3hcddec5eACP_c","3hcmrs7eACP_c","3hcpalm9eACP_c","3hcvac11eACP_c","3hddecACP_c","3hdecACP_c","3hhexACP_c","3hmrsACP_c","3hoctACP_c","3hoctaACP_c","3hpalmACP_c","3hppnl_c","3ocddec5eACP_c","3ocmrs7eACP_c","3ocpalm9eACP_c","3ocvac11eACP_c","3oddecACP_c","3odecACP_c","3ohexACP_c","3omrsACP_c","3ooctACP_c","3ooctdACP_c","3opalmACP_c","3sala_c","4ahmmp_c","4mhetz_c","5phdt_c","5phua_c","5prdmbz_c","ACP_c","Nmtrp_c","acACP_c","acampnt_c","actACP_c","ag_c","alpp_p","ampnt_c","ap5a_c","apoACP_c","aragund_c","aso3_c","aso4_c","bbtcoa_c","btnso_c","but2eACP_c","butACP_c","cddec5eACP_c","cdec3eACP_c","cenchddd_c","cholate_c","cholate_p","cinnm_c","cu_c","cur_c","cyan_c","cysi__L_c","cysi__L_e","cysi__L_p","cyst__L_c","dcaACP_c","ddcaACP_c","dhcholn_c","dhcur_c","dhptdn_c","dkdglcn_c","dmbzid_c","dsbaox_p","dsbard_p","dsbcox_p","dsbcrd_p","dsbdox_c","dsbdrd_c","dsbgox_p","dsbgrd_p","dt5hsu_c","dtgcl_c","dxyl_c","egmeACP_c","epmeACP_c","f_c","f_e","f_p","fe3dcit_c","fe3dhbzs3_p","flxr_c","flxso_c","garagund_c","gbbtn_c","gfgaragund_c","glutrna_c","gmeACP_c","gmplys_c","gp4g_c","grxox_c","grxrd_c","hdeACP_c","hexACP_c","hg2_c","hgmeACP_c","hom__L_c","hpmeACP_c","iprimv_c","iscs_c","iscssh_c","iscu_2fe2s2_c","iscu_2fe2s_c","iscu_4fe4s_c","iscu_c","lpp_p","malACP_c","mercpeth_c","mi1p__D_c","moadamp_c","moadcoo_c","moadcosh_c","mteo2_c","myrsACP_c","nalme_c","o16a2und_p","o16a3und_p","o16a4colipa_e","o16a4colipa_p","o16a4und_p","o16aund_c","o16aund_p","ocACP_c","ocdcaACP_c","octeACP_c","ogmeACP_c","opmeACP_c","oxa_c","oxalcoa_c","palmACP_c","phom_c","pimACP_c","pmeACP_c","psuri_c","psuri_e","psuri_p","ragund_c","rdmbzi_c","sarcs_c","sqg_c","suchms_c","sufbcd_2fe2s2_c","sufbcd_2fe2s_c","sufbcd_4fe4s_c","sufbcd_c","sufse_c","sufsesh_c","t3c11vaceACP_c","t3c5ddeceACP_c","t3c7mrseACP_c","t3c9palmeACP_c","tcynt_c","tddec2eACP_c","tdeACP_c","tdec2eACP_c","teo2_c","thcur_c","thex2eACP_c","thptdn_c","tma_c","tmao_c","tmrs2eACP_c","toct2eACP_c","toctd2eACP_c","tpalm2eACP_c","trdox_c","trdrd_c","trnaglu_c"],"format_type":"count","metric":0.09856153436334576},"test_find_metabolites_not_consumed_with_open_bounds":{"duration":36.992393375000006,"result":"failed","title":"Metabolite Consumption In Complete Medium","summary":"In complete medium, a model should be able to divert flux from every\nmetabolite. This test opens all the boundary reactions i.e. simulates a\ncomplete medium and checks if any metabolite cannot be consumed\nindividually using flux balance analysis. Metabolites that cannot be\nconsumed this way are likely dead-end metabolites or upstream of reactions\nwith fixed constraints. To pass this test all metabolites should be\nconsumable.\n\nImplementation:\nOpen all model boundary reactions, then for each metabolite in the model\nadd a boundary reaction and minimize it with FBA.","message":"A total of 234 (12.47%) metabolites cannot be consumed in complete\nmedium: 23dhbzs3_c, 2dglc_c, 2doxg6p_c, 2hptcl_c, 2hptcoa_c, ...","data":["23dhbzs3_c","2dglc_c","2doxg6p_c","2hptcl_c","2hptcoa_c","2tpr3dpcoa_c","34dhpha_c","34dphacoa_c","3haACP_c","3hbz_c","3hbzcoa_c","3hcddec5eACP_c","3hcmrs7eACP_c","3hcpalm9eACP_c","3hcvac11eACP_c","3hddecACP_c","3hdecACP_c","3hhexACP_c","3hmrsACP_c","3hoctACP_c","3hoctaACP_c","3hpalmACP_c","3ocddec5eACP_c","3ocmrs7eACP_c","3ocpalm9eACP_c","3ocvac11eACP_c","3oddecACP_c","3odecACP_c","3ohexACP_c","3omrsACP_c","3ooctACP_c","3ooctdACP_c","3opalmACP_c","4hbz_p","5phdt_c","5phua_c","ACP_c","N1aspmd_c","acACP_c","acampnt_c","acanth_c","acolipa_e","acolipa_p","aconm_c","actACP_c","adocbi_c","adocbip_c","agdpcbi_c","alpp_p","ampnt_c","apg120_c","apg140_c","apg141_c","apg160_c","apg161_c","apg180_c","apg181_c","apoACP_c","arab__D_c","aragund_c","arbt6p_c","arbt_p","athtp_c","bbtcoa_c","bmoco1gdp_c","bmoco_c","bmocogdp_c","but2eACP_c","butACP_c","bwco1gdp_c","bwco_c","bwcogdp_c","cbi_c","cbi_p","cddec5eACP_c","cdec3eACP_c","cdg_c","cholate_c","cholate_p","chtbs6p_c","colipap_e","colipap_p","cpe160_c","cpe180_c","cpg160_c","cpg180_c","cph4_c","crnDcoa_c","crncoa_c","ctbtcoa_c","cur_c","cxsam_c","cyan_c","cysi__L_c","cysi__L_e","cysi__L_p","dcaACP_c","ddcaACP_c","dgslnt_c","dhcholn_c","dhcur_c","dhptdn_c","didp_c","dkdglcn_c","dms_c","dsbaox_p","dsbard_p","dsbcox_p","dsbcrd_p","dsbdox_c","dsbdrd_c","dsbgox_p","dsbgrd_p","dt5hsu_c","dtgcl_c","egmeACP_c","epmeACP_c","erthrs_c","f_c","f_e","f_p","fe3dhbzs3_c","fe3dhbzs3_p","fe3dhbzs_p","flxr_c","flxso_c","gam_c","garagund_c","gdpddman_c","gdpfuc_c","gdpofuc_c","gfgaragund_c","glutrna_c","gmeACP_c","gmplys_c","grxox_c","grxrd_c","gslnt_c","hdeACP_c","hexACP_c","hgmeACP_c","hpmeACP_c","hqn_c","iscs_c","iscssh_c","iscu_2fe2s2_c","iscu_2fe2s_c","iscu_4fe4s_c","iscu_c","kdo2lipid4p_c","lipa_cold_c","lipa_cold_e","lipa_cold_p","lpp_p","malACP_c","malt6p_c","mchtbs6p_c","mercpeth_c","mercppyr_c","met__D_c","moadamp_c","moadcoo_c","moadcosh_c","mteo2_c","myrsACP_c","n8aspmd_c","na15dap_c","nalme_c","o16a2und_p","o16a3und_p","o16a4colipa_e","o16a4colipa_p","o16a4und_p","o16aund_c","o16aund_p","ocACP_c","ocdcaACP_c","octeACP_c","ogmeACP_c","opmeACP_c","palmACP_c","pimACP_c","pmeACP_c","preq0_c","preq1_c","puacgam_p","ragund_c","rbl__D_c","ribflv_p","sel_c","seln_c","selnp_c","slnt_c","suc6p_c","sufbcd_2fe2s2_c","sufbcd_2fe2s_c","sufbcd_4fe4s_c","sufbcd_c","sufse_c","sufsesh_c","t3c11vaceACP_c","t3c5ddeceACP_c","t3c7mrseACP_c","t3c9palmeACP_c","tcynt_c","tddec2eACP_c","tdeACP_c","tdec2eACP_c","teo2_c","thcur_c","thex2eACP_c","thmnp_c","thptdn_c","tma_c","tmao_c","tmrs2eACP_c","toct2eACP_c","toctd2eACP_c","tpalm2eACP_c","trdox_c","trdrd_c","trnaglu_c","tsul_c","tungs_c","uLa4fn_c","uLa4n_c","uLa4n_p","udpLa4fn_c","udpLa4n_c","udpLa4o_c","udpgalfur_c","udpglcur_c","wco_c","xdp_c"],"format_type":"count","metric":0.12466702184336707},"test_find_reactions_unbounded_flux_default_condition":{"duration":15.43771443999998,"result":"passed","title":"Unbounded Flux In Default Medium","summary":"A large fraction of model reactions able to carry unlimited flux under\ndefault conditions indicates problems with reaction directionality,\nmissing cofactors, incorrectly defined transport reactions and more.\n\nImplementation:\nWithout changing the default constraints run flux variability analysis.\nFrom the FVA results identify those reactions that carry flux equal to the\nmodel's maximal or minimal flux.","message":" A fraction of 4.15% of the non-blocked reactions (in total 66\nreactions) can carry unbounded flux in the default model\ncondition. Unbounded reactions may be involved in\nthermodynamically infeasible cycles: ABUTt2pp, ACCOAL, ACOAD1f,\nACOAD1fr, ACt2rpp, ...","data":["ABUTt2pp","ACCOAL","ACOAD1f","ACOAD1fr","ACt2rpp","ACt4pp","ADK1","ADK3","ADNt2pp_copy1","ADNt2pp_copy2","ALATA_L","ASPtpp","CA2t3pp","CAt6pp","CRNDt2rpp","CRNt2rpp","CRNt8pp","CYTDt2pp_copy1","CYTDt2pp_copy2","EX_fe2_e","EX_fe3_e","EX_h_e","FE2tex","FE3tex","FOMETRi","FUMt1pp","GLBRAN2","GLCtex_copy1","GLDBRAN2","GLUABUTt7pp","GLUt2rpp","GLUt4pp","GLYCLTt2rpp","GLYCLTt4pp","HPYRI","HPYRRx","Htex","ICHORS_copy1","ICHORS_copy2","INDOLEt2pp","INDOLEt2rpp","MN2tipp","MN2tpp","NAt3pp","NDPK1","PPAKr","PPCSCT","PPM","PROt2rpp","PROt4pp","PRPPS","PTA2","R15BPK","R1PK","SUCASPtpp","SUCCt1pp","SUCFUMtpp","SUCOAS","THFAT","THMDt2pp_copy1","THMDt2pp_copy2","TRSARr","URIt2pp_copy1","URIt2pp_copy2","VALTA","VPAMTr"],"format_type":"percent","metric":0.041483343808925204},"test_gene_essentiality_from_data_qualitative":{"duration":{"experiment0":0.00021749499995848964},"result":{"experiment0":"skipped"},"title":"Gene Essentiality Prediction","summary":"The in-silico gene essentiality is compared with experimental\ndata and the accuracy is expected to be better than 0.95.\nIn principal, Matthews' correlation coefficient is a more comprehensive\nmetric but is a little fragile to not having any false negatives or false\npositives in the output.\n\nImplementation:\nRead and validate experimental config file and data tables. Constrain the\nmodel with the parameters provided by a user's definition of the medium,\nthen compute a confusion matrix based on the predicted essential, expected\nessential, predicted nonessential and expected nonessential genes.\nThe individual values of the confusion matrix are calculated as described\nin https://en.wikipedia.org/wiki/Confusion_matrix","message":{},"data":{},"format_type":"percent","metric":{},"score":{}},"test_growth_from_data_qualitative":{"duration":{"experiment0":0.000196374999973159},"result":{"experiment0":"skipped"},"title":"Growth Prediction","summary":"The in-silico growth prediction is compared with experimental\ndata and the accuracy is expected to be better than 0.95.\nIn principal, Matthews' correlation coefficient is a more comprehensive\nmetric but is a little fragile to not having any false negatives or false\npositives in the output.\n\nImplementation:\nRead and validate experimental config file and data tables. Constrain the\nmodel with the parameters provided by a user's definition of the medium,\nthen compute a confusion matrix based on the predicted true, expected\ntrue, predicted false and expected false growth.\nThe individual values of the confusion matrix are calculated as described\nin https://en.wikipedia.org/wiki/Confusion_matrix","message":{},"data":{},"format_type":"percent","metric":{},"score":{}},"test_absolute_extreme_coefficient_ratio":{"duration":0.02269896900003232,"result":"passed","title":"Ratio Min/Max Non-Zero Coefficients","summary":"This test will return the absolute largest and smallest, non-zero\ncoefficients of the stoichiometric matrix. A large ratio of these values\nmay point to potential numerical issues when trying to solve different\nmathematical optimization problems such as flux-balance analysis.\n\nTo pass this test the ratio should not exceed 10^9. This threshold has\nbeen selected based on experience, and is likely to be adapted when more\ndata on solver performance becomes available.\n\nImplementation:\nCompose the stoichiometric matrix, then calculate absolute coefficients and\nlastly use the maximal value and minimal non-zero value to calculate the\nratio.","message":"The ratio of the absolute values of the largest coefficient 75.55223\nand         the lowest, non-zero coefficient 2e-06 is: 3.78E+07.","data":37776115.0,"format_type":"percent","metric":0.0},"test_number_independent_conservation_relations":{"duration":2.2542420329999686,"result":"passed","title":"Independent Conservation Relations","summary":"This test will return the number of conservation relations, i.e.,\nconservation pools through the left null space of the stoichiometric\nmatrix. This test is not scored, as the dimension of the left null space\nis system-specific.\n\nImplementation:\nCalculate the left null space, i.e., the null space of the transposed\nstoichiometric matrix, using an algorithm based on the singular value\ndecomposition adapted from\nhttps://scipy.github.io/old-wiki/pages/Cookbook/RankNullspace.html\nThen, return the estimated dimension of that null space.","message":"The number of independent conservation relations is 31.","data":31,"format_type":"raw","metric":0.016515716568993075},"test_matrix_rank":{"duration":1.2214830350000057,"result":"passed","title":"Rank","summary":"The rank of the stoichiometric matrix is system specific. It is\ncalculated using singular value decomposition (SVD).\n\nImplementation:\nCompose the stoichiometric matrix, then estimate the rank, i.e. the\ndimension of the column space, of a matrix. The algorithm used by this\nfunction is based on the singular value decomposition of the matrix.","message":"The rank of the S-Matrix is 1845.","data":1845,"format_type":"raw","metric":0.6808118081180812},"test_degrees_of_freedom":{"duration":1.2007818600000064,"result":"passed","title":"Degrees Of Freedom","summary":"The degrees of freedom of the stoichiometric matrix, i.e., the number\nof 'free variables' is system specific and corresponds to the dimension\nof the (right) null space of the matrix.\n\nImplementation:\nCompose the stoichiometric matrix, then calculate the dimensionality of the\nnull space using the rank-nullity theorem outlined by\nAlama, J. The Rank+Nullity Theorem. Formalized Mathematics 15, (2007).","message":"The degrees of freedom of the S-Matrix are 865.","data":865,"format_type":"raw","metric":0.3191881918819188},"test_sbml_level":{"duration":0.0002484629999912613,"result":"failed","title":"SBML Level and Version","summary":"This test reports if the model file is represented in the latest edition\n(level) of the Systems Biology Markup Language (SBML) which is Level 3,\nand at least version 1.\n\nImplementation:\nThe level and version are parsed directly from the SBML document.","message":null,"data":null,"format_type":"raw","metric":1.0},"test_fbc_presence":{"duration":0.0002085080000142625,"result":"failed","title":"FBC enabled","summary":"The Flux Balance Constraints (FBC) Package extends SBML with structured\nand semantic descriptions for domain-specific model components such as\nflux bounds, multiple linear objective functions, gene-protein-reaction\nassociations, metabolite chemical formulas, charge and related annotations\nwhich are relevant for parameterized GEMs and FBA models. The SBML and\nconstraint-based modeling communities collaboratively develop this package\nand update it based on user input.\n\nImplementation:\nParse the state of the FBC plugin from the SBML document.","message":null,"data":null,"format_type":"raw","metric":1.0},"test_metabolite_sbo_presence":{"duration":0.004926745999966897,"result":"failed","title":"Metabolite General SBO Presence","summary":"    The Systems Biology Ontology (SBO) allows researchers to annotate a model\n    with terms which indicate the intended function of its individual\n    components. The available terms are controlled and relational and can be\n    viewed here http://www.ebi.ac.uk/sbo/main/tree.\n\n    Implementation:\n    Check if each cobra.Metabolite has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\".","message":"A total of 0 metabolites (0.00%) lack annotation with any type\nof SBO term:","data":[],"format_type":"count","metric":0.0},"test_reaction_sbo_presence":{"duration":0.004229125999984262,"result":"failed","title":"Reaction General SBO Presence","summary":"    The Systems Biology Ontology (SBO) allows researchers to annotate a model\n    with terms which indicate the intended function of its individual\n    components. The available terms are controlled and relational and can be\n    viewed here http://www.ebi.ac.uk/sbo/main/tree.\n\n    Implementation:\n    Check if each cobra.Reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\".","message":"A total of 0 reactions (0.00%) lack annotation with any type\nof SBO term:","data":[],"format_type":"count","metric":0.0},"test_gene_sbo_presence":{"duration":0.002567410999972708,"result":"failed","title":"Gene General SBO Presence","summary":"    The Systems Biology Ontology (SBO) allows researchers to annotate a model\n    with terms which indicate the intended function of its individual\n    components. The available terms are controlled and relational and can be\n    viewed here http://www.ebi.ac.uk/sbo/main/tree.\n\n    Check if each cobra.Gene has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\".","message":"A total of 0 genes (0.00%) lack annotation with any type of\nSBO term:","data":[],"format_type":"count","metric":0.0},"test_metabolic_reaction_specific_sbo_presence":{"duration":0.001613945999963562,"result":"failed","title":"Metabolic Reaction SBO:0000176 Presence","summary":"    SBO:0000176 represents the term 'biochemical reaction'. Every metabolic\n    reaction that is not a transport or boundary reaction should be annotated\n    with this. The results shown are relative to the total amount of pure\n    metabolic reactions.\n\n    Implementation:\n    Check if each pure metabolic reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being the SBO term above.","message":"A total of 0 metabolic reactions (0.00% of all purely\nmetabolic reactions) lack annotation with the SBO term\n\"SBO:0000176\" for 'biochemical reaction':","data":[],"format_type":"count","metric":0.0},"test_transport_reaction_specific_sbo_presence":{"duration":0.0015952210000023115,"result":"failed","title":"Transport Reaction SBO:0000185 Presence","summary":"    'SBO:0000185', 'SBO:0000588', 'SBO:0000587', 'SBO:0000655', 'SBO:0000654',\n    'SBO:0000660', 'SBO:0000659', 'SBO:0000657', and 'SBO:0000658' represent\n    the terms 'transport reaction' and 'translocation reaction', in addition\n    to their children (more specific transport reaction labels). Every\n    transport reaction that is not a pure metabolic or boundary reaction should\n    be annotated with one of these terms. The results shown are relative to the\n    total of all transport reactions.\n\n    Implementation:\n    Check if each transport reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"A total of 10 metabolic reactions (1.20% of all transport\nreactions) lack annotation with one of the SBO terms: ['SBO:0000185',\n'SBO:0000588', 'SBO:0000587', 'SBO:0000655', 'SBO:0000654',\n'SBO:0000660', 'SBO:0000659', 'SBO:0000657', 'SBO:0000658'] for\n'biochemical reaction': URIt2pp_copy2, URIt2pp_copy1, THMDt2pp_copy2,\nADNt2pp_copy1, GLCtex_copy2, ...","data":["URIt2pp_copy2","URIt2pp_copy1","THMDt2pp_copy2","ADNt2pp_copy1","GLCtex_copy2","ADNt2pp_copy2","GLCtex_copy1","THMDt2pp_copy1","CYTDt2pp_copy1","CYTDt2pp_copy2"],"format_type":"count","metric":0.012033694344163659},"test_metabolite_specific_sbo_presence":{"duration":0.002663530000006631,"result":"failed","title":"Metabolite SBO:0000247 Presence","summary":"    SBO:0000247 represents the term 'simple chemical'. Every metabolite should\n    be annotated with this.\n\n    Implementation:\n    Check if each cobra.Metabolite has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"A total of 0 transport reactions (0.00% of all metabolites)\nlack annotation with the SBO term \"SBO:0000247\" for\n'simple chemical':","data":[],"format_type":"count","metric":0.0},"test_gene_specific_sbo_presence":{"duration":0.0022275780000313716,"result":"failed","title":"Gene SBO:0000243 Presence","summary":"    SBO:0000243 represents the term 'gene'. Every gene should\n    be annotated with this.\n\n    Implementation:\n    Check if each cobra.Gene has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"A total of 0 genes (0.00% of all genes) lack             annotation\nwith the SBO term \"SBO:0000243\" for             'gene':","data":[],"format_type":"count","metric":0.0},"test_exchange_specific_sbo_presence":{"duration":0.012169525000047088,"result":"failed","title":"Exchange Reaction SBO:0000627 Presence","summary":"    SBO:0000627 represents the term 'exchange reaction'. The Systems Biology\n    Ontology defines an exchange reaction as follows: 'A modeling process to\n    provide matter influx or efflux to a model, for example to replenish a\n    metabolic network with raw materials (eg carbon / energy sources). Such\n    reactions are conceptual, created solely for modeling purposes, and do not\n    have a  physical correspondence. Exchange reactions, often represented as\n    'R_EX_', can operate in the negative (uptake) direction or positive\n    (secretion) direction. By convention, a negative flux through an exchange\n    reaction represents uptake of the corresponding metabolite, and a positive\n    flux represent discharge.' Every exchange reaction should be annotated with\n    this. Exchange reactions differ from demand reactions in that the\n    metabolites are removed from or added to the extracellular\n    environment only.\n\n    Implementation:\n    Check if each exchange reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"A total of 0 exchange reactions (0.00% of all exchange\nreactions) lack annotation with the SBO term \"SBO:0000627\" for\n'exchange reaction':","data":[],"format_type":"count","metric":0.0},"test_demand_specific_sbo_presence":{"duration":0.011211771000034787,"result":"failed","title":"Demand Reaction SBO:0000628 Presence","summary":"    SBO:0000628 represents the term 'demand reaction'. The Systems Biology\n    Ontology defines a demand reaction as follows: 'A modeling process\n    analogous to exchange reaction, but which operates upon \"internal\"\n    metabolites. Metabolites that are consumed by these reactions are assumed\n    to be used in intra-cellular processes that are not part of the model.\n    Demand reactions, often represented 'R_DM_', can also deliver metabolites\n    (from intra-cellular processes that are not considered in the model).'\n    Every demand reaction should be annotated with\n    this. Demand reactions differ from exchange reactions in that the\n    metabolites are not removed from the extracellular environment, but from\n    any of the organism's compartments. Demand reactions differ from sink\n    reactions in that they are designated as irreversible.\n\n    Implementation:\n    Check if each demand reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"A total of 0 genes (0.00% of all demand reactions) lack\nannotation with the SBO term \"SBO:0000628\" for             'demand\nreaction':","data":[],"format_type":"count","metric":0.0},"test_sink_specific_sbo_presence":{"duration":0.010514562000025762,"result":"skipped","title":"Sink Reactions SBO:0000632 Presence","summary":"    SBO:0000632 represents the term 'sink reaction'. The Systems Biology\n    Ontology defines a sink reaction as follows: 'A modeling process to\n    provide matter influx or efflux to a model, for example to replenish a\n    metabolic network with raw materials (eg carbon / energy sources). Such\n    reactions are conceptual, created solely for modeling purposes, and do not\n    have a physical correspondence. Unlike the analogous demand (SBO:....)\n    reactions, which are usually designated as irreversible, sink reactions\n    always represent a reversible uptake/secretion processes, and act as a\n    metabolite source with no cost to the cell. Sink reactions, also referred\n    to as R_SINK_, are generally used for compounds that are metabolized by\n    the cell but are produced by non-metabolic, un-modeled cellular processes.'\n    Every sink reaction should be annotated with\n    this. Sink reactions differ from exchange reactions in that the metabolites\n    are not removed from the extracellular environment, but from any of the\n    organism's compartments.\n\n    Implementation:\n    Check if each sink reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"No sink reactions found.","data":[],"format_type":"count","metric":1.0},"test_biomass_specific_sbo_presence":{"duration":0.00027165599999534606,"result":"passed","title":"Biomass Reactions SBO:0000629 Presence","summary":"    SBO:0000629 represents the term 'biomass production'. The Systems Biology\n    Ontology defines an exchange reaction as follows: 'Biomass production,\n    often represented 'R_BIOMASS_', is usually the optimization target reaction\n    of constraint-based models, and can consume multiple reactants to produce\n    multiple products. It is also assumed that parts of the reactants are also\n    consumed in unrepresented processes and hence products do not have to\n    reflect all the atom composition of the reactants. Formulation of a\n    biomass production process entails definition of the macromolecular\n    content (eg. cellular protein fraction), metabolic constitution of\n    each fraction (eg. amino acids), and subsequently the atomic composition\n    (eg. nitrogen atoms). More complex biomass functions can additionally\n    incorporate details of essential vitamins and cofactors required for\n    growth.'\n    Every reaction representing the biomass production should be annotated with\n    this.\n\n    Implementation:\n    Check if each biomass reaction has a non-zero \"annotation\"\n    attribute that contains the key \"sbo\" with the associated\n    value being one of the SBO terms above.","message":"A total of 0 biomass reactions (0.00% of all biomass reactions)\nlack annotation with the SBO term \"SBO:0000629\" for         'biomass\nproduction':","data":[],"format_type":"count","metric":0.0}},"score":{"sections":[{"section":"consistency","score":0.9940135561745521},{"section":"annotation_met","score":0.7878142102968955},{"section":"annotation_rxn","score":0.8085383353833537},{"section":"annotation_gene","score":0.633245382585752},{"section":"annotation_sbo","score":0.9079969368778034}],"total_score":0.9099141411380651},"cards":{"scored":{"title":"Core Tests","sections":{"consistency":{"title":"Consistency","weight":3.0,"cases":["test_stoichiometric_consistency","test_reaction_mass_balance","test_reaction_charge_balance","test_find_disconnected","test_find_reactions_unbounded_flux_default_condition"]},"annotation_met":{"title":"Annotation - Metabolites","weight":1.0,"cases":["test_metabolite_annotation_presence","test_metabolite_annotation_overview","test_metabolite_annotation_wrong_ids","test_metabolite_id_namespace_consistency"]},"annotation_rxn":{"title":"Annotation - Reactions","weight":1.0,"cases":["test_reaction_annotation_presence","test_reaction_annotation_overview","test_reaction_annotation_wrong_ids","test_reaction_id_namespace_consistency"]},"annotation_gene":{"title":"Annotation - Genes","weight":1.0,"cases":["test_gene_product_annotation_presence","test_gene_product_annotation_overview","test_gene_product_annotation_wrong_ids"]},"annotation_sbo":{"title":"Annotation - SBO Terms","weight":2.0,"cases":["test_metabolite_sbo_presence","test_metabolite_specific_sbo_presence","test_reaction_sbo_presence","test_metabolic_reaction_specific_sbo_presence","test_transport_reaction_specific_sbo_presence","test_exchange_specific_sbo_presence","test_demand_specific_sbo_presence","test_sink_specific_sbo_presence","test_gene_sbo_presence","test_gene_specific_sbo_presence","test_biomass_specific_sbo_presence"]}}},"sbml_format":{"title":"SBML","cases":["test_sbml_level","test_fbc_presence"]},"basic_info":{"title":"Basic Information","cases":["test_model_id_presence","test_metabolites_presence","test_reactions_presence","test_genes_presence","test_compartments_presence","test_metabolic_coverage","test_unconserved_metabolites","test_inconsistent_min_stoichiometry"]},"basic_met":{"title":"Metabolite Information","cases":["test_find_unique_metabolites","test_find_duplicate_metabolites_in_compartments","test_metabolites_charge_presence","test_metabolites_formula_presence","test_find_medium_metabolites"]},"basic_rxn":{"title":"Reaction Information","cases":["test_find_pure_metabolic_reactions","test_find_constrained_pure_metabolic_reactions","test_find_transport_reactions","test_find_constrained_transport_reactions","test_find_candidate_irreversible_reactions","test_find_reactions_with_partially_identical_annotations","test_find_duplicate_reactions","test_find_reactions_with_identical_genes"]},"gpr_calculations":{"title":"Gene-Protein-Reaction (GPR) Associations","cases":["test_gene_protein_reaction_rule_presence","test_transport_reaction_gpr_presence","test_protein_complex_presence"]},"test_biomass":{"title":"Biomass","cases":["test_biomass_presence","test_biomass_consistency","test_biomass_default_production","test_fast_growth_default","test_biomass_open_production","test_biomass_precursors_default_production","test_biomass_precursors_open_production","test_direct_metabolites_in_biomass","test_essential_precursors_not_in_biomass"]},"energy_metabolism":{"title":"Energy Metabolism","cases":["test_ngam_presence","test_gam_in_biomass","test_find_reversible_oxygen_reactions","test_detect_energy_generating_cycles"]},"gap_finding":{"title":"Network Topology","cases":["test_blocked_reactions","test_find_orphans","test_find_deadends","test_find_stoichiometrically_balanced_cycles","test_find_metabolites_not_produced_with_open_bounds","test_find_metabolites_not_consumed_with_open_bounds"]},"matrix":{"title":"Matrix Conditioning","cases":["test_absolute_extreme_coefficient_ratio","test_number_independent_conservation_relations","test_matrix_rank","test_degrees_of_freedom"]},"experimental":{"title":"Experimental Data Comparison","cases":["test_growth_from_data_qualitative","test_gene_essentiality_from_data_qualitative"]},"misc":{"title":"Misc. Tests","cases":[]}},"weights":{"test_reaction_mass_balance":1.0,"test_find_disconnected":1.0,"test_stoichiometric_consistency":3.0,"test_reaction_charge_balance":1.0,"test_metabolite_annotation_presence":1.0,"test_reaction_annotation_presence":1.0,"test_metabolite_annotation_overview":1.0,"test_reaction_annotation_overview":1.0,"test_metabolite_annotation_wrong_ids":1.0,"test_reaction_annotation_wrong_ids":1.0,"test_metabolite_id_namespace_consistency":1.0,"test_reaction_id_namespace_consistency":1.0}};
     window.reportType = 'snapshot';
   </script>
 <script type="text/javascript">
diff --git a/model/Ecoli-GEM.json b/model/Ecoli-GEM.json
index d7f0aa4..42c98fe 100644
--- a/model/Ecoli-GEM.json
+++ b/model/Ecoli-GEM.json
@@ -50553,7 +50553,7 @@
 },
 "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":{
 "bigg.reaction":"3NTD4pp",
@@ -59044,7 +59044,7 @@
 },
 "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":{
 "bigg.reaction":"ARGabcpp",
@@ -60717,7 +60717,7 @@
 },
 "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":{
 "bigg.reaction":"BMOGDS1",
@@ -60737,7 +60737,7 @@
 },
 "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":{
 "bigg.reaction":"BMOGDS2",
@@ -61033,7 +61033,7 @@
 },
 "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":{
 "bigg.reaction":"BWCOGDS1",
@@ -61053,7 +61053,7 @@
 },
 "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":{
 "bigg.reaction":"BWCOGDS2",
@@ -70285,7 +70285,7 @@
 },
 "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":{
 "bigg.reaction":"ECAP1pp",
@@ -70305,7 +70305,7 @@
 },
 "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":{
 "bigg.reaction":"ECAP2pp",
@@ -70325,7 +70325,7 @@
 },
 "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":{
 "bigg.reaction":"ECAP3pp",
@@ -80146,7 +80146,7 @@
 },
 "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":{
 "bigg.reaction":"FADRx2",
@@ -82109,7 +82109,7 @@
 },
 "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":{
 "bigg.reaction":"FMNRx2",
@@ -85180,7 +85180,7 @@
 "ser__L_c":-1.0,
 "thf_c":-1.0
 },
-"lower_bound":-1000.0,
+"lower_bound":0.0,
 "upper_bound":1000.0,
 "gene_reaction_rule":"b2551",
 "subsystem":"Glycine and Serine Metabolism",
@@ -86122,7 +86122,7 @@
 },
 "lower_bound":-1000.0,
 "upper_bound":1000.0,
-"gene_reaction_rule":"b1761 or (b3213 and b3212)",
+"gene_reaction_rule":"b1761",
 "subsystem":"Glutamate Metabolism",
 "annotation":{
 "bigg.reaction":"GLUDy",
@@ -87002,51 +87002,6 @@
 }
 },
 {
-"id":"GLYCK",
-"name":"Glycerate kinase",
-"metabolites":{
-"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":{
-"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"
-}
-},
-{
 "id":"GLYCK2",
 "name":"Glycerate kinase",
 "metabolites":{
@@ -87058,7 +87013,7 @@
 },
 "lower_bound":0.0,
 "upper_bound":1000.0,
-"gene_reaction_rule":"b3124",
+"gene_reaction_rule":"b3124 or b0514",
 "subsystem":"Glycine and Serine Metabolism",
 "annotation":{
 "bigg.reaction":"GLYCK2",
@@ -91715,7 +91670,7 @@
 "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",
@@ -100167,7 +100122,7 @@
 },
 "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":{
 "bigg.reaction":"MOGDS",
@@ -116342,7 +116297,7 @@
 "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",
@@ -117348,8 +117303,8 @@
 "id":"THD2pp",
 "name":"NAD(P) transhydrogenase (periplasm)",
 "metabolites":{
-"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,
@@ -117943,7 +117898,7 @@
 },
 "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":{
 "bigg.reaction":"THZPSN3",
@@ -121868,7 +121823,7 @@
 "biocyc":"META:XYLISOM-RXN",
 "ec-code":"5.3.1.5",
 "kegg.reaction":"R01432",
-"metanetx.reaction":"MNXR105253",
+"metanetx.reaction":"MNXR146751",
 "rhea":[
 "22818",
 "22816",
@@ -121880,34 +121835,6 @@
 }
 },
 {
-"id":"XYLI2",
-"name":"Xylose isomerase",
-"metabolites":{
-"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":{
-"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"
-}
-},
-{
 "id":"XYLK",
 "name":"Xylulokinase",
 "metabolites":{
diff --git a/model/Ecoli-GEM.mat b/model/Ecoli-GEM.mat
index 11a23bc..c67abd6 100644
Binary files a/model/Ecoli-GEM.mat and b/model/Ecoli-GEM.mat differ
diff --git a/model/Ecoli-GEM.txt b/model/Ecoli-GEM.txt
index ec86ccf..8bfb7a6 100644
--- a/model/Ecoli-GEM.txt
+++ b/model/Ecoli-GEM.txt
@@ -96,7 +96,7 @@ R_3HPPtex	3-Hydroxypropanoate[e] <=> 3-Hydroxypropanoate[p] 	G_b1377 or G_b0929
 R_3HPPtpp	3-Hydroxypropanoate[c] + H+[c] => 3-Hydroxypropanoate[p] + H+[p] 		  0.00	1000.00	  0.00
 R_3KGK	3-Dehydro-L-gulonate[c] + ATP C10H12N5O13P3[c] => 3-keto-L-gulonate-6-phosphate[c] + ADP C10H12N5O10P2[c] + H+[c] 	G_b3580	  0.00	1000.00	  0.00
 R_3NTD2pp	3  UMP C9H11N2O9P[p] + H2O H2O[p] => Phosphate[p] + Uridine[p] 	G_b4213 or G_b0383	  0.00	1000.00	  0.00
-R_3NTD4pp	3  CMP C9H12N3O8P[p] + H2O H2O[p] => Cytidine[p] + Phosphate[p] 	G_b4213 or G_b0383 or G_b0383	  0.00	1000.00	  0.00
+R_3NTD4pp	3  CMP C9H12N3O8P[p] + H2O H2O[p] => Cytidine[p] + Phosphate[p] 	G_b0383 or G_b4213 or G_b2744	  0.00	1000.00	  0.00
 R_3NTD7pp	3  AMP C10H12N5O7P[p] + H2O H2O[p] => Adenosine[p] + Phosphate[p] 	G_b4213 or G_b0383	  0.00	1000.00	  0.00
 R_3NTD9pp	Guanosine 3  phosphate C10H12N5O8P[p] + H2O H2O[p] => Guanosine[p] + Phosphate[p] 	G_b4213 or G_b0383	  0.00	1000.00	  0.00
 R_3OAR100	3-Oxodecanoyl-[acyl-carrier protein][c] + H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] <=> (R)-3-Hydroxydecanoyl-[acyl-carrier protein][c] + Nicotinamide adenine dinucleotide phosphate[c] 	G_b1093	-1000.00	1000.00	  0.00
@@ -406,7 +406,7 @@ R_ARGDCpp	L-Arginine[p] + H+[p] => Agmatine[p] + CO2 CO2[p] 	G_b2938	  0.00	1000
 R_ARGORNt7pp	L-Arginine[p] + Ornithine[c] <=> L-Arginine[c] + Ornithine[p] 	G_b1605	-1000.00	1000.00	  0.00
 R_ARGSL	N(omega)-(L-Arginino)succinate[c] <=> L-Arginine[c] + Fumarate[c] 	G_b3960	-1000.00	1000.00	  0.00
 R_ARGSS	L-Aspartate[c] + ATP C10H12N5O13P3[c] + L-Citrulline[c] => AMP C10H12N5O7P[c] + N(omega)-(L-Arginino)succinate[c] + H+[c] + Diphosphate[c] 	G_b3172	  0.00	1000.00	  0.00
-R_ARGabcpp	L-Arginine[p] + ATP C10H12N5O13P3[c] + H2O H2O[c] => ADP C10H12N5O10P2[c] + L-Arginine[c] + H+[c] + Phosphate[c] 	(G_b2308 and G_b2306 and G_b2310 and G_b2307) or (G_b0864 and G_b0860 and G_b0863 and G_b0862 and G_b0861)	  0.00	1000.00	  0.00
+R_ARGabcpp	L-Arginine[p] + ATP C10H12N5O13P3[c] + H2O H2O[c] => ADP C10H12N5O10P2[c] + L-Arginine[c] + H+[c] + Phosphate[c] 	(G_b2310 and G_b2308 and G_b2306 and G_b2307) or (G_b0862 and G_b0860 and G_b0864 and G_b0861) or (G_b0862 and G_b0864 and G_b0863 and G_b0861)	  0.00	1000.00	  0.00
 R_ARGt3pp	L-Arginine[c] + H+[p] => L-Arginine[p] + H+[c] 	G_b2923	  0.00	1000.00	  0.00
 R_ARGtex	L-Arginine[e] <=> L-Arginine[p] 	G_b0241 or G_b0929 or G_b1377 or G_b2215	-1000.00	1000.00	  0.00
 R_ARHGDx	Nicotinamide adenine dinucleotide[c] + (R)-2-Hydroxyglutarate[c] <=> 2-Oxoglutarate[c] + H+[c] + Nicotinamide adenine dinucleotide - reduced[c] 	G_b2913	-1000.00	1000.00	  0.00
@@ -453,8 +453,8 @@ R_BGLA1	6-Phospho-beta-D-glucosyl-(1,4)-D-glucose[c] + H2O H2O[c] => D-Glucose 6
 R_BIOMASS_Ec_iML1515_WT_75p37M	0.000223 10-Formyltetrahydrofolate[c] + 0.000223 2-Demethylmenaquinol 8[c] + 2.5e-05 [2Fe-2S] iron-sulfur cluster[c] + 0.000248 [4Fe-4S] iron-sulfur cluster[c] + 0.000223 5-Methyltetrahydrofolate[c] + 0.000279 Acetyl-CoA[c] + 0.000223 Adenosylcobalamin[c] + 0.49915 L-Alanine[c] + 0.000223 S-Adenosyl-L-methionine[c] + 0.28742 L-Arginine[c] + 0.23423 L-Asparagine[c] + 0.23423 L-Aspartate[c] + 75.5522 ATP C10H12N5O13P3[c] + 2e-06 Biotin[c] + 0.004952 Calcium[c] + 0.000223 Chorismate[c] + 0.004952 Chloride[c] + 0.002944 Cardiolipin (tetrahexadecanoyl, n-C16:0)[p] + 0.00229 Cardiolipin (tetrahexadec-9-enoyl, n-C16:1)[p] + 0.00118 Cardiolipin (tetraoctadec-11-enoyl, n-C18:1)[p] + 0.000168 Coenzyme A[c] + 2.4e-05 Co2+[c] + 0.008151 Core oligosaccharide lipid A[e] + 0.1298 CTP C9H12N3O14P3[c] + 0.000674 Copper[c] + 0.088988 L-Cysteine[c] + 0.024805 DATP C10H12N5O12P3[c] + 0.025612 DCTP C9H12N3O13P3[c] + 0.025612 DGTP C10H12N5O13P3[c] + 0.024805 DTTP C10H13N2O14P3[c] + 0.000223 Enterochelin[c] + 0.000223 Flavin adenine dinucleotide oxidized[c] + 0.006388 Fe2+ mitochondria[c] + 0.007428 Iron (Fe3+)[c] + 0.25571 L-Glutamine[c] + 0.25571 L-Glutamate[c] + 0.5953 Glycine[c] + 0.15419 Glycogen C6H10O5[c] + 0.000223 Reduced glutathione[c] + 0.20912 GTP C10H12N5O14P3[c] + 70.0288 H2O H2O[c] + 0.000223 Heme O C49H56FeN4O5[c] + 0.092056 L-Histidine[c] + 0.28231 L-Isoleucine[c] + 0.18569 Potassium[c] + 0.43778 L-Leucine[c] + 3e-06 Lipoate (protein bound)[c] + 0.33345 L-Lysine[c] + 3.1e-05 Malonyl CoA C24H33N7O19P3S[c] + 0.14934 L-Methionine[c] + 0.008253 Magnesium[c] + 0.000223 5,10-Methylenetetrahydrofolate[c] + 0.000658 Manganese[c] + 7e-06 Molybdate[c] + 7e-06 Molybdopterin cytosine dinucleotide[c] + 7e-06 Molybdopterin guanine dinucleotide[c] + 0.000223 Menaquinol 8[c] + 0.001345 Two linked disacharide tripeptide murein units (uncrosslinked, middle of chain)[p] + 0.000605 Two disacharide linked murein units, tripeptide crosslinked tetrapeptide (A2pm->D-ala) (middle of chain)[p] + 0.005381 Two linked disacharide tetrapeptide murein units (uncrosslinked, middle of chain)[p] + 0.005448 Two disacharide linked murein units, tetrapeptide corsslinked tetrapeptide (A2pm->D-ala) (middle of chain)[p] + 0.000673 Three disacharide linked murein units (tetrapeptide crosslinked tetrapeptide (A2pm->D-ala) & tetrapeptide corsslinked tetrapeptide (A2pm->D-ala)) (middle of chain)[p] + 0.001787 Nicotinamide adenine dinucleotide[c] + 4.5e-05 Nicotinamide adenine dinucleotide - reduced[c] + 0.000112 Nicotinamide adenine dinucleotide phosphate[c] + 0.000335 Nicotinamide adenine dinucleotide phosphate - reduced[c] + 0.012379 Ammonium[c] + 0.000307 Nickel[c] + 0.044164 Phosphatidylethanolamine (dihexadecanoyl, n-C16:0)[p] + 0.03435 Phosphatidylethanolamine (dihexadec-9enoyl, n-C16:1)[p] + 0.017704 Phosphatidylethanolamine (dioctadec-11-enoyl, n-C18:1)[p] + 0.010599 Phosphatidylglycerol (dihexadecanoyl, n-C16:0)[p] + 0.008244 Phosphatidylglycerol (dihexadec-9-enoyl, n-C16:1)[p] + 0.004249 Phosphatidylglycerol (dioctadec-11-enoyl, n-C18:1)[p] + 0.18002 L-Phenylalanine[c] + 0.000223 Protoheme C34H30FeN4O4[c] + 0.2148 L-Proline[c] + 0.03327 Putrescine[c] + 0.000223 Pyridoxal 5'-phosphate[c] + 0.000223 Ubiquinol-8[c] + 0.000223 Riboflavin C17H20N4O6[c] + 0.20968 L-Serine[c] + 0.000223 Siroheme C42H36FeN4O16[c] + 0.004126 Sulfate[c] + 0.006744 Spermidine[c] + 9.8e-05 Succinyl-CoA[c] + 0.000223 5,6,7,8-Tetrahydrofolate[c] + 0.000223 Thiamine diphosphate[c] + 0.24651 L-Threonine[c] + 0.055234 L-Tryptophan[c] + 0.13399 L-Tyrosine[c] + 5.5e-05 Undecaprenyl diphosphate[c] + 0.1401 UTP C9H11N2O15P3[c] + 0.41118 L-Valine[c] + 0.000324 Zinc[c] => 75.3772 ADP C10H12N5O10P2[c] + 75.3772 H+[c] + 75.3732 Phosphate[c] + 0.74983 Diphosphate[c] 		  0.00	1000.00	  0.00
 R_BIOMASS_Ec_iML1515_core_75p37M	0.000223 10-Formyltetrahydrofolate[c] + 2.6e-05 [2Fe-2S] iron-sulfur cluster[c] + 0.000223 2-Octaprenyl-6-hydroxyphenol[c] + 0.00026 [4Fe-4S] iron-sulfur cluster[c] + 0.51369 L-Alanine[c] + 0.000223 S-Adenosyl-L-methionine[c] + 0.29579 L-Arginine[c] + 0.24105 L-Asparagine[c] + 0.24105 L-Aspartate[c] + 75.5522 ATP C10H12N5O13P3[c] + 2e-06 Biotin[c] + 0.005205 Calcium[c] + 0.005205 Chloride[c] + 0.000576 Coenzyme A[c] + 2.5e-05 Co2+[c] + 0.13351 CTP C9H12N3O14P3[c] + 0.000709 Copper[c] + 0.09158 L-Cysteine[c] + 0.026166 DATP C10H12N5O12P3[c] + 0.027017 DCTP C9H12N3O13P3[c] + 0.027017 DGTP C10H12N5O13P3[c] + 0.026166 DTTP C10H13N2O14P3[c] + 0.000223 Flavin adenine dinucleotide oxidized[c] + 0.006715 Fe2+ mitochondria[c] + 0.007808 Iron (Fe3+)[c] + 0.26316 L-Glutamine[c] + 0.26316 L-Glutamate[c] + 0.61264 Glycine[c] + 0.2151 GTP C10H12N5O14P3[c] + 70.0288 H2O H2O[c] + 0.094738 L-Histidine[c] + 0.29053 L-Isoleucine[c] + 0.19519 Potassium[c] + 0.019456 KDO(2)-lipid IV(A)[e] + 0.45053 L-Leucine[c] + 0.34316 L-Lysine[c] + 0.15369 L-Methionine[c] + 0.008675 Magnesium[c] + 0.000223 5,10-Methylenetetrahydrofolate[c] + 0.000691 Manganese[c] + 7e-06 Molybdate[c] + 0.013894 Two disacharide linked murein units, pentapeptide crosslinked tetrapeptide (A2pm->D-ala) (middle of chain)[p] + 0.001831 Nicotinamide adenine dinucleotide[c] + 0.000447 Nicotinamide adenine dinucleotide phosphate[c] + 0.013013 Ammonium[c] + 0.000323 Nickel[c] + 0.063814 Phosphatidylethanolamine (dihexadecanoyl, n-C16:0)[p] + 0.075214 Phosphatidylethanolamine (dihexadec-9enoyl, n-C16:1)[p] + 0.18527 L-Phenylalanine[c] + 0.000223 Protoheme C34H30FeN4O4[c] + 0.22106 L-Proline[c] + 0.000223 Pyridoxal 5'-phosphate[c] + 0.000223 Riboflavin C17H20N4O6[c] + 0.21579 L-Serine[c] + 0.000223 Siroheme C42H36FeN4O16[c] + 0.004338 Sulfate[c] + 9.8e-05 Succinyl-CoA[c] + 0.000223 5,6,7,8-Tetrahydrofolate[c] + 0.000223 Thiamine diphosphate[c] + 0.25369 L-Threonine[c] + 0.056843 L-Tryptophan[c] + 0.1379 L-Tyrosine[c] + 5.5e-05 Undecaprenyl diphosphate[c] + 0.1441 UTP C9H11N2O15P3[c] + 0.42316 L-Valine[c] + 0.000341 Zinc[c] => 75.3772 ADP C10H12N5O10P2[c] + 75.3772 H+[c] + 75.3732 Phosphate[c] + 0.7739 Diphosphate[c] 		  0.00	1000.00	  1.00
 R_BMOCOS	Molybdenum cofactor[c] + Adenylated molybdopterin[c] => AMP C10H12N5O7P[c] + Bis-molybdenum cofactor[c] + Copper[c] 	G_b0827	  0.00	1000.00	  0.00
-R_BMOGDS1	Bis-molybdenum cofactor[c] + GTP C10H12N5O14P3[c] + H+[c] => Bis-molybdopterin mono-guanine dinucleotide[c] + Diphosphate[c] 	G_b3857 or (G_b3857 and G_b3856)	  0.00	1000.00	  0.00
-R_BMOGDS2	Bis-molybdopterin mono-guanine dinucleotide[c] + GTP C10H12N5O14P3[c] + H+[c] => Bis-molybdopterin guanine dinucleotide[c] + Diphosphate[c] 	(G_b3857 and G_b3856) or G_b3857	  0.00	1000.00	  0.00
+R_BMOGDS1	Bis-molybdenum cofactor[c] + GTP C10H12N5O14P3[c] + H+[c] => Bis-molybdopterin mono-guanine dinucleotide[c] + Diphosphate[c] 	G_b3857	  0.00	1000.00	  0.00
+R_BMOGDS2	Bis-molybdopterin mono-guanine dinucleotide[c] + GTP C10H12N5O14P3[c] + H+[c] => Bis-molybdopterin guanine dinucleotide[c] + Diphosphate[c] 	G_b3857	  0.00	1000.00	  0.00
 R_BPNT	H2O H2O[c] + Adenosine 3',5'-bisphosphate[c] => AMP C10H12N5O7P[c] + Phosphate[c] 	G_b4214	  0.00	1000.00	  0.00
 R_BSORx	D-biotin d-sulfoxide[c] + H+[c] + Nicotinamide adenine dinucleotide - reduced[c] => Biotin[c] + H2O H2O[c] + Nicotinamide adenine dinucleotide[c] 	G_b3551	  0.00	1000.00	  0.00
 R_BSORy	D-biotin d-sulfoxide[c] + H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] => Biotin[c] + H2O H2O[c] + Nicotinamide adenine dinucleotide phosphate[c] 	G_b3551	  0.00	1000.00	  0.00
@@ -466,8 +466,8 @@ R_BUTSO3abcpp	ATP C10H12N5O13P3[c] + Butanesulfonate[p] + H2O H2O[c] => ADP C10H
 R_BUTSO3tex	Butanesulfonate[e] <=> Butanesulfonate[p] 	G_b0241 or G_b0929 or G_b1377 or G_b2215	-1000.00	1000.00	  0.00
 R_BUTt2rpp	Butyrate (n-C4:0)[p] + H+[p] <=> Butyrate (n-C4:0)[c] + H+[c] 	G_b2223	-1000.00	1000.00	  0.00
 R_BUTtex	Butyrate (n-C4:0)[e] <=> Butyrate (n-C4:0)[p] 	G_b0241 or G_b0929 or G_b1377 or G_b2215	-1000.00	1000.00	  0.00
-R_BWCOGDS1	Tungsten bispterin cofactor[c] + GTP C10H12N5O14P3[c] + H+[c] => Tungsten bispterin cofactor mono-guanine dinucleotide[c] + Diphosphate[c] 	(G_b3857 and G_b3856) or G_b3857	  0.00	1000.00	  0.00
-R_BWCOGDS2	Tungsten bispterin cofactor mono-guanine dinucleotide[c] + GTP C10H12N5O14P3[c] + H+[c] => Tungsten bispterin cofactor guanine dinucleotide[c] + Diphosphate[c] 	(G_b3857 and G_b3856) or G_b3857	  0.00	1000.00	  0.00
+R_BWCOGDS1	Tungsten bispterin cofactor[c] + GTP C10H12N5O14P3[c] + H+[c] => Tungsten bispterin cofactor mono-guanine dinucleotide[c] + Diphosphate[c] 	G_b3857	  0.00	1000.00	  0.00
+R_BWCOGDS2	Tungsten bispterin cofactor mono-guanine dinucleotide[c] + GTP C10H12N5O14P3[c] + H+[c] => Tungsten bispterin cofactor guanine dinucleotide[c] + Diphosphate[c] 	G_b3857	  0.00	1000.00	  0.00
 R_BWCOS	Adenylated molybdopterin[c] + Tungsten binding cofactor[c] => AMP C10H12N5O7P[c] + Tungsten bispterin cofactor[c] + Copper[c] 	G_b0827	  0.00	1000.00	  0.00
 R_CA2t3pp	Calcium[c] + H+[p] => Calcium[p] + H+[c] 	G_b1216	  0.00	1000.00	  0.00
 R_CA2tex	Calcium[e] <=> Calcium[p] 	G_b0241 or G_b0929 or G_b1377 or G_b2215	-1000.00	1000.00	  0.00
@@ -813,9 +813,9 @@ R_EAR80x	H+[c] + Nicotinamide adenine dinucleotide - reduced[c] + Trans-Oct-2-en
 R_EAR80y	H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] + Trans-Oct-2-enoyl-[acyl-carrier protein][c] => Nicotinamide adenine dinucleotide phosphate[c] + Octanoyl-ACP (n-C8:0ACP)[c] 	G_b1288	  0.00	1000.00	  0.00
 R_ECA4COLIPAabctex	ATP C10H12N5O13P3[c] + (enterobacterial common antigen)x4 core oligosaccharide lipid A[p] + H2O H2O[c] => ADP C10H12N5O10P2[c] + (enterobacterial common antigen)x4 core oligosaccharide lipid A[e] + H+[c] + Phosphate[c] 	G_b4262 and G_b4261 and G_b3199 and G_b3201 and G_b3200 and G_b0054 and G_b0641	  0.00	1000.00	  0.00
 R_ECA4OALpp	Core oligosaccharide lipid A[p] + (enterobacterial common antigen)x4 undecaprenyl-diphosphate[p] => (enterobacterial common antigen)x4 core oligosaccharide lipid A[p] + H+[p] + Undecaprenyl diphosphate[p] 	G_b3622	  0.00	1000.00	  0.00
-R_ECAP1pp	2 Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose[p] => (enterobacterial common antigen)x2 undecaprenyl-diphosphate[p] + H+[p] + Undecaprenyl diphosphate[p] 	G_b3785 and G_b3793	  0.00	1000.00	  0.00
-R_ECAP2pp	(enterobacterial common antigen)x2 undecaprenyl-diphosphate[p] + Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose[p] => (enterobacterial common antigen)x3 undecaprenyl-diphosphate[p] + H+[p] + Undecaprenyl diphosphate[p] 	G_b3785 and G_b3793	  0.00	1000.00	  0.00
-R_ECAP3pp	(enterobacterial common antigen)x3 undecaprenyl-diphosphate[p] + Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose[p] => (enterobacterial common antigen)x4 undecaprenyl-diphosphate[p] + H+[p] + Undecaprenyl diphosphate[p] 	G_b3785 and G_b3793	  0.00	1000.00	  0.00
+R_ECAP1pp	2 Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose[p] => (enterobacterial common antigen)x2 undecaprenyl-diphosphate[p] + H+[p] + Undecaprenyl diphosphate[p] 	G_b3785 and G_b3793 and G_b3792	  0.00	1000.00	  0.00
+R_ECAP2pp	(enterobacterial common antigen)x2 undecaprenyl-diphosphate[p] + Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose[p] => (enterobacterial common antigen)x3 undecaprenyl-diphosphate[p] + H+[p] + Undecaprenyl diphosphate[p] 	G_b3785 and G_b3793 and G_b3792	  0.00	1000.00	  0.00
+R_ECAP3pp	(enterobacterial common antigen)x3 undecaprenyl-diphosphate[p] + Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose[p] => (enterobacterial common antigen)x4 undecaprenyl-diphosphate[p] + H+[p] + Undecaprenyl diphosphate[p] 	G_b3785 and G_b3793 and G_b3792	  0.00	1000.00	  0.00
 R_ECAtpp	Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose[c] => Undecaprenyl-diphospho N-acetylglucosamine-N-acetylmannosaminuronate-N-acetamido-4,6-dideoxy-D-galactose[p] 	G_b3792	  0.00	1000.00	  0.00
 R_ECOAH1	(S)-3-Hydroxybutanoyl-CoA[c] <=> Crotonoyl-CoA[c] + H2O H2O[c] 	G_b2341 or G_b3846	-1000.00	1000.00	  0.00
 R_ECOAH2	(S)-3-Hydroxyhexanoyl-CoA[c] <=> H2O H2O[c] + Trans-Hex-2-enoyl-CoA[c] 	G_b2341 or G_b3846	-1000.00	1000.00	  0.00
@@ -1208,7 +1208,7 @@ R_FACOAL181t2pp	ATP C10H12N5O13P3[c] + Coenzyme A[c] + H+[p] + Octadecenoate (n-
 R_FACOAL60t2pp	ATP C10H12N5O13P3[c] + Coenzyme A[c] + H+[p] + Hexanoate (n-C6:0)[p] => AMP C10H12N5O7P[c] + H+[c] + Hexanoyl-CoA (n-C6:0CoA)[c] + Diphosphate[c] 	G_b1805 or G_b1701	  0.00	1000.00	  0.00
 R_FACOAL80t2pp	ATP C10H12N5O13P3[c] + Coenzyme A[c] + H+[p] + Octanoate (n-C8:0)[p] => AMP C10H12N5O7P[c] + H+[c] + Octanoyl-CoA (n-C8:0CoA)[c] + Diphosphate[c] 	G_b1805 or G_b1701	  0.00	1000.00	  0.00
 R_FADRx	Flavin adenine dinucleotide oxidized[c] + H+[c] + Nicotinamide adenine dinucleotide - reduced[c] => Flavin adenine dinucleotide reduced[c] + Nicotinamide adenine dinucleotide[c] 	G_b3844	  0.00	1000.00	  0.00
-R_FADRx2	Flavin adenine dinucleotide oxidized[c] + H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] => Flavin adenine dinucleotide reduced[c] + Nicotinamide adenine dinucleotide phosphate[c] 	G_b2764 and G_b2763	  0.00	1000.00	  0.00
+R_FADRx2	Flavin adenine dinucleotide oxidized[c] + H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] => Flavin adenine dinucleotide reduced[c] + Nicotinamide adenine dinucleotide phosphate[c] 	G_b2764	  0.00	1000.00	  0.00
 R_FADt	Flavin adenine dinucleotide oxidized[c] => Flavin adenine dinucleotide oxidized[p] 	G_b1985	  0.00	1000.00	  0.00
 R_FADtex	Flavin adenine dinucleotide oxidized[p] <=> Flavin adenine dinucleotide oxidized[e] 	G_b0241 or G_b2215 or G_b1377 or G_b0929	-1000.00	1000.00	  0.00
 R_FALDH2	Hydroxymethylglutathione[c] + Nicotinamide adenine dinucleotide[c] <=> S-Formylglutathione[c] + H+[c] + Nicotinamide adenine dinucleotide - reduced[c] 	G_b0356	-1000.00	1000.00	  0.00
@@ -1287,7 +1287,7 @@ R_FLVR	H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] + Ribofl
 R_FLVRx	H+[c] + Nicotinamide adenine dinucleotide - reduced[c] + Riboflavin C17H20N4O6[c] => Nicotinamide adenine dinucleotide[c] + Reduced riboflavin[c] 	G_b3844	  0.00	1000.00	  0.00
 R_FMNAT	ATP C10H12N5O13P3[c] + FMN C17H19N4O9P[c] + H+[c] => Flavin adenine dinucleotide oxidized[c] + Diphosphate[c] 	G_b0025	  0.00	1000.00	  0.00
 R_FMNRx	FMN C17H19N4O9P[c] + H+[c] + Nicotinamide adenine dinucleotide - reduced[c] => Reduced FMN[c] + Nicotinamide adenine dinucleotide[c] 	G_b0937 or G_b3844	  0.00	1000.00	  0.00
-R_FMNRx2	FMN C17H19N4O9P[c] + H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] => Reduced FMN[c] + Nicotinamide adenine dinucleotide phosphate[c] 	G_b3844 or G_b0937 or (G_b2764 and G_b2763)	  0.00	1000.00	  0.00
+R_FMNRx2	FMN C17H19N4O9P[c] + H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] => Reduced FMN[c] + Nicotinamide adenine dinucleotide phosphate[c] 	G_b0937 or G_b3844 or G_b2764	  0.00	1000.00	  0.00
 R_FMNt	FMN C17H19N4O9P[c] => FMN C17H19N4O9P[p] 	G_b1985	  0.00	1000.00	  0.00
 R_FMNtex	FMN C17H19N4O9P[p] <=> FMN C17H19N4O9P[e] 	G_b0929 or G_b0241 or G_b2215 or G_b1377	-1000.00	1000.00	  0.00
 R_FOMETRi	5-Formyltetrahydrofolate[c] + H+[c] => H2O H2O[c] + 5,10-Methenyltetrahydrofolate[c] 	G_b2912	  0.00	1000.00	  0.00
@@ -1404,7 +1404,7 @@ R_GGGABAH	Gamma-glutamyl-gamma aminobutyric acid[c] + H2O H2O[c] => 4-Aminobutan
 R_GGPTRCO	Gamma-glutamyl-putrescine[c] + H2O H2O[c] + O2 O2[c] => Gamma-glutamyl-gamma-butyraldehyde[c] + Hydrogen peroxide[c] + Ammonium[c] 	G_b1301	  0.00	1000.00	  0.00
 R_GGPTRCS	ATP C10H12N5O13P3[c] + L-Glutamate[c] + Putrescine[c] => ADP C10H12N5O10P2[c] + Gamma-glutamyl-putrescine[c] + H+[c] + Phosphate[c] 	G_b1297	  0.00	1000.00	  0.00
 R_GHBDHx	H+[c] + Nicotinamide adenine dinucleotide - reduced[c] + Succinic semialdehyde[c] <=> Gamma-hydroxybutyrate[c] + Nicotinamide adenine dinucleotide[c] 	G_b3882	-1000.00	1000.00	  0.00
-R_GHMT2r	L-Serine[c] + 5,6,7,8-Tetrahydrofolate[c] <=> Glycine[c] + H2O H2O[c] + 5,10-Methylenetetrahydrofolate[c] 	G_b2551	-1000.00	1000.00	  0.00
+R_GHMT2r	L-Serine[c] + 5,6,7,8-Tetrahydrofolate[c] => Glycine[c] + H2O H2O[c] + 5,10-Methylenetetrahydrofolate[c] 	G_b2551	  0.00	1000.00	  0.00
 R_GK1	ATP C10H12N5O13P3[c] + GMP C10H12N5O8P[c] <=> ADP C10H12N5O10P2[c] + GDP C10H12N5O11P2[c] 	G_b3648	-1000.00	1000.00	  0.00
 R_GLBRAN2	Glycogen C6H10O5[c] => Branching glycogen[c] 	G_b3432	  0.00	1000.00	  0.00
 R_GLCATr	Acetyl-CoA[c] + D-Glucose[c] <=> 6-Acetyl-D-glucose[c] + Coenzyme A[c] 	G_b0459	-1000.00	1000.00	  0.00
@@ -1439,7 +1439,7 @@ R_GLU5K	ATP C10H12N5O13P3[c] + L-Glutamate[c] => ADP C10H12N5O10P2[c] + L-Glutam
 R_GLUABUTt7pp	4-Aminobutanoate[c] + L-Glutamate[p] <=> 4-Aminobutanoate[p] + L-Glutamate[c] 	G_b1492	-1000.00	1000.00	  0.00
 R_GLUCYS	ATP C10H12N5O13P3[c] + L-Cysteine[c] + L-Glutamate[c] => ADP C10H12N5O10P2[c] + Gamma-L-Glutamyl-L-cysteine[c] + H+[c] + Phosphate[c] 	G_b2688	  0.00	1000.00	  0.00
 R_GLUDC	L-Glutamate[c] + H+[c] => 4-Aminobutanoate[c] + CO2 CO2[c] 	G_b3517 or G_b1493	  0.00	1000.00	  0.00
-R_GLUDy	L-Glutamate[c] + H2O H2O[c] + Nicotinamide adenine dinucleotide phosphate[c] <=> 2-Oxoglutarate[c] + H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] + Ammonium[c] 	G_b1761 or (G_b3213 and G_b3212)	-1000.00	1000.00	  0.00
+R_GLUDy	L-Glutamate[c] + H2O H2O[c] + Nicotinamide adenine dinucleotide phosphate[c] <=> 2-Oxoglutarate[c] + H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] + Ammonium[c] 	G_b1761	-1000.00	1000.00	  0.00
 R_GLUN	L-Glutamine[c] + H2O H2O[c] => L-Glutamate[c] + Ammonium[c] 	G_b0485 or G_b1524	  0.00	1000.00	  0.00
 R_GLUNpp	L-Glutamine[p] + H2O H2O[p] => L-Glutamate[p] + Ammonium[p] 	G_b2957	  0.00	1000.00	  0.00
 R_GLUPRT	L-Glutamine[c] + H2O H2O[c] + 5-Phospho-alpha-D-ribose 1-diphosphate[c] => L-Glutamate[c] + Diphosphate[c] + 5-Phospho-beta-D-ribosylamine[c] 	G_b2312	  0.00	1000.00	  0.00
@@ -1467,8 +1467,7 @@ R_GLYC3Ptex	Glycerol 3-phosphate[e] <=> Glycerol 3-phosphate[p] 	G_b0241 or G_b0
 R_GLYCAt2rpp	(R)-Glycerate[p] + H+[p] <=> (R)-Glycerate[c] + H+[c] 	G_b3127 or G_b2789	-1000.00	1000.00	  0.00
 R_GLYCAtex	(R)-Glycerate[e] <=> (R)-Glycerate[p] 	G_b0241 or G_b0929 or G_b1377 or G_b2215	-1000.00	1000.00	  0.00
 R_GLYCDx	Glycerol[c] + Nicotinamide adenine dinucleotide[c] => Dihydroxyacetone[c] + H+[c] + Nicotinamide adenine dinucleotide - reduced[c] 	G_b3945	  0.00	1000.00	  0.00
-R_GLYCK	ATP C10H12N5O13P3[c] + (R)-Glycerate[c] => 3-Phospho-D-glycerate[c] + ADP C10H12N5O10P2[c] + H+[c] 	G_b0514	  0.00	1000.00	  0.00
-R_GLYCK2	ATP C10H12N5O13P3[c] + (R)-Glycerate[c] => D-Glycerate 2-phosphate[c] + ADP C10H12N5O10P2[c] + H+[c] 	G_b3124	  0.00	1000.00	  0.00
+R_GLYCK2	ATP C10H12N5O13P3[c] + (R)-Glycerate[c] => D-Glycerate 2-phosphate[c] + ADP C10H12N5O10P2[c] + H+[c] 	G_b3124 or G_b0514	  0.00	1000.00	  0.00
 R_GLYCL	Glycine[c] + Nicotinamide adenine dinucleotide[c] + 5,6,7,8-Tetrahydrofolate[c] => CO2 CO2[c] + 5,10-Methylenetetrahydrofolate[c] + Nicotinamide adenine dinucleotide - reduced[c] + Ammonium[c] 	G_b2904 and G_b2903 and G_b0116 and G_b2905	  0.00	1000.00	  0.00
 R_GLYCLTDx	Glyoxylate[c] + H+[c] + Nicotinamide adenine dinucleotide - reduced[c] => Glycolate C2H3O3[c] + Nicotinamide adenine dinucleotide[c] 	G_b3553 or G_b1033	  0.00	1000.00	  0.00
 R_GLYCLTDy	Glyoxylate[c] + H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] => Glycolate C2H3O3[c] + Nicotinamide adenine dinucleotide phosphate[c] 	G_b1033 or G_b3553	  0.00	1000.00	  0.00
@@ -1602,7 +1601,7 @@ R_HPYRI	Hydroxypyruvate[c] <=> 2-Hydroxy-3-oxopropanoate[c] 	G_b0508	-1000.00	10
 R_HPYRP	3-Phosphohydroxypyruvate[c] + H2O H2O[c] => Hydroxypyruvate[c] + Phosphate[c] 	G_b1813	  0.00	1000.00	  0.00
 R_HPYRRx	H+[c] + Hydroxypyruvate[c] + Nicotinamide adenine dinucleotide - reduced[c] => (R)-Glycerate[c] + Nicotinamide adenine dinucleotide[c] 	G_b1033 or G_b3553	  0.00	1000.00	  0.00
 R_HPYRRy	H+[c] + Hydroxypyruvate[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] => (R)-Glycerate[c] + Nicotinamide adenine dinucleotide phosphate[c] 	G_b1033 or G_b3553	  0.00	1000.00	  0.00
-R_HSDy	L-Homoserine[c] + Nicotinamide adenine dinucleotide phosphate[c] <=> L-Aspartate 4-semialdehyde[c] + H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] 	G_b3940 or G_b0002	-1000.00	1000.00	  0.00
+R_HSDy	L-Homoserine[c] + Nicotinamide adenine dinucleotide phosphate[c] => L-Aspartate 4-semialdehyde[c] + H+[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] 	G_b3940 or G_b0002	  0.00	1000.00	  0.00
 R_HSK	ATP C10H12N5O13P3[c] + L-Homoserine[c] => ADP C10H12N5O10P2[c] + H+[c] + O-Phospho-L-homoserine[c] 	G_b0003	  0.00	1000.00	  0.00
 R_HSST	L-Homoserine[c] + Succinyl-CoA[c] => Coenzyme A[c] + O-Succinyl-L-homoserine[c] 	G_b4013	  0.00	1000.00	  0.00
 R_HSTPT	L-Glutamate[c] + 3-(Imidazol-4-yl)-2-oxopropyl phosphate[c] => 2-Oxoglutarate[c] + L-Histidinol phosphate[c] 	G_b2021	  0.00	1000.00	  0.00
@@ -1922,7 +1921,7 @@ R_MOBDabcpp	ATP C10H12N5O13P3[c] + H2O H2O[c] + Molybdate[p] => ADP C10H12N5O10P
 R_MOBDtex	Molybdate[e] <=> Molybdate[p] 	G_b0241 or G_b0929 or G_b1377 or G_b2215	-1000.00	1000.00	  0.00
 R_MOCDS	CTP C9H12N3O14P3[c] + H+[c] + Molybdenum cofactor[c] => Molybdopterin cytosine dinucleotide[c] + Diphosphate[c] 	G_b2877	  0.00	1000.00	  0.00
 R_MOCOS	2 H+[c] + Molybdate[c] + Adenylated molybdopterin[c] => AMP C10H12N5O7P[c] + Copper[c] + H2O H2O[c] + Molybdenum cofactor[c] 	G_b0827	  0.00	1000.00	  0.00
-R_MOGDS	GTP C10H12N5O14P3[c] + H+[c] + Molybdenum cofactor[c] => Molybdopterin guanine dinucleotide[c] + Diphosphate[c] 	(G_b3857 and G_b3856) or G_b3857	  0.00	1000.00	  0.00
+R_MOGDS	GTP C10H12N5O14P3[c] + H+[c] + Molybdenum cofactor[c] => Molybdopterin guanine dinucleotide[c] + Diphosphate[c] 	G_b3857	  0.00	1000.00	  0.00
 R_MOHMT	3-Methyl-2-oxobutanoate[c] + H2O H2O[c] + 5,10-Methylenetetrahydrofolate[c] => 2-Dehydropantoate[c] + 5,6,7,8-Tetrahydrofolate[c] 	G_b0134	  0.00	1000.00	  0.00
 R_MOX	L-Malate[c] + O2 O2[c] => Hydrogen peroxide[c] + Oxaloacetate[c] 		  0.00	1000.00	  0.00
 R_MPTAT	ATP C10H12N5O13P3[c] + H+[c] + Molybdopterin[c] => Adenylated molybdopterin[c] + Diphosphate[c] 	G_b0009	  0.00	1000.00	  0.00
@@ -2501,7 +2500,7 @@ R_SSALy	H2O H2O[c] + Nicotinamide adenine dinucleotide phosphate[c] + Succinic s
 R_SUCASPtpp	L-Aspartate[p] + Succinate[c] <=> L-Aspartate[c] + Succinate[p] 	G_b4138 or G_b4123 or G_b0621	-1000.00	1000.00	  0.00
 R_SUCBZL	ATP C10H12N5O13P3[c] + Coenzyme A[c] + O-Succinylbenzoate[c] => AMP C10H12N5O7P[c] + Diphosphate[c] + O-Succinylbenzoyl-CoA[c] 	G_b2260	  0.00	1000.00	  0.00
 R_SUCBZS	2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate[c] => H2O H2O[c] + O-Succinylbenzoate[c] 	G_b2261	  0.00	1000.00	  0.00
-R_SUCCt1pp	Succinate[p] <=> Succinate[c] 	G_b1206	-1000.00	1000.00	  0.00
+R_SUCCt1pp	Succinate[p] => Succinate[c] 	G_b1206	  0.00	1000.00	  0.00
 R_SUCCt2_2pp	2 H+[p] + Succinate[p] => 2 H+[c] + Succinate[c] 	G_b3528 or G_b0010	  0.00	1000.00	  0.00
 R_SUCCt2_3pp	3 H+[p] + Succinate[p] => 3 H+[c] + Succinate[c] 	G_b4123 or G_b4138	  0.00	1000.00	  0.00
 R_SUCCtex	Succinate[e] <=> Succinate[p] 	G_b0241 or G_b0929 or G_b1377 or G_b2215	-1000.00	1000.00	  0.00
@@ -2539,7 +2538,7 @@ R_TDSR1	Protein disulfide isomerase II (oxidized)[p] + Fused thiol:disulfide int
 R_TDSR2	Fused thiol:disulfide interchange protein (reduced)[c] + Periplasmic disulfide isomerase/thiol-disulphide oxidase (oxidized)[p] => Fused thiol:disulfide interchange protein (oxidized)[c] + Periplasmic disulfide isomerase/thiol-disulphide oxidase (reduced)[p] 	G_b0604 and G_b4136	  0.00	1000.00	  0.00
 R_TEO2M	S-Adenosyl-L-methionine[c] + Tellurite[c] => S-Adenosyl-L-homocysteine[c] + Methanetelluronate[c] 	G_b1430	  0.00	1000.00	  0.00
 R_TGBPA	D-Tagatose 1,6-biphosphate[c] <=> Dihydroxyacetone phosphate[c] + Glyceraldehyde 3-phosphate[c] 	(G_b3132 and G_b3137) or (G_b2095 and G_b2096)	-1000.00	1000.00	  0.00
-R_THD2pp	2 H+[p] + Nicotinamide adenine dinucleotide - reduced[c] + Nicotinamide adenine dinucleotide phosphate[c] => 2 H+[c] + Nicotinamide adenine dinucleotide[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] 	G_b1602 and G_b1603	  0.00	1000.00	  0.00
+R_THD2pp	H+[p] + Nicotinamide adenine dinucleotide - reduced[c] + Nicotinamide adenine dinucleotide phosphate[c] => H+[c] + Nicotinamide adenine dinucleotide[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] 	G_b1602 and G_b1603	  0.00	1000.00	  0.00
 R_THDPS	H2O H2O[c] + Succinyl-CoA[c] + 2,3,4,5-Tetrahydrodipicolinate[c] => Coenzyme A[c] + N-Succinyl-2-L-amino-6-oxoheptanedioate[c] 	G_b0166	  0.00	1000.00	  0.00
 R_THFAT	H2O H2O[c] + 5,10-Methenyltetrahydrofolate[c] => 5-Formyltetrahydrofolate[c] + H+[c] 	G_b2551	  0.00	1000.00	  0.00
 R_THIORDXi	Hydrogen peroxide[c] + Reduced thioredoxin[c] => 2 H2O H2O[c] + Oxidized thioredoxin[c] 	(G_b3781 and G_b2480) or G_b1710 or (G_b2582 and G_b2480)	  0.00	1000.00	  0.00
@@ -2561,7 +2560,7 @@ R_THRt4pp	Sodium[p] + L-Threonine[p] => Sodium[c] + L-Threonine[c] 	G_b3089	  0.
 R_THRtex	L-Threonine[e] <=> L-Threonine[p] 	G_b0241 or G_b0929 or G_b1377 or G_b2215	-1000.00	1000.00	  0.00
 R_THYMt3pp	H+[p] + Thymine C5H6N2O2[c] => H+[c] + Thymine C5H6N2O2[p] 		  0.00	1000.00	  0.00
 R_THYMtex	Thymine C5H6N2O2[e] <=> Thymine C5H6N2O2[p] 	G_b0241 or G_b1377 or G_b2215 or G_b0929	-1000.00	1000.00	  0.00
-R_THZPSN3	ATP C10H12N5O13P3[c] + Dehydroglycine[c] + 1-deoxy-D-xylulose 5-phosphate[c] + H+[c] + IscS with bound sulfur[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] => 4-Methyl-5-(2-phosphoethyl)-thiazole[c] + AMP C10H12N5O7P[c] + CO2 CO2[c] + 2 H2O H2O[c] + IscS sulfur acceptor protein[c] + Nicotinamide adenine dinucleotide phosphate[c] + Diphosphate[c] 	G_b0423 and G_b3990 and G_b2530 and G_b3992 and G_b4407	  0.00	1000.00	  0.00
+R_THZPSN3	ATP C10H12N5O13P3[c] + Dehydroglycine[c] + 1-deoxy-D-xylulose 5-phosphate[c] + H+[c] + IscS with bound sulfur[c] + Nicotinamide adenine dinucleotide phosphate - reduced[c] => 4-Methyl-5-(2-phosphoethyl)-thiazole[c] + AMP C10H12N5O7P[c] + CO2 CO2[c] + 2 H2O H2O[c] + IscS sulfur acceptor protein[c] + Nicotinamide adenine dinucleotide phosphate[c] + Diphosphate[c] 	G_b3992 and G_b3990 and G_b0423 and G_b2530 and G_b4407 and G_b3991	  0.00	1000.00	  0.00
 R_TKT1	Alpha-D-Ribose 5-phosphate[c] + D-Xylulose 5-phosphate[c] <=> Glyceraldehyde 3-phosphate[c] + Sedoheptulose 7-phosphate[c] 	G_b2935 or G_b2465	-1000.00	1000.00	  0.00
 R_TKT2	D-Erythrose 4-phosphate[c] + D-Xylulose 5-phosphate[c] <=> D-Fructose 6-phosphate[c] + Glyceraldehyde 3-phosphate[c] 	G_b2935 or G_b2465	-1000.00	1000.00	  0.00
 R_TMAOR1	H+[c] + Menaquinol 8[c] + Trimethylamine N-oxide[c] => H2O H2O[c] + Menaquinone 8[c] + Trimethylamine[c] 	(G_b0895 and G_b0896 and G_b0894) or (G_b1589 and G_b1590 and G_b1588 and G_b1587)	  0.00	1000.00	  0.00
@@ -2697,7 +2696,6 @@ R_XTSNt2rpp	H+[p] + Xanthosine[p] <=> H+[c] + Xanthosine[c] 	G_b2406	-1000.00	10
 R_XTSNtex	Xanthosine[e] <=> Xanthosine[p] 	G_b0241 or G_b0929 or G_b1377 or G_b2215	-1000.00	1000.00	  0.00
 R_XYHDL	H2O H2O[c] + Isoprimeverose[c] => D-Glucose[c] + D-Xylose[c] 	G_b3656	  0.00	1000.00	  0.00
 R_XYLI1	D-Xylose[c] <=> D-Xylulose[c] 	G_b3565	-1000.00	1000.00	  0.00
-R_XYLI2	D-Glucose[c] <=> D-Fructose[c] 	G_b3565	-1000.00	1000.00	  0.00
 R_XYLK	ATP C10H12N5O13P3[c] + D-Xylulose[c] => ADP C10H12N5O10P2[c] + H+[c] + D-Xylulose 5-phosphate[c] 	G_b0063 or G_b3564	  0.00	1000.00	  0.00
 R_XYLK2	ATP C10H12N5O13P3[c] + L-Xylulose[c] => ADP C10H12N5O10P2[c] + H+[c] + L-Xylulose 5-phosphate[c] 	G_b0063 or G_b3580	  0.00	1000.00	  0.00
 R_XYLUt2pp	H+[p] + L-Xylulose[p] => H+[c] + L-Xylulose[c] 	G_b3577 and G_b3578 and G_b3579	  0.00	1000.00	  0.00
diff --git a/model/Ecoli-GEM.xlsx b/model/Ecoli-GEM.xlsx
index e59cffb..c6c6378 100644
Binary files a/model/Ecoli-GEM.xlsx and b/model/Ecoli-GEM.xlsx differ
diff --git a/model/Ecoli-GEM.xml b/model/Ecoli-GEM.xml
index 0977dcf..7587d7c 100644
--- a/model/Ecoli-GEM.xml
+++ b/model/Ecoli-GEM.xml
@@ -49116,9 +49116,9 @@
         </listOfProducts>
         <fbc:geneProductAssociation>
           <fbc:or>
-            <fbc:geneProductRef fbc:geneProduct="G_b4213"/>
-            <fbc:geneProductRef fbc:geneProduct="G_b0383"/>
             <fbc:geneProductRef fbc:geneProduct="G_b0383"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b4213"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2744"/>
           </fbc:or>
         </fbc:geneProductAssociation>
       </reaction>
@@ -59504,16 +59504,21 @@
         <fbc:geneProductAssociation>
           <fbc:or>
             <fbc:and>
+              <fbc:geneProductRef fbc:geneProduct="G_b2310"/>
               <fbc:geneProductRef fbc:geneProduct="G_b2308"/>
               <fbc:geneProductRef fbc:geneProduct="G_b2306"/>
-              <fbc:geneProductRef fbc:geneProduct="G_b2310"/>
               <fbc:geneProductRef fbc:geneProduct="G_b2307"/>
             </fbc:and>
             <fbc:and>
-              <fbc:geneProductRef fbc:geneProduct="G_b0864"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0862"/>
               <fbc:geneProductRef fbc:geneProduct="G_b0860"/>
-              <fbc:geneProductRef fbc:geneProduct="G_b0863"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0864"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0861"/>
+            </fbc:and>
+            <fbc:and>
               <fbc:geneProductRef fbc:geneProduct="G_b0862"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0864"/>
+              <fbc:geneProductRef fbc:geneProduct="G_b0863"/>
               <fbc:geneProductRef fbc:geneProduct="G_b0861"/>
             </fbc:and>
           </fbc:or>
@@ -61433,13 +61438,7 @@
           <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
         </listOfProducts>
         <fbc:geneProductAssociation>
-          <fbc:or>
-            <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
-            <fbc:and>
-              <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
-              <fbc:geneProductRef fbc:geneProduct="G_b3856"/>
-            </fbc:and>
-          </fbc:or>
+          <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
         </fbc:geneProductAssociation>
       </reaction>
       <reaction metaid="meta_R_BMOGDS2" sboTerm="SBO:0000176" id="R_BMOGDS2" name="Bis-molybdopterin guanine dinucleotide synthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
@@ -61465,13 +61464,7 @@
           <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
         </listOfProducts>
         <fbc:geneProductAssociation>
-          <fbc:or>
-            <fbc:and>
-              <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
-              <fbc:geneProductRef fbc:geneProduct="G_b3856"/>
-            </fbc:and>
-            <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
-          </fbc:or>
+          <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
         </fbc:geneProductAssociation>
       </reaction>
       <reaction metaid="meta_R_BPNT" sboTerm="SBO:0000176" id="R_BPNT" name="3&apos;,5&apos;-bisphosphate nucleotidase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
@@ -61849,13 +61842,7 @@
           <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
         </listOfProducts>
         <fbc:geneProductAssociation>
-          <fbc:or>
-            <fbc:and>
-              <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
-              <fbc:geneProductRef fbc:geneProduct="G_b3856"/>
-            </fbc:and>
-            <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
-          </fbc:or>
+          <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
         </fbc:geneProductAssociation>
       </reaction>
       <reaction metaid="meta_R_BWCOGDS2" sboTerm="SBO:0000176" id="R_BWCOGDS2" name="Tungsten bispterin guanine dinucleotide synthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
@@ -61881,13 +61868,7 @@
           <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
         </listOfProducts>
         <fbc:geneProductAssociation>
-          <fbc:or>
-            <fbc:and>
-              <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
-              <fbc:geneProductRef fbc:geneProduct="G_b3856"/>
-            </fbc:and>
-            <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
-          </fbc:or>
+          <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
         </fbc:geneProductAssociation>
       </reaction>
       <reaction metaid="meta_R_BWCOS" sboTerm="SBO:0000176" id="R_BWCOS" name="Tungsten bispterin cofactor synthase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
@@ -73144,6 +73125,7 @@
           <fbc:and>
             <fbc:geneProductRef fbc:geneProduct="G_b3785"/>
             <fbc:geneProductRef fbc:geneProduct="G_b3793"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3792"/>
           </fbc:and>
         </fbc:geneProductAssociation>
       </reaction>
@@ -73173,6 +73155,7 @@
           <fbc:and>
             <fbc:geneProductRef fbc:geneProduct="G_b3785"/>
             <fbc:geneProductRef fbc:geneProduct="G_b3793"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3792"/>
           </fbc:and>
         </fbc:geneProductAssociation>
       </reaction>
@@ -73202,6 +73185,7 @@
           <fbc:and>
             <fbc:geneProductRef fbc:geneProduct="G_b3785"/>
             <fbc:geneProductRef fbc:geneProduct="G_b3793"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3792"/>
           </fbc:and>
         </fbc:geneProductAssociation>
       </reaction>
@@ -83177,10 +83161,7 @@
           <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
         </listOfProducts>
         <fbc:geneProductAssociation>
-          <fbc:and>
-            <fbc:geneProductRef fbc:geneProduct="G_b2764"/>
-            <fbc:geneProductRef fbc:geneProduct="G_b2763"/>
-          </fbc:and>
+          <fbc:geneProductRef fbc:geneProduct="G_b2764"/>
         </fbc:geneProductAssociation>
       </reaction>
       <reaction metaid="meta_R_FADt" sboTerm="SBO:0000185" id="R_FADt" name="FAD transporter, periplasm" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
@@ -85641,12 +85622,9 @@
         </listOfProducts>
         <fbc:geneProductAssociation>
           <fbc:or>
-            <fbc:geneProductRef fbc:geneProduct="G_b3844"/>
             <fbc:geneProductRef fbc:geneProduct="G_b0937"/>
-            <fbc:and>
-              <fbc:geneProductRef fbc:geneProduct="G_b2764"/>
-              <fbc:geneProductRef fbc:geneProduct="G_b2763"/>
-            </fbc:and>
+            <fbc:geneProductRef fbc:geneProduct="G_b3844"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b2764"/>
           </fbc:or>
         </fbc:geneProductAssociation>
       </reaction>
@@ -89468,7 +89446,7 @@
           <fbc:geneProductRef fbc:geneProduct="G_b3882"/>
         </fbc:geneProductAssociation>
       </reaction>
-      <reaction metaid="meta_R_GHMT2r" sboTerm="SBO:0000176" id="R_GHMT2r" name="Glycine hydroxymethyltransferase, reversible" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+      <reaction metaid="meta_R_GHMT2r" sboTerm="SBO:0000176" id="R_GHMT2r" name="Glycine hydroxymethyltransferase, reversible" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
             <rdf:Description rdf:about="#meta_R_GHMT2r">
@@ -90666,13 +90644,7 @@
           <speciesReference species="M_nh4_c" stoichiometry="1" constant="true"/>
         </listOfProducts>
         <fbc:geneProductAssociation>
-          <fbc:or>
-            <fbc:geneProductRef fbc:geneProduct="G_b1761"/>
-            <fbc:and>
-              <fbc:geneProductRef fbc:geneProduct="G_b3213"/>
-              <fbc:geneProductRef fbc:geneProduct="G_b3212"/>
-            </fbc:and>
-          </fbc:or>
+          <fbc:geneProductRef fbc:geneProduct="G_b1761"/>
         </fbc:geneProductAssociation>
       </reaction>
       <reaction metaid="meta_R_GLUN" sboTerm="SBO:0000176" id="R_GLUN" name="Glutaminase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
@@ -91680,53 +91652,6 @@
           <fbc:geneProductRef fbc:geneProduct="G_b3945"/>
         </fbc:geneProductAssociation>
       </reaction>
-      <reaction metaid="meta_R_GLYCK" sboTerm="SBO:0000176" id="R_GLYCK" name="Glycerate kinase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-            <rdf:Description rdf:about="#meta_R_GLYCK">
-              <bqbiol:is>
-                <rdf:Bag>
-                  <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/GLYCK"/>
-                  <rdf:li rdf:resource="https://identifiers.org/biocyc/META:GLY3KIN-RXN"/>
-                  <rdf:li rdf:resource="https://identifiers.org/ec-code/2.7.1.31"/>
-                  <rdf:li rdf:resource="https://identifiers.org/kegg.reaction/R01514"/>
-                  <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR100328"/>
-                  <rdf:li rdf:resource="https://identifiers.org/reactome.reaction/R-MMU-6799495"/>
-                  <rdf:li rdf:resource="https://identifiers.org/reactome.reaction/R-TGU-6799495"/>
-                  <rdf:li rdf:resource="https://identifiers.org/reactome.reaction/R-DME-6799495"/>
-                  <rdf:li rdf:resource="https://identifiers.org/reactome.reaction/R-GGA-6799495"/>
-                  <rdf:li rdf:resource="https://identifiers.org/reactome.reaction/R-RNO-6799495"/>
-                  <rdf:li rdf:resource="https://identifiers.org/reactome.reaction/R-XTR-6799495"/>
-                  <rdf:li rdf:resource="https://identifiers.org/reactome.reaction/R-DRE-6799495"/>
-                  <rdf:li rdf:resource="https://identifiers.org/reactome.reaction/R-HSA-6799495"/>
-                  <rdf:li rdf:resource="https://identifiers.org/reactome.reaction/R-SSC-6799495"/>
-                  <rdf:li rdf:resource="https://identifiers.org/reactome.reaction/R-BTA-6799495"/>
-                  <rdf:li rdf:resource="https://identifiers.org/reactome.reaction/R-CEL-6799495"/>
-                  <rdf:li rdf:resource="https://identifiers.org/reactome.reaction/R-CFA-6799495"/>
-                  <rdf:li rdf:resource="https://identifiers.org/rhea/23518"/>
-                  <rdf:li rdf:resource="https://identifiers.org/rhea/23519"/>
-                  <rdf:li rdf:resource="https://identifiers.org/rhea/23516"/>
-                  <rdf:li rdf:resource="https://identifiers.org/rhea/23517"/>
-                  <rdf:li rdf:resource="https://identifiers.org/sabiork/428"/>
-                  <rdf:li rdf:resource="https://identifiers.org/seed.reaction/rxn01102"/>
-                </rdf:Bag>
-              </bqbiol:is>
-            </rdf:Description>
-          </rdf:RDF>
-        </annotation>
-        <listOfReactants>
-          <speciesReference species="M_atp_c" stoichiometry="1" constant="true"/>
-          <speciesReference species="M_glyc__R_c" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="M_3pg_c" stoichiometry="1" constant="true"/>
-          <speciesReference species="M_adp_c" stoichiometry="1" constant="true"/>
-          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
-        </listOfProducts>
-        <fbc:geneProductAssociation>
-          <fbc:geneProductRef fbc:geneProduct="G_b0514"/>
-        </fbc:geneProductAssociation>
-      </reaction>
       <reaction metaid="meta_R_GLYCK2" sboTerm="SBO:0000176" id="R_GLYCK2" name="Glycerate kinase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
@@ -91760,7 +91685,10 @@
           <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
         </listOfProducts>
         <fbc:geneProductAssociation>
-          <fbc:geneProductRef fbc:geneProduct="G_b3124"/>
+          <fbc:or>
+            <fbc:geneProductRef fbc:geneProduct="G_b3124"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0514"/>
+          </fbc:or>
         </fbc:geneProductAssociation>
       </reaction>
       <reaction metaid="meta_R_GLYCL" sboTerm="SBO:0000176" id="R_GLYCL" name="Glycine Cleavage System" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
@@ -97001,7 +96929,7 @@
           </fbc:or>
         </fbc:geneProductAssociation>
       </reaction>
-      <reaction metaid="meta_R_HSDy" sboTerm="SBO:0000176" id="R_HSDy" name="Homoserine dehydrogenase (NADPH)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+      <reaction metaid="meta_R_HSDy" sboTerm="SBO:0000176" id="R_HSDy" name="Homoserine dehydrogenase (NADPH)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
             <rdf:Description rdf:about="#meta_R_HSDy">
@@ -107632,13 +107560,7 @@
           <speciesReference species="M_ppi_c" stoichiometry="1" constant="true"/>
         </listOfProducts>
         <fbc:geneProductAssociation>
-          <fbc:or>
-            <fbc:and>
-              <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
-              <fbc:geneProductRef fbc:geneProduct="G_b3856"/>
-            </fbc:and>
-            <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
-          </fbc:or>
+          <fbc:geneProductRef fbc:geneProduct="G_b3857"/>
         </fbc:geneProductAssociation>
       </reaction>
       <reaction metaid="meta_R_MOHMT" sboTerm="SBO:0000176" id="R_MOHMT" name="3-methyl-2-oxobutanoate hydroxymethyltransferase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
@@ -127424,7 +127346,7 @@
           <fbc:geneProductRef fbc:geneProduct="G_b2261"/>
         </fbc:geneProductAssociation>
       </reaction>
-      <reaction metaid="meta_R_SUCCt1pp" sboTerm="SBO:0000185" id="R_SUCCt1pp" name="Succinate transport via diffusion in (periplasm)" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
+      <reaction metaid="meta_R_SUCCt1pp" sboTerm="SBO:0000185" id="R_SUCCt1pp" name="Succinate transport via diffusion in (periplasm)" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
             <rdf:Description rdf:about="#meta_R_SUCCt1pp">
@@ -128721,12 +128643,12 @@
           </rdf:RDF>
         </annotation>
         <listOfReactants>
-          <speciesReference species="M_h_p" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_p" stoichiometry="1" constant="true"/>
           <speciesReference species="M_nadh_c" stoichiometry="1" constant="true"/>
           <speciesReference species="M_nadp_c" stoichiometry="1" constant="true"/>
         </listOfReactants>
         <listOfProducts>
-          <speciesReference species="M_h_c" stoichiometry="2" constant="true"/>
+          <speciesReference species="M_h_c" stoichiometry="1" constant="true"/>
           <speciesReference species="M_nad_c" stoichiometry="1" constant="true"/>
           <speciesReference species="M_nadph_c" stoichiometry="1" constant="true"/>
         </listOfProducts>
@@ -129460,11 +129382,12 @@
         </listOfProducts>
         <fbc:geneProductAssociation>
           <fbc:and>
-            <fbc:geneProductRef fbc:geneProduct="G_b0423"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3992"/>
             <fbc:geneProductRef fbc:geneProduct="G_b3990"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b0423"/>
             <fbc:geneProductRef fbc:geneProduct="G_b2530"/>
-            <fbc:geneProductRef fbc:geneProduct="G_b3992"/>
             <fbc:geneProductRef fbc:geneProduct="G_b4407"/>
+            <fbc:geneProductRef fbc:geneProduct="G_b3991"/>
           </fbc:and>
         </fbc:geneProductAssociation>
       </reaction>
@@ -134130,7 +134053,7 @@
                   <rdf:li rdf:resource="https://identifiers.org/biocyc/META:XYLISOM-RXN"/>
                   <rdf:li rdf:resource="https://identifiers.org/ec-code/5.3.1.5"/>
                   <rdf:li rdf:resource="https://identifiers.org/kegg.reaction/R01432"/>
-                  <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR105253"/>
+                  <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR146751"/>
                   <rdf:li rdf:resource="https://identifiers.org/rhea/22818"/>
                   <rdf:li rdf:resource="https://identifiers.org/rhea/22816"/>
                   <rdf:li rdf:resource="https://identifiers.org/rhea/22819"/>
@@ -134151,38 +134074,6 @@
           <fbc:geneProductRef fbc:geneProduct="G_b3565"/>
         </fbc:geneProductAssociation>
       </reaction>
-      <reaction metaid="meta_R_XYLI2" sboTerm="SBO:0000176" id="R_XYLI2" name="Xylose isomerase" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
-        <annotation>
-          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
-            <rdf:Description rdf:about="#meta_R_XYLI2">
-              <bqbiol:is>
-                <rdf:Bag>
-                  <rdf:li rdf:resource="https://identifiers.org/bigg.reaction/XYLI2"/>
-                  <rdf:li rdf:resource="https://identifiers.org/biocyc/META:GLUCISOM-RXN"/>
-                  <rdf:li rdf:resource="https://identifiers.org/ec-code/5.3.1.5"/>
-                  <rdf:li rdf:resource="https://identifiers.org/kegg.reaction/R00307"/>
-                  <rdf:li rdf:resource="https://identifiers.org/metanetx.reaction/MNXR105254"/>
-                  <rdf:li rdf:resource="https://identifiers.org/rhea/28546"/>
-                  <rdf:li rdf:resource="https://identifiers.org/rhea/28547"/>
-                  <rdf:li rdf:resource="https://identifiers.org/rhea/28549"/>
-                  <rdf:li rdf:resource="https://identifiers.org/rhea/28548"/>
-                  <rdf:li rdf:resource="https://identifiers.org/sabiork/800"/>
-                  <rdf:li rdf:resource="https://identifiers.org/seed.reaction/rxn00223"/>
-                </rdf:Bag>
-              </bqbiol:is>
-            </rdf:Description>
-          </rdf:RDF>
-        </annotation>
-        <listOfReactants>
-          <speciesReference species="M_glc__D_c" stoichiometry="1" constant="true"/>
-        </listOfReactants>
-        <listOfProducts>
-          <speciesReference species="M_fru_c" stoichiometry="1" constant="true"/>
-        </listOfProducts>
-        <fbc:geneProductAssociation>
-          <fbc:geneProductRef fbc:geneProduct="G_b3565"/>
-        </fbc:geneProductAssociation>
-      </reaction>
       <reaction metaid="meta_R_XYLK" sboTerm="SBO:0000176" id="R_XYLK" name="Xylulokinase" reversible="false" fast="false" fbc:lowerFluxBound="cobra_0_bound" fbc:upperFluxBound="cobra_default_ub">
         <annotation>
           <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:vCard4="http://www.w3.org/2006/vcard/ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/" xmlns:bqmodel="http://biomodels.net/model-qualifiers/">
@@ -168196,1347 +168087,1346 @@
     <groups:listOfGroups>
       <groups:group metaid="meta_G_group1" sboTerm="SBO:0000633" groups:id="G_group1" groups:name="Alanine and Aspartate Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="L-asparaginase" groups:idRef="R_ASNN"/>
-          <groups:member groups:name="L-aspartase" groups:idRef="R_ASPT"/>
+          <groups:member groups:name="D-Amino acid dehydrogenase" groups:idRef="R_DAAD"/>
+          <groups:member groups:name="L-alanine transaminase" groups:idRef="R_ALATA_L"/>
           <groups:member groups:name="Aspartate transaminase" groups:idRef="R_ASPTA"/>
+          <groups:member groups:name="L-asparaginase" groups:idRef="R_ASNNpp"/>
           <groups:member groups:name="Asparagine synthase (glutamine-hydrolysing)" groups:idRef="R_ASNS1"/>
-          <groups:member groups:name="D-Amino acid dehydrogenase" groups:idRef="R_DAAD"/>
+          <groups:member groups:name="L-aspartase" groups:idRef="R_ASPT"/>
           <groups:member groups:name="Alanine racemase" groups:idRef="R_ALAR"/>
-          <groups:member groups:name="L-alanine transaminase" groups:idRef="R_ALATA_L"/>
           <groups:member groups:name="Asparagine synthetase" groups:idRef="R_ASNS2"/>
-          <groups:member groups:name="L-asparaginase" groups:idRef="R_ASNNpp"/>
+          <groups:member groups:name="L-asparaginase" groups:idRef="R_ASNN"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group2" sboTerm="SBO:0000633" groups:id="G_group2" groups:name="Alternate Carbon Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="6-phospho-beta-glucosidase" groups:idRef="R_BGLA1"/>
-          <groups:member groups:name="Xylose isomerase" groups:idRef="R_XYLI1"/>
-          <groups:member groups:name="Phenylhydantoinase" groups:idRef="R_PHDA"/>
-          <groups:member groups:name="Galactitol-1-phosphate dehydrogenase" groups:idRef="R_GLTPD"/>
-          <groups:member groups:name="Uridine hydrolase" groups:idRef="R_URIH"/>
-          <groups:member groups:name="Phosphomannomutase" groups:idRef="R_PMANM"/>
           <groups:member groups:name="Phenylpropanoate Dioxygenase" groups:idRef="R_PPPNDO"/>
-          <groups:member groups:name="Phytase (periplasm)" groups:idRef="R_PHYTSpp"/>
-          <groups:member groups:name="Phosphoglycolate phosphatase" groups:idRef="R_PGLYCP"/>
-          <groups:member groups:name="Sulfoquinovosidase" groups:idRef="R_SQGH"/>
-          <groups:member groups:name="Xylulokinase" groups:idRef="R_XYLK"/>
-          <groups:member groups:name="D-xylonate dehydratase" groups:idRef="R_DXYLTD"/>
-          <groups:member groups:name="2,3-dihydroxypheylpropionate 1,2-dioxygenase" groups:idRef="R_HPPPNDO"/>
-          <groups:member groups:name="Maltodextrin glucosidase (maltotriose)" groups:idRef="R_MLTG1"/>
-          <groups:member groups:name="Phenylacetyl-CoA thioesterase" groups:idRef="R_PACOAT"/>
-          <groups:member groups:name="Maltodextrin phosphorylase (maltoheptaose)" groups:idRef="R_MLTP3"/>
-          <groups:member groups:name="Maltodextrin glucosidase (maltohexaose)" groups:idRef="R_MLTG4"/>
-          <groups:member groups:name="Acetyl-CoA:acetoacetyl-CoA transferase" groups:idRef="R_ACACCT"/>
-          <groups:member groups:name="Gluconokinase" groups:idRef="R_GNK"/>
-          <groups:member groups:name="Maltodextrin phosphorylase (maltohexaose)" groups:idRef="R_MLTP2"/>
-          <groups:member groups:name="Trehalose-phosphatase" groups:idRef="R_TRE6PP"/>
-          <groups:member groups:name="Cinnamate dioxygenase" groups:idRef="R_CINNDO"/>
-          <groups:member groups:name="Glucuronate isomerase (D-galacturonate)" groups:idRef="R_GUI2"/>
-          <groups:member groups:name="RPnTP hydrolase" groups:idRef="R_RPNTPH"/>
-          <groups:member groups:name="L-indonate 5-dehydrogenase (NADP)" groups:idRef="R_IDOND2"/>
-          <groups:member groups:name="UDPglucose pyrophosphohydrolase" groups:idRef="R_UDPGPpp"/>
-          <groups:member groups:name="Alcohol dehydrogenase (glycerol)" groups:idRef="R_ALCD19"/>
-          <groups:member groups:name="Glycolate oxidase" groups:idRef="R_GLYCTO3"/>
-          <groups:member groups:name="N-acetyl-D-galactosamine 1-phosphatase (periplasm)" groups:idRef="R_ACGAL1PPpp"/>
-          <groups:member groups:name="Ribose 1-phosphokinase" groups:idRef="R_R1PK"/>
-          <groups:member groups:name="Mannose 6-phosphate phosphatase" groups:idRef="R_MN6PP"/>
-          <groups:member groups:name="Propane-1,2-diol:NADP+ 1-oxidoreductase" groups:idRef="R_PPDOy"/>
-          <groups:member groups:name="2-dehydro-3-deoxygluconokinase" groups:idRef="R_DDGLK"/>
-          <groups:member groups:name="2,3-diaminopropionate amonnia lyase" groups:idRef="R_DAPAL"/>
-          <groups:member groups:name="L-idonate 5-dehydrogenase" groups:idRef="R_IDOND"/>
-          <groups:member groups:name="Sulfoquinovose isomerase" groups:idRef="R_SQVOSI"/>
-          <groups:member groups:name="Ureidoglycolate dehydrogenase" groups:idRef="R_URDGLYCD"/>
-          <groups:member groups:name="Erythrose-4-phosphate phosphatase" groups:idRef="R_E4PP"/>
-          <groups:member groups:name="N-acetyl-D-glucosamine 1-phosphatase (periplasm)" groups:idRef="R_ACGAM1PPpp"/>
-          <groups:member groups:name="Phosphopentomutase 2 (deoxyribose)" groups:idRef="R_PPM2"/>
-          <groups:member groups:name="3-Hydroxypropanal Dehydrogenase" groups:idRef="R_3HPADHi"/>
-          <groups:member groups:name="2-methylisocitrate dehydratase" groups:idRef="R_MICITDr"/>
-          <groups:member groups:name="3-hydroxycinnamate hydroxylase" groups:idRef="R_3HCINNMH"/>
-          <groups:member groups:name="Hydroxypyruvate reductase (NADH)" groups:idRef="R_HPYRRx"/>
-          <groups:member groups:name="Phosphopentomutase" groups:idRef="R_PPM"/>
-          <groups:member groups:name="Phosphofructokinase" groups:idRef="R_PFK_2"/>
-          <groups:member groups:name="Alpha,alpha-trehalase (periplasm)" groups:idRef="R_TREHpp"/>
-          <groups:member groups:name="4-hydroxy-2-oxopentanoate aldolase" groups:idRef="R_HOPNTAL"/>
-          <groups:member groups:name="2-methylcitrate dehydratase" groups:idRef="R_MCITD"/>
-          <groups:member groups:name="UDPgalactose pyrophosphohydrolase" groups:idRef="R_UDPGALPpp"/>
-          <groups:member groups:name="3-keto-L-gulonate kinase" groups:idRef="R_3KGK"/>
-          <groups:member groups:name="Aldehyde dehydrogenase (phenylacetaldehyde, NAD)" groups:idRef="R_ALDD19xr"/>
-          <groups:member groups:name="Gamma glutamyl putrescine synthase" groups:idRef="R_GGPTRCS"/>
-          <groups:member groups:name="Acetate-CoA ligase (ADP-forming)" groups:idRef="R_ACCOAL"/>
-          <groups:member groups:name="Glucarate dehydratase" groups:idRef="R_GLCRD"/>
-          <groups:member groups:name="Glycerol kinase" groups:idRef="R_GLYK"/>
-          <groups:member groups:name="Glucosamine-6-phosphate deaminase" groups:idRef="R_G6PDA"/>
-          <groups:member groups:name="L-xylulokinase" groups:idRef="R_XYLK2"/>
-          <groups:member groups:name="Phosphogluconate phosphatase" groups:idRef="R_GNP"/>
-          <groups:member groups:name="B-galactosidase" groups:idRef="R_LACZpp"/>
-          <groups:member groups:name="Ribose-1,5-bisphosphokinase" groups:idRef="R_R15BPK"/>
-          <groups:member groups:name="Tagatose-bisphosphate aldolase" groups:idRef="R_TGBPA"/>
-          <groups:member groups:name="UDP-D-glucuronate pyrophosphohydrolase (periplasm)" groups:idRef="R_UGLCURPpp"/>
-          <groups:member groups:name="Adenosine hydrolase" groups:idRef="R_ADNUC"/>
-          <groups:member groups:name="Gamma glutamyl putrescine oxidase" groups:idRef="R_GGPTRCO"/>
-          <groups:member groups:name="Propanoyl-CoA:NADP+ 2-oxidoreductase" groups:idRef="R_PCNO"/>
-          <groups:member groups:name="UDPglucose 4-epimerase" groups:idRef="R_UDPG4E"/>
-          <groups:member groups:name="Dihydropteridine reductase" groups:idRef="R_DHPTDNR"/>
-          <groups:member groups:name="Methylmalonyl-CoA mutase" groups:idRef="R_MMM"/>
           <groups:member groups:name="2-oxopent-4-enoate hydratase" groups:idRef="R_OP4ENH"/>
-          <groups:member groups:name="7-?-hydroxysteroid dehydrogenase" groups:idRef="R_CHOLID"/>
-          <groups:member groups:name="2-dehydro-3-deoxy-6-phosphogalactonate aldolase" groups:idRef="R_DDPGALA"/>
-          <groups:member groups:name="Dihydropteridine reductase (NADH)" groups:idRef="R_DHPTDNRN"/>
-          <groups:member groups:name="Tartronate semialdehyde reductase" groups:idRef="R_TRSARr"/>
-          <groups:member groups:name="2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase" groups:idRef="R_HKNDDH"/>
-          <groups:member groups:name="Ribose 5-phosphate phosphatase" groups:idRef="R_R5PP"/>
+          <groups:member groups:name="L-idonate 5-dehydrogenase" groups:idRef="R_IDOND"/>
+          <groups:member groups:name="Maltose O-acetyltransferase" groups:idRef="R_MALTATr"/>
+          <groups:member groups:name="UDP-N-acetyl-D-glucosamine pyrophosphohydrolase (periplasm)" groups:idRef="R_UACGAMPpp"/>
+          <groups:member groups:name="Glycerol-3-phosphate dehydrogenase (NADP)" groups:idRef="R_G3PD2"/>
+          <groups:member groups:name="Alpha,alpha-trehalase" groups:idRef="R_TREH"/>
           <groups:member groups:name="D-fructose 6-phosphate phosphatase" groups:idRef="R_F6PP"/>
           <groups:member groups:name="B-galactosidase" groups:idRef="R_LACZ"/>
-          <groups:member groups:name="Lyxose isomerase" groups:idRef="R_LYXI"/>
-          <groups:member groups:name="3-oxoadipyl-CoA thiolase" groups:idRef="R_3OXCOAT"/>
-          <groups:member groups:name="Arbutin 6-phosphate glucohydrolase" groups:idRef="R_AB6PGH"/>
-          <groups:member groups:name="3-phosphohydroxypyruvate phosphatase" groups:idRef="R_HPYRP"/>
+          <groups:member groups:name="Phosphoglucomutase" groups:idRef="R_PGMT"/>
+          <groups:member groups:name="Sorbitol-6-phosphate dehydrogenase" groups:idRef="R_SBTPD"/>
+          <groups:member groups:name="Uridine hydrolase" groups:idRef="R_URIH"/>
+          <groups:member groups:name="N-acetyl-D-mannosamine kinase" groups:idRef="R_AMANK"/>
+          <groups:member groups:name="A-galactosidase (melibiose)" groups:idRef="R_GALS3"/>
+          <groups:member groups:name="Cytidine hydrolase" groups:idRef="R_CYTDH"/>
+          <groups:member groups:name="Ribulose-5-Phosphate Phosphatase" groups:idRef="R_RU5PP"/>
+          <groups:member groups:name="2-Dehydro-L-gulonate reductase to gluconate (NADH)" groups:idRef="R_2DGULRGx"/>
+          <groups:member groups:name="Alpha-amylase (periplasm)" groups:idRef="R_AAMYLpp"/>
+          <groups:member groups:name="Ureidoglycolate dehydrogenase" groups:idRef="R_URDGLYCD"/>
+          <groups:member groups:name="Gamma-glutamyl-gamma-aminobutyric acid hydrolase" groups:idRef="R_GGGABAH"/>
+          <groups:member groups:name="Mannose-6-phosphate isomerase" groups:idRef="R_MAN6PI"/>
+          <groups:member groups:name="2-methylcitrate synthase" groups:idRef="R_MCITS"/>
+          <groups:member groups:name="Aldehyde dehydrogenase (propanal, NADP)" groups:idRef="R_ALDD3y"/>
+          <groups:member groups:name="Ribose 1-phosphokinase" groups:idRef="R_R1PK"/>
+          <groups:member groups:name="Gamma-glutamyl-gamma aminobutyric acid dehydrogenase" groups:idRef="R_GGGABADr"/>
+          <groups:member groups:name="D-mannonate hydrolyase" groups:idRef="R_MNNH"/>
+          <groups:member groups:name="RPnTP hydrolase" groups:idRef="R_RPNTPH"/>
+          <groups:member groups:name="Hexokinase (D-fructose:ATP)" groups:idRef="R_HEX7"/>
+          <groups:member groups:name="1-O-Methyl-Beta-D-glucuronidase" groups:idRef="R_METGLCUR"/>
+          <groups:member groups:name="Maltodextrin phosphorylase (maltohexaose)" groups:idRef="R_MLTP2"/>
+          <groups:member groups:name="2,3-dehydroadipyl-CoA hydratase" groups:idRef="R_DHACOAH"/>
+          <groups:member groups:name="Ring 1,2-epoxyphenylacetyl-CoA isomerase (oxepin-CoA forming)" groups:idRef="R_REPHACCOAI"/>
+          <groups:member groups:name="Glucuronate isomerase (D-galacturonate)" groups:idRef="R_GUI2"/>
+          <groups:member groups:name="Aldose-1-epimerase" groups:idRef="R_GALM2pp"/>
+          <groups:member groups:name="2-Oxobutanoate formate lyase" groups:idRef="R_OBTFL"/>
+          <groups:member groups:name="Xylose isomerase" groups:idRef="R_XYLI1"/>
           <groups:member groups:name="1,3-propanediol dehydrogenase" groups:idRef="R_13PPDH2"/>
-          <groups:member groups:name="2,3 dioxo-L-gulonate reductase" groups:idRef="R_DOGULNR"/>
-          <groups:member groups:name="Glycolate oxidase" groups:idRef="R_GLYCTO4"/>
-          <groups:member groups:name="Myo-Inositol:oxygen oxidoreductase" groups:idRef="R_INOSTO"/>
+          <groups:member groups:name="D(-)-tartrate dehydratase" groups:idRef="R_DTARTD"/>
+          <groups:member groups:name="3-phosphohydroxypyruvate phosphatase" groups:idRef="R_HPYRP"/>
+          <groups:member groups:name="Sulfoquinovosidase" groups:idRef="R_SQGH"/>
+          <groups:member groups:name="6-phospho-beta-glucosidase" groups:idRef="R_BGLA1"/>
           <groups:member groups:name="Maltodextrin glucosidase (maltotetraose)" groups:idRef="R_MLTG2"/>
-          <groups:member groups:name="2-dehydro-L-gulonate reductase (NADH)" groups:idRef="R_2DGULRx"/>
-          <groups:member groups:name="Aldehyde dehydrogenase (acetaldehyde, NADP)" groups:idRef="R_ALDD2y"/>
+          <groups:member groups:name="Trehalose-phosphatase" groups:idRef="R_TRE6PP"/>
+          <groups:member groups:name="Glycolate oxidase" groups:idRef="R_GLYCTO4"/>
+          <groups:member groups:name="5-phospho-?-D-ribosyl 1,2-cyclic phosphate phosphodiesterase" groups:idRef="R_PRCPD"/>
+          <groups:member groups:name="Ribose-1,5-bisphosphokinase" groups:idRef="R_R15BPK"/>
+          <groups:member groups:name="5-dehydro-D-gluconate reductase" groups:idRef="R_5DGLCNR"/>
+          <groups:member groups:name="Glucarate dehydratase" groups:idRef="R_GLCRD"/>
+          <groups:member groups:name="Maltodextrin glucosidase (maltopentaose)" groups:idRef="R_MLTG3"/>
+          <groups:member groups:name="Phosphofructokinase" groups:idRef="R_PFK_2"/>
+          <groups:member groups:name="Ribose 5-phosphate phosphatase" groups:idRef="R_R5PPpp"/>
+          <groups:member groups:name="L-rhamnonate dehydratase" groups:idRef="R_RHMND"/>
           <groups:member groups:name="2,3-dihydroxyphenylpropionate dehydrogenase" groups:idRef="R_DHPPD"/>
-          <groups:member groups:name="Hydroxypyruvate reductase (NADPH)" groups:idRef="R_HPYRRy"/>
+          <groups:member groups:name="D-galactose 1-phosphatase" groups:idRef="R_GAL1PPpp"/>
+          <groups:member groups:name="Glycolate oxidase" groups:idRef="R_GLYCTO2"/>
+          <groups:member groups:name="Lacaldehyde reductase (S-propane-1,2-diol forming)" groups:idRef="R_LCARSyi"/>
+          <groups:member groups:name="Rhamnulose-1-phosphate aldolase" groups:idRef="R_RMPA"/>
+          <groups:member groups:name="Trehalose-6-phosphate hydrolase" groups:idRef="R_TRE6PH"/>
+          <groups:member groups:name="Adenosine hydrolase" groups:idRef="R_ADNUC"/>
+          <groups:member groups:name="Methylisocitrate lyase" groups:idRef="R_MCITL2"/>
+          <groups:member groups:name="Phenylhydantoinase" groups:idRef="R_PHDA"/>
+          <groups:member groups:name="Arbutin 6-phosphate glucohydrolase" groups:idRef="R_AB6PGH"/>
+          <groups:member groups:name="Galactarate dehydratase" groups:idRef="R_GALCTD"/>
+          <groups:member groups:name="Hydroxypyruvate isomerase" groups:idRef="R_HPYRI"/>
+          <groups:member groups:name="L-xylulose 5-phosphate 3-epimerase" groups:idRef="R_X5PL3E"/>
+          <groups:member groups:name="Aldehyde dehydrogenase (butanal, NAD)" groups:idRef="R_ALDD4"/>
+          <groups:member groups:name="2,3-dihydroxycinnamate dehydrogenase" groups:idRef="R_DHCIND"/>
+          <groups:member groups:name="2-methylcitrate dehydratase" groups:idRef="R_MCITD"/>
           <groups:member groups:name="5-keto-D-gluconate 5-reductase" groups:idRef="R_5DKGR"/>
-          <groups:member groups:name="Chito-oligosaccharide mono-deacetylase" groups:idRef="R_DC6PDA"/>
-          <groups:member groups:name="Lactaldehyde dehydrogenase" groups:idRef="R_LCADi"/>
-          <groups:member groups:name="3-hydroxyadipyl-CoA dehydrogenase (NAD+)" groups:idRef="R_HADPCOADH3"/>
+          <groups:member groups:name="N-acetylglucosamine-6-phosphate deacetylase" groups:idRef="R_AGDC"/>
+          <groups:member groups:name="Altronate hydrolase" groups:idRef="R_ALTRH"/>
+          <groups:member groups:name="Allulose 6-phosphate epimerase" groups:idRef="R_ALLULPE"/>
+          <groups:member groups:name="2,3-dihydroxycinnamate 1,2-dioxygenase" groups:idRef="R_DHCINDO"/>
+          <groups:member groups:name="Taurine dioxygenase" groups:idRef="R_TAUDO"/>
+          <groups:member groups:name="2-dehydro-3-deoxy-6-phosphogalactonate aldolase" groups:idRef="R_DDPGALA"/>
+          <groups:member groups:name="Aldehyde dehydrogenase (phenylacetaldehyde, NAD)" groups:idRef="R_ALDD19xr"/>
+          <groups:member groups:name="Myo-Inositol:oxygen oxidoreductase" groups:idRef="R_INOSTO"/>
+          <groups:member groups:name="L-ascorbate 6-phosphate lactonase" groups:idRef="R_ASCBPL"/>
+          <groups:member groups:name="NADPH-dependent curcumin reductase" groups:idRef="R_CURR"/>
+          <groups:member groups:name="Glycerol-2-phosphate phosphatase" groups:idRef="R_G2PP"/>
+          <groups:member groups:name="2-dehydro-3-deoxy-D-arabinonate Aldolase" groups:idRef="R_2DDARAA"/>
+          <groups:member groups:name="Alcohol dehydrogenase (glycerol)" groups:idRef="R_ALCD19"/>
+          <groups:member groups:name="Formyl-CoA Transferase" groups:idRef="R_FORCT"/>
+          <groups:member groups:name="Amylomaltase (maltohexaose)" groups:idRef="R_AMALT4"/>
+          <groups:member groups:name="N-acetylmannosamine 6-phosphate epimerase" groups:idRef="R_AMANAPEr"/>
+          <groups:member groups:name="L-galactonate oxidoreductase" groups:idRef="R_GALCTLO"/>
+          <groups:member groups:name="Alkaline phosphatase" groups:idRef="R_ALKP"/>
           <groups:member groups:name="Lacaldehyde reductase (S-propane-1,2-diol forming)" groups:idRef="R_LCARS"/>
+          <groups:member groups:name="Maltodextrin glucosidase (maltotriose)" groups:idRef="R_MLTG1"/>
+          <groups:member groups:name="Amylomaltase (maltopentaose)" groups:idRef="R_AMALT3"/>
+          <groups:member groups:name="Propionate kinase" groups:idRef="R_PPAKr"/>
+          <groups:member groups:name="L-xylulokinase" groups:idRef="R_XYLK2"/>
+          <groups:member groups:name="Galactonate dehydratase" groups:idRef="R_GALCTND"/>
+          <groups:member groups:name="Phosphoglycolate phosphatase" groups:idRef="R_PGLYCP"/>
+          <groups:member groups:name="Ribose 5-phosphate phosphatase" groups:idRef="R_R5PP"/>
+          <groups:member groups:name="Aldehyde dehydrogenase (acetaldehyde, NADP)" groups:idRef="R_ALDD2y"/>
+          <groups:member groups:name="Glycerol kinase" groups:idRef="R_GLYK"/>
           <groups:member groups:name="Mannitol-1-phosphate 5-dehydrogenase" groups:idRef="R_M1PD"/>
-          <groups:member groups:name="2-hydroxycyclohepta-1,4,6-triene-1-carboxyl-CoA thioesterase" groups:idRef="R_2HPTCOAT"/>
-          <groups:member groups:name="N-acetylmannosamine 6-phosphate epimerase" groups:idRef="R_AMANAPEr"/>
+          <groups:member groups:name="Gamma glutamyl putrescine oxidase" groups:idRef="R_GGPTRCO"/>
+          <groups:member groups:name="2-methylisocitrate dehydratase" groups:idRef="R_MICITDr"/>
+          <groups:member groups:name="Sulfoquinovose isomerase" groups:idRef="R_SQVOSI"/>
+          <groups:member groups:name="Allose 6-phosphate isomerase" groups:idRef="R_ALLPI"/>
+          <groups:member groups:name="Deoxyribose-phosphate aldolase" groups:idRef="R_DRPA"/>
           <groups:member groups:name="Maltodextrin glucosidase (maltoheptaose)" groups:idRef="R_MLTG5"/>
-          <groups:member groups:name="Fructoselysine 3-epimerase" groups:idRef="R_FRULYSE"/>
-          <groups:member groups:name="Rhamnulokinase" groups:idRef="R_RMK"/>
-          <groups:member groups:name="L-xylulose 5-phosphate 3-epimerase" groups:idRef="R_X5PL3E"/>
-          <groups:member groups:name="2 deoxyglucose 6 phosphatase" groups:idRef="R_2DOXG6PP"/>
-          <groups:member groups:name="Alpha-amylase" groups:idRef="R_AAMYL"/>
-          <groups:member groups:name="Formyl-CoA Transferase" groups:idRef="R_FORCT"/>
-          <groups:member groups:name="Glycerol-3-phosphatase" groups:idRef="R_G3PT"/>
           <groups:member groups:name="5-dehydro-4-deoxyglucarate aldolase" groups:idRef="R_GLCRAL"/>
-          <groups:member groups:name="2-hydroxy-6-ketononotrienedioate hydrolase" groups:idRef="R_HKNTDH"/>
-          <groups:member groups:name="6-deoxy-6-sulfofructose kinase" groups:idRef="R_6D6SFK"/>
-          <groups:member groups:name="Alpha-amylase (periplasm)" groups:idRef="R_AAMYLpp"/>
-          <groups:member groups:name="2-methylcitrate synthase" groups:idRef="R_MCITS"/>
-          <groups:member groups:name="?-D-ribose 1-methylphosphonate 5-triphosphate synthase" groups:idRef="R_ARMEPNS"/>
-          <groups:member groups:name="Monoacetylchitobiose-6-phosphate hydrolase" groups:idRef="R_MC6PH"/>
-          <groups:member groups:name="2,3-dihydroxycinnamate 1,2-dioxygenase" groups:idRef="R_DHCINDO"/>
-          <groups:member groups:name="2,3-dihydroxycinnamate dehydrogenase" groups:idRef="R_DHCIND"/>
+          <groups:member groups:name="3-keto-L-gulonate 6-phosphate decarboxylase" groups:idRef="R_KG6PDC"/>
+          <groups:member groups:name="Methylmalonyl-CoA decarboxylase" groups:idRef="R_MMCD"/>
+          <groups:member groups:name="NADPH-dependent dihydrocurcumin reductase" groups:idRef="R_DHCURR"/>
+          <groups:member groups:name="Fructose-1-phosphate kinase" groups:idRef="R_FRUK"/>
+          <groups:member groups:name="Maltodextrin phosphorylase (maltoheptaose)" groups:idRef="R_MLTP3"/>
+          <groups:member groups:name="2,5-diketo-D-gluconate reductase (NADPH)" groups:idRef="R_DKGLCNR2y"/>
+          <groups:member groups:name="D-fructose 1-phosphate phosphatase" groups:idRef="R_F1PP"/>
+          <groups:member groups:name="UDP-N-acetyl-D-galactosamine pyrophosphohydrolase (periplasm)" groups:idRef="R_UACGALPpp"/>
+          <groups:member groups:name="2,5-diketo-D-gluconate reductase" groups:idRef="R_DKGLCNR1"/>
+          <groups:member groups:name="2,5-diketo-D-gluconate reductase (NADH)" groups:idRef="R_DKGLCNR2x"/>
+          <groups:member groups:name="Allose kinase" groups:idRef="R_ALLK"/>
+          <groups:member groups:name="Arabinose-5-phosphate isomerase" groups:idRef="R_A5PISO"/>
+          <groups:member groups:name="Glycerol 2-phosphate phosphatase (periplasmic)" groups:idRef="R_G2PPpp"/>
+          <groups:member groups:name="Hexokinase (D-mannose:ATP)" groups:idRef="R_HEX4"/>
           <groups:member groups:name="2-dehydro-3-deoxygalactonokinase" groups:idRef="R_DDGALK"/>
-          <groups:member groups:name="N-acetyl-D-mannosamine kinase" groups:idRef="R_AMANK"/>
           <groups:member groups:name="L-arabinose isomerase" groups:idRef="R_ARAI"/>
-          <groups:member groups:name="L-fucose isomerase" groups:idRef="R_FCI"/>
-          <groups:member groups:name="N-acetylglucosamine-6-phosphate deacetylase" groups:idRef="R_AGDC"/>
-          <groups:member groups:name="Carbon-phosphorous lyase" groups:idRef="R_CPL"/>
-          <groups:member groups:name="Glucuronate isomerase (D-glucuronate)" groups:idRef="R_GUI1"/>
-          <groups:member groups:name="3-sulfolactaldehyde reductase" groups:idRef="R_3SLAR"/>
-          <groups:member groups:name="Fructoselysine Kinase" groups:idRef="R_FRULYSK"/>
-          <groups:member groups:name="Glucuronate 1-phosphate phosphatase (periplasm)" groups:idRef="R_GUR1PPpp"/>
-          <groups:member groups:name="Fructoselysine phosphate deglycase" groups:idRef="R_FRULYSDG"/>
-          <groups:member groups:name="Hydroxyphenylacetyl-CoA thioesterase" groups:idRef="R_HPACOAT"/>
-          <groups:member groups:name="Maltodextrin glucosidase (maltopentaose)" groups:idRef="R_MLTG3"/>
-          <groups:member groups:name="Aldehyde dehydrogenase (butanal, NAD)" groups:idRef="R_ALDD4"/>
-          <groups:member groups:name="Deoxyribose-phosphate aldolase" groups:idRef="R_DRPA"/>
-          <groups:member groups:name="Glycerol dehydrogenase" groups:idRef="R_GLYCDx"/>
-          <groups:member groups:name="2-O-alpha-mannosyl-6-phosphate-D-glycerate hydrolase" groups:idRef="R_MANPGH"/>
           <groups:member groups:name="Oxalyl-CoA decarboxylase" groups:idRef="R_OXCDC"/>
-          <groups:member groups:name="Propionate kinase" groups:idRef="R_PPAKr"/>
-          <groups:member groups:name="1-O-Methyl-Beta-D-glucuronidase" groups:idRef="R_METGLCUR"/>
-          <groups:member groups:name="Xylose isomerase" groups:idRef="R_XYLI2"/>
+          <groups:member groups:name="3-oxo-5,6-dehydrosuberyl-CoA thiolase" groups:idRef="R_OXDHCOAT"/>
+          <groups:member groups:name="L-ribulose-phosphate 4-epimerase" groups:idRef="R_RBP4E"/>
+          <groups:member groups:name="Alpha,alpha-trehalase (periplasm)" groups:idRef="R_TREHpp"/>
+          <groups:member groups:name="Phosphomannomutase" groups:idRef="R_PMANM"/>
+          <groups:member groups:name="Xylulokinase" groups:idRef="R_XYLK"/>
+          <groups:member groups:name="Phosphopentomutase" groups:idRef="R_PPM"/>
+          <groups:member groups:name="3-keto-L-gulonate kinase" groups:idRef="R_3KGK"/>
+          <groups:member groups:name="Ring 1,2-phenylacetyl-CoA epoxidase (NADPH)" groups:idRef="R_PACCOAE"/>
+          <groups:member groups:name="2-Dehydro-L-gulonate reductase to gluconate (NADPH)" groups:idRef="R_2DGULRGy"/>
           <groups:member groups:name="Mannonate oxidoreductase" groups:idRef="R_MANAO"/>
-          <groups:member groups:name="L-fuculose 1-phosphate aldolase" groups:idRef="R_FCLPA"/>
+          <groups:member groups:name="L-indonate 5-dehydrogenase (NADP)" groups:idRef="R_IDOND2"/>
+          <groups:member groups:name="Phosphopentomutase 2 (deoxyribose)" groups:idRef="R_PPM2"/>
+          <groups:member groups:name="Malate decarboxylating oxidoreductase (decarboxylating)" groups:idRef="R_MALDDH"/>
+          <groups:member groups:name="Oxepin-CoA hydrolase/ 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase (NADP+)" groups:idRef="R_OXCOAHDH"/>
+          <groups:member groups:name="D-xylonate dehydratase" groups:idRef="R_DXYLTD"/>
+          <groups:member groups:name="Phenylacetate-CoA ligase" groups:idRef="R_PACCOAL"/>
+          <groups:member groups:name="UDP-D-glucuronate pyrophosphohydrolase (periplasm)" groups:idRef="R_UGLCURPpp"/>
+          <groups:member groups:name="Mannose 6-phosphate phosphatase" groups:idRef="R_MN6PP"/>
+          <groups:member groups:name="Phenylacetyl-CoA thioesterase" groups:idRef="R_PACOAT"/>
+          <groups:member groups:name="Fructoselysine 3-epimerase" groups:idRef="R_FRULYSE"/>
+          <groups:member groups:name="Amylomaltase (maltotriose)" groups:idRef="R_AMALT1"/>
+          <groups:member groups:name="Cinnamate dioxygenase" groups:idRef="R_CINNDO"/>
           <groups:member groups:name="N-Acetylneuraminate lyase" groups:idRef="R_ACNML"/>
-          <groups:member groups:name="UDPglucose--hexose-1-phosphate uridylyltransferase" groups:idRef="R_UGLT"/>
-          <groups:member groups:name="3-oxo-5,6-dehydrosuberyl-CoA thiolase" groups:idRef="R_OXDHCOAT"/>
-          <groups:member groups:name="Maltose O-acetyltransferase" groups:idRef="R_MALTATr"/>
-          <groups:member groups:name="Cytidine hydrolase" groups:idRef="R_CYTDH"/>
-          <groups:member groups:name="Allose kinase" groups:idRef="R_ALLK"/>
-          <groups:member groups:name="Phosphate acetyltransferase" groups:idRef="R_PTA2"/>
-          <groups:member groups:name="Glycerol 2-phosphate phosphatase (periplasmic)" groups:idRef="R_G2PPpp"/>
-          <groups:member groups:name="Allose 6-phosphate isomerase" groups:idRef="R_ALLPI"/>
           <groups:member groups:name="L-fuculokinase" groups:idRef="R_FCLK"/>
-          <groups:member groups:name="Alkaline phosphatase" groups:idRef="R_ALKP"/>
-          <groups:member groups:name="Gamma-glutamyl-gamma-aminobutyric acid hydrolase" groups:idRef="R_GGGABAH"/>
-          <groups:member groups:name="2-Oxobutanoate formate lyase" groups:idRef="R_OBTFL"/>
-          <groups:member groups:name="Acetyl-CoA:butyrate-CoA transferase" groups:idRef="R_BUTCT"/>
-          <groups:member groups:name="Gamma-glutamyl-gamma aminobutyric acid dehydrogenase" groups:idRef="R_GGGABADr"/>
-          <groups:member groups:name="Methylisocitrate lyase" groups:idRef="R_MCITL2"/>
-          <groups:member groups:name="Lacaldehyde reductase (S-propane-1,2-diol forming)" groups:idRef="R_LCARSyi"/>
-          <groups:member groups:name="L(+)-tartrate dehydratase" groups:idRef="R_TARTD"/>
+          <groups:member groups:name="2-dehydro-L-gulonate reductase (NADH)" groups:idRef="R_2DGULRx"/>
+          <groups:member groups:name="2-O-alpha-mannosyl-6-phosphate-D-glycerate hydrolase" groups:idRef="R_MANPGH"/>
+          <groups:member groups:name="L-fucose isomerase" groups:idRef="R_ARABDI"/>
           <groups:member groups:name="D-glucose O-acetyltransferase" groups:idRef="R_GLCATr"/>
-          <groups:member groups:name="Tagaturonate reductase" groups:idRef="R_TAGURr"/>
-          <groups:member groups:name="L-ascorbate 6-phosphate lactonase" groups:idRef="R_ASCBPL"/>
-          <groups:member groups:name="D(-)-tartrate dehydratase" groups:idRef="R_DTARTD"/>
+          <groups:member groups:name="2-dehydro-3-deoxygluconokinase" groups:idRef="R_DDGLK"/>
+          <groups:member groups:name="B-galactosidase" groups:idRef="R_LACZpp"/>
+          <groups:member groups:name="L-fucose isomerase" groups:idRef="R_FCI"/>
           <groups:member groups:name="3-(3-hydroxy-phenyl)propionate hydroxylase" groups:idRef="R_3HPPPNH"/>
-          <groups:member groups:name="Oxepin-CoA hydrolase/ 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase (NADP+)" groups:idRef="R_OXCOAHDH"/>
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-          <groups:member groups:name="Dihydroxyacetone phosphotransferase" groups:idRef="R_DHAPT"/>
-          <groups:member groups:name="2-keto-3-deoxy-L-rhamnonate aldolase" groups:idRef="R_LKDRA"/>
-          <groups:member groups:name="Rhamnulose-1-phosphate aldolase" groups:idRef="R_RMPA"/>
-          <groups:member groups:name="Phosphoglucomutase" groups:idRef="R_PGMT"/>
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-          <groups:member groups:name="D-galactose 1-phosphatase" groups:idRef="R_GAL1PPpp"/>
-          <groups:member groups:name="L-rhamnose isomerase" groups:idRef="R_RMI"/>
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-          <groups:member groups:name="2-hydroxyethyldisulfide reductase" groups:idRef="R_2HESR"/>
+          <groups:member groups:name="2,3-diaminopropionate amonnia lyase" groups:idRef="R_DAPAL"/>
+          <groups:member groups:name="2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase" groups:idRef="R_HKNDDH"/>
+          <groups:member groups:name="3-hydroxycinnamate hydroxylase" groups:idRef="R_3HCINNMH"/>
+          <groups:member groups:name="Hydroxyphenylacetyl-CoA thioesterase" groups:idRef="R_HPACOAT"/>
+          <groups:member groups:name="Monoacetylchitobiose-6-phosphate hydrolase" groups:idRef="R_MC6PH"/>
+          <groups:member groups:name="Acetate-CoA ligase (ADP-forming)" groups:idRef="R_ACCOAL"/>
+          <groups:member groups:name="Lyxose isomerase" groups:idRef="R_LYXI"/>
           <groups:member groups:name="Propanoyl-CoA: succinate CoA-transferase" groups:idRef="R_PPCSCT"/>
+          <groups:member groups:name="3-Hydroxypropanal Dehydrogenase" groups:idRef="R_3HPADHi"/>
+          <groups:member groups:name="Maltodextrin phosphorylase (maltopentaose)" groups:idRef="R_MLTP1"/>
+          <groups:member groups:name="2-hydroxycyclohepta-1,4,6-triene-1-carboxyl-CoA thioesterase" groups:idRef="R_2HPTCOAT"/>
+          <groups:member groups:name="Hydroxypyruvate reductase (NADH)" groups:idRef="R_HPYRRx"/>
+          <groups:member groups:name="Amylomaltase (maltotetraose)" groups:idRef="R_AMALT2"/>
+          <groups:member groups:name="?-D-ribose 1-methylphosphonate 5-triphosphate synthase" groups:idRef="R_ARMEPNS"/>
+          <groups:member groups:name="2-hydroxy-6-ketononotrienedioate hydrolase" groups:idRef="R_HKNTDH"/>
+          <groups:member groups:name="Dihydroxyacetone phosphotransferase" groups:idRef="R_DHAPT"/>
+          <groups:member groups:name="Glucosamine-6-phosphate deaminase" groups:idRef="R_G6PDA"/>
+          <groups:member groups:name="Acetyl-CoA:hexanoate-CoA transferase" groups:idRef="R_HXCT"/>
+          <groups:member groups:name="Maltodextrin glucosidase (maltohexaose)" groups:idRef="R_MLTG4"/>
+          <groups:member groups:name="UDPglucose pyrophosphohydrolase" groups:idRef="R_UDPGPpp"/>
+          <groups:member groups:name="2 deoxyglucose 6 phosphatase" groups:idRef="R_2DOXG6PP"/>
           <groups:member groups:name="N-acetylmuramate 6-phosphate hydrolase" groups:idRef="R_ACM6PH"/>
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-          <groups:member groups:name="Arabinose-5-phosphate isomerase" groups:idRef="R_A5PISO"/>
           <groups:member groups:name="Glyceraldehyde-3-phosphate phosphatase" groups:idRef="R_GAPP"/>
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-          <groups:member groups:name="Galactarate dehydratase" groups:idRef="R_GALCTD"/>
+          <groups:member groups:name="Acetyl-CoA:acetoacetyl-CoA transferase" groups:idRef="R_ACACCT"/>
+          <groups:member groups:name="N-acetyl-D-glucosamine 1-phosphatase (periplasm)" groups:idRef="R_ACGAM1PPpp"/>
+          <groups:member groups:name="Fructoselysine phosphate deglycase" groups:idRef="R_FRULYSDG"/>
+          <groups:member groups:name="Alpha-amylase" groups:idRef="R_AAMYL"/>
+          <groups:member groups:name="Chito-oligosaccharide mono-deacetylase" groups:idRef="R_DC6PDA"/>
           <groups:member groups:name="Galactokinase" groups:idRef="R_GALKr"/>
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-          <groups:member groups:name="Ring 1,2-epoxyphenylacetyl-CoA isomerase (oxepin-CoA forming)" groups:idRef="R_REPHACCOAI"/>
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-          <groups:member groups:name="L-galactonate oxidoreductase" groups:idRef="R_GALCTLO"/>
+          <groups:member groups:name="Propane-1,2-diol:NADP+ 1-oxidoreductase" groups:idRef="R_PPDOy"/>
+          <groups:member groups:name="L(+)-tartrate dehydratase" groups:idRef="R_TARTD"/>
+          <groups:member groups:name="Phosphate acetyltransferase" groups:idRef="R_PTA2"/>
+          <groups:member groups:name="UDPgalactose pyrophosphohydrolase" groups:idRef="R_UDPGALPpp"/>
+          <groups:member groups:name="Glycolate oxidase" groups:idRef="R_GLYCTO3"/>
           <groups:member groups:name="Alpha,alpha-trehalose-phosphate synthase (UDP-forming)" groups:idRef="R_TRE6PS"/>
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-          <groups:member groups:name="D-fructose 1-phosphate phosphatase" groups:idRef="R_F1PP"/>
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-          <groups:member groups:name="Ribulose-5-Phosphate Phosphatase" groups:idRef="R_RU5PP"/>
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-          <groups:member groups:name="NADPH-dependent dihydrocurcumin reductase" groups:idRef="R_DHCURR"/>
+          <groups:member groups:name="6-deoxy-6-sulfofructose-1-phosphate aldolase" groups:idRef="R_6D6SPA"/>
+          <groups:member groups:name="3-hydroxyadipyl-CoA dehydrogenase (NAD+)" groups:idRef="R_HADPCOADH3"/>
+          <groups:member groups:name="Rhamnulokinase" groups:idRef="R_RMK"/>
+          <groups:member groups:name="Dihydropteridine reductase (NADH)" groups:idRef="R_DHPTDNRN"/>
           <groups:member groups:name="3,5-cyclic-nucleotide phosphodiesterase" groups:idRef="R_CDGUNPD"/>
-        </groups:listOfMembers>
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-        </groups:listOfMembers>
-      </groups:group>
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-          <groups:member groups:name="Proline dehydrogenase (q8)" groups:idRef="R_PROD3"/>
+          <groups:member groups:name="7-?-hydroxysteroid dehydrogenase" groups:idRef="R_CHOLID"/>
+          <groups:member groups:name="6-deoxy-6-sulfofructose kinase" groups:idRef="R_6D6SFK"/>
+          <groups:member groups:name="2,3-dihydroxypheylpropionate 1,2-dioxygenase" groups:idRef="R_HPPPNDO"/>
+          <groups:member groups:name="Tagatose-bisphosphate aldolase" groups:idRef="R_TGBPA"/>
+          <groups:member groups:name="N-acetyl-D-galactosamine 1-phosphatase (periplasm)" groups:idRef="R_ACGAL1PPpp"/>
+          <groups:member groups:name="UDPglucose--hexose-1-phosphate uridylyltransferase" groups:idRef="R_UGLT"/>
+          <groups:member groups:name="L-fuculose 1-phosphate aldolase" groups:idRef="R_FCLPA"/>
+          <groups:member groups:name="Phosphogluconate phosphatase" groups:idRef="R_GNP"/>
+          <groups:member groups:name="2-keto-3-deoxy-L-rhamnonate aldolase" groups:idRef="R_LKDRA"/>
+          <groups:member groups:name="Propanoyl-CoA:NADP+ 2-oxidoreductase" groups:idRef="R_PCNO"/>
+          <groups:member groups:name="L-ribulokinase (L-ribulose)" groups:idRef="R_RBK_L1"/>
+          <groups:member groups:name="Tagaturonate reductase" groups:idRef="R_TAGURr"/>
+          <groups:member groups:name="2,3 dioxo-L-gulonate reductase" groups:idRef="R_DOGULNR"/>
+          <groups:member groups:name="UDPglucose 4-epimerase" groups:idRef="R_UDPG4E"/>
+          <groups:member groups:name="Tartronate semialdehyde reductase" groups:idRef="R_TRSARr"/>
+          <groups:member groups:name="3-sulfolactaldehyde reductase" groups:idRef="R_3SLAR"/>
+          <groups:member groups:name="Fructoselysine Kinase" groups:idRef="R_FRULYSK"/>
+          <groups:member groups:name="L-rhamnose isomerase" groups:idRef="R_RMI"/>
+          <groups:member groups:name="Glycerol-3-phosphatase" groups:idRef="R_G3PT"/>
+          <groups:member groups:name="Gamma glutamyl putrescine synthase" groups:idRef="R_GGPTRCS"/>
+          <groups:member groups:name="Glycerol dehydrogenase" groups:idRef="R_GLYCDx"/>
+          <groups:member groups:name="Acetyl-CoA:butyrate-CoA transferase" groups:idRef="R_BUTCT"/>
+          <groups:member groups:name="Carbon-phosphorous lyase" groups:idRef="R_CPL"/>
+          <groups:member groups:name="4-hydroxy-2-oxopentanoate aldolase" groups:idRef="R_HOPNTAL"/>
+          <groups:member groups:name="Dihydropteridine reductase" groups:idRef="R_DHPTDNR"/>
+          <groups:member groups:name="Hydroxypyruvate reductase (NADPH)" groups:idRef="R_HPYRRy"/>
+          <groups:member groups:name="Phytase (periplasm)" groups:idRef="R_PHYTSpp"/>
+          <groups:member groups:name="2-hydroxyethyldisulfide reductase" groups:idRef="R_2HESR"/>
+          <groups:member groups:name="Galactitol-1-phosphate dehydrogenase" groups:idRef="R_GLTPD"/>
+          <groups:member groups:name="Gluconokinase" groups:idRef="R_GNK"/>
+          <groups:member groups:name="3-oxoadipyl-CoA thiolase" groups:idRef="R_3OXCOAT"/>
+          <groups:member groups:name="Glucuronate isomerase (D-glucuronate)" groups:idRef="R_GUI1"/>
+          <groups:member groups:name="Glucuronate 1-phosphate phosphatase (periplasm)" groups:idRef="R_GUR1PPpp"/>
+          <groups:member groups:name="Lactaldehyde dehydrogenase" groups:idRef="R_LCADi"/>
+          <groups:member groups:name="Methylmalonyl-CoA mutase" groups:idRef="R_MMM"/>
+          <groups:member groups:name="Ribokinase" groups:idRef="R_RBK"/>
+          <groups:member groups:name="2-dehydro-L-gulonate reductase (NADPH)" groups:idRef="R_2DGULRy"/>
+          <groups:member groups:name="Erythrose-4-phosphate phosphatase" groups:idRef="R_E4PP"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="meta_G_group3" sboTerm="SBO:0000633" groups:id="G_group3" groups:name="Anaplerotic Reactions" groups:kind="partonomy">
+        <groups:listOfMembers>
+          <groups:member groups:name="Phosphoenolpyruvate carboxylase" groups:idRef="R_PPC"/>
+          <groups:member groups:name="Malic enzyme (NAD)" groups:idRef="R_ME1"/>
+          <groups:member groups:name="Malic enzyme (NADP)" groups:idRef="R_ME2"/>
+          <groups:member groups:name="Isocitrate lyase" groups:idRef="R_ICL"/>
+          <groups:member groups:name="Inorganic triphosphatase" groups:idRef="R_PPA2"/>
+          <groups:member groups:name="Inorganic diphosphatase" groups:idRef="R_PPA"/>
+          <groups:member groups:name="Malate synthase" groups:idRef="R_MALS"/>
+          <groups:member groups:name="Phosphoenolpyruvate carboxykinase" groups:idRef="R_PPCK"/>
+        </groups:listOfMembers>
+      </groups:group>
+      <groups:group metaid="meta_G_group4" sboTerm="SBO:0000633" groups:id="G_group4" groups:name="Arginine and Proline Metabolism" groups:kind="partonomy">
+        <groups:listOfMembers>
+          <groups:member groups:name="Adenosylmethionine decarboxylase" groups:idRef="R_ADMDC"/>
+          <groups:member groups:name="Acetylglutamate kinase" groups:idRef="R_ACGK"/>
+          <groups:member groups:name="L-glutamate 5-semialdehyde dehydratase (spontaneous)" groups:idRef="R_G5SADs"/>
+          <groups:member groups:name="Ornithine carbamoyltransferase" groups:idRef="R_OCBT"/>
+          <groups:member groups:name="Succinylarginine dihydrolase" groups:idRef="R_SADH"/>
+          <groups:member groups:name="Succinate-semialdehyde dehydrogenase (NAD)" groups:idRef="R_SSALx"/>
+          <groups:member groups:name="Acetylornithine deacetylase" groups:idRef="R_ACODA"/>
+          <groups:member groups:name="Succinate-semialdehyde dehydrogenase (NADP)" groups:idRef="R_SSALy"/>
           <groups:member groups:name="Methylthioadenosine nucleosidase" groups:idRef="R_MTAN"/>
-          <groups:member groups:name="Argininosuccinate synthase" groups:idRef="R_ARGSS"/>
-          <groups:member groups:name="Ornithine Decarboxylase" groups:idRef="R_ORNDC"/>
-          <groups:member groups:name="Succinylglutamate desuccinylase" groups:idRef="R_SGDS"/>
-          <groups:member groups:name="Pyrroline-5-carboxylate reductase" groups:idRef="R_P5CR"/>
+          <groups:member groups:name="Arginine decarboxylase" groups:idRef="R_ARGDC"/>
+          <groups:member groups:name="Argininosuccinate lyase" groups:idRef="R_ARGSL"/>
+          <groups:member groups:name="Aminopeptidase (pro-gly)" groups:idRef="R_AMPTASEPG"/>
+          <groups:member groups:name="Arginine succinyltransferase" groups:idRef="R_AST"/>
+          <groups:member groups:name="Putrescine Transaminase" groups:idRef="R_PTRCTA"/>
           <groups:member groups:name="Glutamate 5-kinase" groups:idRef="R_GLU5K"/>
-          <groups:member groups:name="Glutathionylspermidine synthetase" groups:idRef="R_GSPMDS"/>
+          <groups:member groups:name="1-pyrroline-5-carboxylate dehydrogenase" groups:idRef="R_P5CD"/>
+          <groups:member groups:name="Spermidine acetyltransferase (N8)" groups:idRef="R_SPMDAT2"/>
           <groups:member groups:name="Glutamate-5-semialdehyde dehydrogenase" groups:idRef="R_G5SD"/>
           <groups:member groups:name="Gamma-hydroxybutyrate dehydrogenase (NADH)" groups:idRef="R_GHBDHx"/>
-          <groups:member groups:name="Glutathionylspermidine amidase" groups:idRef="R_GSPMDA"/>
+          <groups:member groups:name="N-acetyl-g-glutamyl-phosphate reductase" groups:idRef="R_AGPR"/>
+          <groups:member groups:name="Proline dehydrogenase (q8)" groups:idRef="R_PROD3"/>
+          <groups:member groups:name="Acetylornithine transaminase" groups:idRef="R_ACOTA"/>
+          <groups:member groups:name="Succinylornithine transaminase" groups:idRef="R_SOTA"/>
+          <groups:member groups:name="Spermidine acetyltransferase" groups:idRef="R_SPMDAT1"/>
+          <groups:member groups:name="Agmatinase" groups:idRef="R_AGMT"/>
+          <groups:member groups:name="Succinylglutamate desuccinylase" groups:idRef="R_SGDS"/>
           <groups:member groups:name="Succinylglutamic semialdehyde dehydrogenase" groups:idRef="R_SGSAD"/>
+          <groups:member groups:name="Arginine decarboxylase" groups:idRef="R_ARGDCpp"/>
+          <groups:member groups:name="Glutathionylspermidine synthetase" groups:idRef="R_GSPMDS"/>
+          <groups:member groups:name="Argininosuccinate synthase" groups:idRef="R_ARGSS"/>
+          <groups:member groups:name="Glutathionylspermidine amidase" groups:idRef="R_GSPMDA"/>
+          <groups:member groups:name="Pyrroline-5-carboxylate reductase" groups:idRef="R_P5CR"/>
           <groups:member groups:name="4-aminobutyrate transaminase" groups:idRef="R_ABTA"/>
-          <groups:member groups:name="Aminopeptidase (pro-gly)" groups:idRef="R_AMPTASEPG"/>
-          <groups:member groups:name="N-acetyl-g-glutamyl-phosphate reductase" groups:idRef="R_AGPR"/>
           <groups:member groups:name="N-acetylglutamate synthase" groups:idRef="R_ACGS"/>
+          <groups:member groups:name="Aminopropylcadaverine synthase" groups:idRef="R_APCS"/>
           <groups:member groups:name="Spermidine synthase" groups:idRef="R_SPMS"/>
-          <groups:member groups:name="Succinate-semialdehyde dehydrogenase (NAD)" groups:idRef="R_SSALx"/>
-          <groups:member groups:name="Putrescine Transaminase" groups:idRef="R_PTRCTA"/>
-          <groups:member groups:name="Spermidine acetyltransferase (N8)" groups:idRef="R_SPMDAT2"/>
-          <groups:member groups:name="Argininosuccinate lyase" groups:idRef="R_ARGSL"/>
           <groups:member groups:name="Carbamoyl-phosphate synthase (glutamine-hydrolysing)" groups:idRef="R_CBPS"/>
-          <groups:member groups:name="Ornithine carbamoyltransferase" groups:idRef="R_OCBT"/>
-          <groups:member groups:name="1-pyrroline-5-carboxylate dehydrogenase" groups:idRef="R_P5CD"/>
-          <groups:member groups:name="Agmatinase" groups:idRef="R_AGMT"/>
-          <groups:member groups:name="Acetylglutamate kinase" groups:idRef="R_ACGK"/>
           <groups:member groups:name="Aminobutyraldehyde dehydrogenase" groups:idRef="R_ABUTD"/>
-          <groups:member groups:name="Arginine decarboxylase" groups:idRef="R_ARGDC"/>
-          <groups:member groups:name="Arginine decarboxylase" groups:idRef="R_ARGDCpp"/>
-          <groups:member groups:name="Arginine succinyltransferase" groups:idRef="R_AST"/>
+          <groups:member groups:name="Ornithine Decarboxylase" groups:idRef="R_ORNDC"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group5" sboTerm="SBO:0000633" groups:id="G_group5" groups:name="Biomass and maintenance functions" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="Nucleoside-triphosphatase (ATP)" groups:idRef="R_NTP1"/>
-          <groups:member groups:name="ATP maintenance requirement" groups:idRef="R_ATPM"/>
           <groups:member groups:name="E. coli biomass objective function (iML1515) - WT - with 75.37 GAM estimate" groups:idRef="R_BIOMASS_Ec_iML1515_WT_75p37M"/>
+          <groups:member groups:name="Nucleoside-triphosphatase (ATP)" groups:idRef="R_NTP1"/>
           <groups:member groups:name="E. coli biomass objective function (iML1515) - core - with 75.37 GAM estimate" groups:idRef="R_BIOMASS_Ec_iML1515_core_75p37M"/>
+          <groups:member groups:name="ATP maintenance requirement" groups:idRef="R_ATPM"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group6" sboTerm="SBO:0000633" groups:id="G_group6" groups:name="Cell Envelope Biosynthesis" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="GDP-4-dehydro-6-deoxy-D-mannose epimerase" groups:idRef="R_GDMANE"/>
-          <groups:member groups:name="Fatty-acid-CoA thioesterase (octadecanoate)" groups:idRef="R_FACOAE180"/>
-          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C10:0)" groups:idRef="R_3HAD100"/>
-          <groups:member groups:name="GDP-mannose mannosyl hydrolase" groups:idRef="R_GDPMNH"/>
+          <groups:member groups:name="Fatty-acid-CoA ligase (dodecanoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL120t2pp"/>
+          <groups:member groups:name="Fatty-acid-CoA thioesterase (octanoate)" groups:idRef="R_FACOAE80"/>
           <groups:member groups:name="Undecaprenyl-phosphate glucose phosphotransferase" groups:idRef="R_UDPGPT"/>
-          <groups:member groups:name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate synthetase" groups:idRef="R_UAAGDS"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C12:1)" groups:idRef="R_3OAS121"/>
-          <groups:member groups:name="DTDP-4-dehydrorhamnose reductase" groups:idRef="R_TDPDRR"/>
-          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C18:0)" groups:idRef="R_AACPS6"/>
+          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase (n-C14:0)" groups:idRef="R_AACPS1"/>
           <groups:member groups:name="Fatty-acid-CoA thioesterase (dodecanoate)" groups:idRef="R_FACOAE120"/>
-          <groups:member groups:name="Phospho-N-acetylmuramoyl-pentapeptide-transferase (meso-2,6-diaminopimelate)" groups:idRef="R_PAPPT3"/>
-          <groups:member groups:name="DTDP-N-4-acetamido-4,6-dideoxy-D-galactose transferase" groups:idRef="R_AADDGT"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C14:0)" groups:idRef="R_EAR140x"/>
-          <groups:member groups:name="UDPgalactopyranose mutase" groups:idRef="R_UDPGALM"/>
-          <groups:member groups:name="Fatty-acid-CoA ligase (hexadecanoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL160t2pp"/>
-          <groups:member groups:name="GDP-mannose phyrophosphatase" groups:idRef="R_GDPMNP"/>
-          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C18:1)" groups:idRef="R_3HAD181"/>
-          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C18:0)" groups:idRef="R_3HAD180"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C18:1)" groups:idRef="R_3OAR181"/>
-          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA120ACPHi"/>
-          <groups:member groups:name="Phosphoglucosamine mutase" groups:idRef="R_PGAMT"/>
-          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C8:0)" groups:idRef="R_AACPS9"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C12:1)" groups:idRef="R_EAR121y"/>
-          <groups:member groups:name="D-alanine-D-alanine ligase (reversible)" groups:idRef="R_ALAALAr"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C14:0)" groups:idRef="R_3OAS140"/>
-          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C12:1)" groups:idRef="R_3HAD121"/>
-          <groups:member groups:name="UDP-N-acetylglucosamine:undecaprenylphosphate N-acetylglucosamine -1-phosphate transferase" groups:idRef="R_ACGAMT"/>
-          <groups:member groups:name="DTDP-4-amino-4,6-dideoxy-D-glucose transaminase" groups:idRef="R_TDPAGTA"/>
-          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C14:0)" groups:idRef="R_3HAD140"/>
-          <groups:member groups:name="DTDPglucose 4,6-dehydratase" groups:idRef="R_TDPGDH"/>
-          <groups:member groups:name="UDP-N-acetyl-D-mannosamine oxidoreductase" groups:idRef="R_UACMAMO"/>
-          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C12:0)" groups:idRef="R_3HAD120"/>
-          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C6:0)" groups:idRef="R_3HAD60"/>
           <groups:member groups:name="Fatty-acid-CoA thioesterase (hexanoate)" groups:idRef="R_FACOAE60"/>
-          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C4:0)" groups:idRef="R_3HAD40"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C18:0)" groups:idRef="R_EAR180x"/>
-          <groups:member groups:name="Poly-?-1,6-N-acetyl-D-glucosamine synthase" groups:idRef="R_PUACGAMS"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C4:0)" groups:idRef="R_EAR40x"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C14:0)" groups:idRef="R_EAR140y"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C14:1)" groups:idRef="R_3OAR141"/>
-          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C14:1)" groups:idRef="R_3HAD141"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C16:1)" groups:idRef="R_3OAR161"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C8:0)" groups:idRef="R_3OAS80"/>
-          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C12:0)" groups:idRef="R_AACPS7"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C10:0)" groups:idRef="R_EAR100y"/>
-          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA141ACPHi"/>
-          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA140ACPHi"/>
-          <groups:member groups:name="GDP-4-oxo-L-fucose reductase" groups:idRef="R_GOFUCR"/>
           <groups:member groups:name="DTDP-4-dehydrorhamnose 3,5-epimerase" groups:idRef="R_TDPDRE"/>
-          <groups:member groups:name="Fatty-acid-CoA thioesterase (octadecenoate)" groups:idRef="R_FACOAE181"/>
-          <groups:member groups:name="UTP-glucose-1-phosphate uridylyltransferase (irreversible)" groups:idRef="R_GALUi"/>
+          <groups:member groups:name="UDP-N-acetylglucosamine:undecaprenylphosphate N-acetylglucosamine -1-phosphate transferase" groups:idRef="R_ACGAMT"/>
+          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA160ACPHi"/>
+          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA141ACPHi"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C16:0)" groups:idRef="R_3OAS160"/>
           <groups:member groups:name="UDP-N-acetylglucosamine 2-epimerase" groups:idRef="R_UAG2E"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C18:0)" groups:idRef="R_3OAS180"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C16:0)" groups:idRef="R_3OAR160"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C10:0)" groups:idRef="R_3OAS100"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C10:0)" groups:idRef="R_EAR100x"/>
-          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C8:0)" groups:idRef="R_3HAD80"/>
-          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C18:1)" groups:idRef="R_AACPS5"/>
-          <groups:member groups:name="Fatty-acid-CoA ligase (tetradecenoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL141t2pp"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C12:0)" groups:idRef="R_EAR120y"/>
-          <groups:member groups:name="Fatty-acid-CoA thioesterase (octanoate)" groups:idRef="R_FACOAE80"/>
-          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA100ACPHi"/>
           <groups:member groups:name="?-D-xyloside xylohydrolase" groups:idRef="R_XYHDL"/>
-          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C14:1)" groups:idRef="R_AACPS2"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C18:1)" groups:idRef="R_EAR181y"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C12:1)" groups:idRef="R_EAR121x"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C8:0)" groups:idRef="R_EAR80y"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C18:0)" groups:idRef="R_3OAR180"/>
+          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C8:0)" groups:idRef="R_AACPS9"/>
+          <groups:member groups:name="Glutamine-fructose-6-phosphate transaminase" groups:idRef="R_GF6PTA"/>
+          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C18:0)" groups:idRef="R_3HAD180"/>
+          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C16:1)" groups:idRef="R_3HAD161"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C6:0)" groups:idRef="R_EAR60x"/>
+          <groups:member groups:name="Fatty-acid-CoA ligase (octadecenoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL181t2pp"/>
+          <groups:member groups:name="DTDP-4-dehydrorhamnose reductase" groups:idRef="R_TDPDRR"/>
           <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C4:0)" groups:idRef="R_3OAR40"/>
+          <groups:member groups:name="UDP-N-acetyl-D-mannosamine oxidoreductase" groups:idRef="R_UACMAMO"/>
+          <groups:member groups:name="UDP-N-acetylmuramoyl-L-alanine synthetase" groups:idRef="R_UAMAS"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C10:0)" groups:idRef="R_3OAR100"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C14:0)" groups:idRef="R_3OAS140"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C8:0)" groups:idRef="R_3OAS80"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C14:1)" groups:idRef="R_EAR141x"/>
+          <groups:member groups:name="Myo-inositol 1-phosphatase" groups:idRef="R_MI1PP"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C18:1)" groups:idRef="R_3OAR181"/>
+          <groups:member groups:name="GDP-4-oxo-L-fucose reductase" groups:idRef="R_GOFUCR"/>
+          <groups:member groups:name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase" groups:idRef="R_UAMAGS"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C14:1)" groups:idRef="R_3OAS141"/>
+          <groups:member groups:name="DTDP-N-4-acetamido-4,6-dideoxy-D-galactose transferase" groups:idRef="R_AADDGT"/>
+          <groups:member groups:name="Undecaprenyl-diphosphatase" groups:idRef="R_UDCPDP"/>
+          <groups:member groups:name="UDP-N-acetylenolpyruvoylglucosamine reductase" groups:idRef="R_UAPGR"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C12:1)" groups:idRef="R_3OAR121"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C12:1)" groups:idRef="R_EAR121x"/>
+          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA140ACPHi"/>
+          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C16:0)" groups:idRef="R_AACPS3"/>
+          <groups:member groups:name="DTDP-4-amino-4,6-dideoxy-D-glucose acetyltransferase" groups:idRef="R_TDPADGAT"/>
+          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C14:1)" groups:idRef="R_AACPS2"/>
+          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C10:0)" groups:idRef="R_AACPS8"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C10:0)" groups:idRef="R_EAR100y"/>
+          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA100ACPHi"/>
           <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C12:0)" groups:idRef="R_EAR120x"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C14:1)" groups:idRef="R_EAR141y"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C4:0)" groups:idRef="R_EAR40y"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C12:0)" groups:idRef="R_EAR120y"/>
+          <groups:member groups:name="Fatty-acid-CoA thioesterase (decanoate)" groups:idRef="R_FACOAE100"/>
+          <groups:member groups:name="Ethanolamine ammonia-lyase" groups:idRef="R_ETHAAL"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C12:1)" groups:idRef="R_3OAS121"/>
+          <groups:member groups:name="Fatty-acid-CoA thioesterase (octadecenoate)" groups:idRef="R_FACOAE181"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C12:0)" groups:idRef="R_3OAR120"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C14:0)" groups:idRef="R_3OAR140"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C6:0)" groups:idRef="R_3OAR60"/>
           <groups:member groups:name="Fatty-acid-CoA thioesterase (tetradecenoate)" groups:idRef="R_FACOAE141"/>
+          <groups:member groups:name="Fatty-acid-CoA ligase (tetradecenoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL141t2pp"/>
+          <groups:member groups:name="Fatty-acid-CoA ligase (hexanoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL60t2pp"/>
+          <groups:member groups:name="D-alanine-D-alanine ligase (reversible)" groups:idRef="R_ALAALAr"/>
+          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA80ACPHi"/>
+          <groups:member groups:name="UDP-N-acetylglucosamine diphosphorylase" groups:idRef="R_UAGDP"/>
+          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C12:0)" groups:idRef="R_AACPS7"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C12:1)" groups:idRef="R_EAR121y"/>
+          <groups:member groups:name="Fatty-acid-CoA ligase (tetradecanoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL140t2pp"/>
+          <groups:member groups:name="Phosphoglucosamine mutase" groups:idRef="R_PGAMT"/>
+          <groups:member groups:name="GDP-D-mannose dehydratase" groups:idRef="R_GMAND"/>
+          <groups:member groups:name="Glutamate racemase" groups:idRef="R_GLUR"/>
+          <groups:member groups:name="Glucosamine-1-phosphate N-acetyltransferase" groups:idRef="R_G1PACT"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C16:0)" groups:idRef="R_EAR160y"/>
+          <groups:member groups:name="UTP-glucose-1-phosphate uridylyltransferase (irreversible)" groups:idRef="R_GALUi"/>
+          <groups:member groups:name="Fatty-acid-CoA ligase (hexadecanoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL160t2pp"/>
+          <groups:member groups:name="Undecaprenyl-diphosphatase (periplasm)" groups:idRef="R_UDCPDPpp"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C4:0)" groups:idRef="R_EAR40x"/>
           <groups:member groups:name="Fatty-acid-CoA ligase (decanoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL100t2pp"/>
-          <groups:member groups:name="Glucose-1-phosphate thymidylyltransferase" groups:idRef="R_G1PTT"/>
-          <groups:member groups:name="Myo-inositol 1-phosphatase" groups:idRef="R_MI1PP"/>
+          <groups:member groups:name="GDP-mannose mannosyl hydrolase" groups:idRef="R_GDPMNH"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C16:1)" groups:idRef="R_3OAS161"/>
           <groups:member groups:name="UDPglucose 6-dehydrogenase" groups:idRef="R_UDPGD"/>
-          <groups:member groups:name="Undecaprenyl-diphosphatase" groups:idRef="R_UDCPDP"/>
-          <groups:member groups:name="Undecaprenyl-diphosphatase (periplasm)" groups:idRef="R_UDCPDPpp"/>
           <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C18:1)" groups:idRef="R_3OAS181"/>
-          <groups:member groups:name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase" groups:idRef="R_UAMAGS"/>
-          <groups:member groups:name="Fatty-acid-CoA thioesterase (hexadecenoate)" groups:idRef="R_FACOAE161"/>
           <groups:member groups:name="UDP-N-acetylglucosamine 1-carboxyvinyltransferase" groups:idRef="R_UAGCVT"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C14:1)" groups:idRef="R_3OAS141"/>
-          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C16:1)" groups:idRef="R_AACPS4"/>
-          <groups:member groups:name="Glutamate racemase" groups:idRef="R_GLUR"/>
-          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C16:0)" groups:idRef="R_AACPS3"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C6:0)" groups:idRef="R_EAR60x"/>
-          <groups:member groups:name="Fatty-acid-CoA ligase (hexanoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL60t2pp"/>
-          <groups:member groups:name="Glutamine-fructose-6-phosphate transaminase" groups:idRef="R_GF6PTA"/>
+          <groups:member groups:name="5-keto-4-deoxyuronate isomerase" groups:idRef="R_KDUI"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C8:0)" groups:idRef="R_EAR80x"/>
+          <groups:member groups:name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelate synthetase" groups:idRef="R_UAAGDS"/>
+          <groups:member groups:name="Fatty-acid-CoA thioesterase (octadecanoate)" groups:idRef="R_FACOAE180"/>
+          <groups:member groups:name="UDP-N-acetyl-D-mannosaminuronic acid transferase" groups:idRef="R_ACMAMUT"/>
+          <groups:member groups:name="Fatty-acid-CoA thioesterase (tetradecanoate)" groups:idRef="R_FACOAE140"/>
+          <groups:member groups:name="Fatty-acid-CoA ligase (octanoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL80t2pp"/>
           <groups:member groups:name="Trans-2-decenoyl-ACP isomerase" groups:idRef="R_T2DECAI"/>
-          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C16:1)" groups:idRef="R_3HAD161"/>
-          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C16:0)" groups:idRef="R_3HAD160"/>
-          <groups:member groups:name="DTDP-4-amino-4,6-dideoxy-D-glucose acetyltransferase" groups:idRef="R_TDPADGAT"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C14:0)" groups:idRef="R_EAR140x"/>
           <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C18:0)" groups:idRef="R_EAR180y"/>
-          <groups:member groups:name="5-keto-4-deoxyuronate isomerase" groups:idRef="R_KDUI"/>
-          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase (n-C14:0)" groups:idRef="R_AACPS1"/>
-          <groups:member groups:name="Fatty-acid-CoA ligase (octadecenoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL181t2pp"/>
+          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C4:0)" groups:idRef="R_3HAD40"/>
+          <groups:member groups:name="GDP-mannose phyrophosphatase" groups:idRef="R_GDPMNP"/>
+          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C18:1)" groups:idRef="R_3HAD181"/>
+          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C14:1)" groups:idRef="R_3HAD141"/>
+          <groups:member groups:name="Mannose-1-phosphate guanylyltransferase (GDP)" groups:idRef="R_MAN1PT2"/>
+          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C16:1)" groups:idRef="R_AACPS4"/>
+          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA161ACPHi"/>
+          <groups:member groups:name="UDPgalactopyranose mutase" groups:idRef="R_UDPGALM"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C16:0)" groups:idRef="R_3OAR160"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C10:0)" groups:idRef="R_3OAS100"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C18:1)" groups:idRef="R_EAR181y"/>
+          <groups:member groups:name="Glucose-1-phosphate thymidylyltransferase" groups:idRef="R_G1PTT"/>
           <groups:member groups:name="UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimeloyl-D-alanyl-D-alanine synthetase" groups:idRef="R_UGMDDS"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C6:0)" groups:idRef="R_3OAS60"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C16:1)" groups:idRef="R_EAR161y"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C18:0)" groups:idRef="R_3OAS180"/>
+          <groups:member groups:name="GDP-4-dehydro-6-deoxy-D-mannose epimerase" groups:idRef="R_GDMANE"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C8:0)" groups:idRef="R_EAR80y"/>
+          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C14:0)" groups:idRef="R_3HAD140"/>
+          <groups:member groups:name="DTDP-4-amino-4,6-dideoxy-D-glucose transaminase" groups:idRef="R_TDPAGTA"/>
           <groups:member groups:name="UDP-N-acetylglucosamine-N-acetylmuramyl-(pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase" groups:idRef="R_UAGPT3"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C16:0)" groups:idRef="R_3OAS160"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C14:1)" groups:idRef="R_EAR141x"/>
-          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA160ACPHi"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C16:1)" groups:idRef="R_EAR161x"/>
+          <groups:member groups:name="Phospho-N-acetylmuramoyl-pentapeptide-transferase (meso-2,6-diaminopimelate)" groups:idRef="R_PAPPT3"/>
+          <groups:member groups:name="Poly-?-1,6-N-acetyl-D-glucosamine synthase" groups:idRef="R_PUACGAMS"/>
+          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C16:0)" groups:idRef="R_3HAD160"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C6:0)" groups:idRef="R_EAR60y"/>
+          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C8:0)" groups:idRef="R_3HAD80"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C10:0)" groups:idRef="R_EAR100x"/>
           <groups:member groups:name="Fatty-acid-CoA ligase (octadecanoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL180t2pp"/>
+          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C6:0)" groups:idRef="R_3HAD60"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C16:1)" groups:idRef="R_3OAR161"/>
+          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C12:0)" groups:idRef="R_3HAD120"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C14:1)" groups:idRef="R_3OAR141"/>
           <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C8:0)" groups:idRef="R_3OAR80"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C12:0)" groups:idRef="R_3OAR120"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C16:1)" groups:idRef="R_EAR161y"/>
-          <groups:member groups:name="Mannose-1-phosphate guanylyltransferase (GDP)" groups:idRef="R_MAN1PT2"/>
+          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C10:0)" groups:idRef="R_3HAD100"/>
+          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C18:1)" groups:idRef="R_AACPS5"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C18:1)" groups:idRef="R_EAR181x"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C16:0)" groups:idRef="R_EAR160x"/>
           <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C12:0)" groups:idRef="R_3OAS120"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C16:1)" groups:idRef="R_EAR161x"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C8:0)" groups:idRef="R_EAR80x"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C6:0)" groups:idRef="R_EAR60y"/>
-          <groups:member groups:name="Ethanolamine ammonia-lyase" groups:idRef="R_ETHAAL"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C14:0)" groups:idRef="R_EAR140y"/>
           <groups:member groups:name="Fatty-acid-CoA ligase (hexadecenoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL161t2pp"/>
-          <groups:member groups:name="Fatty-acid-CoA thioesterase (tetradecanoate)" groups:idRef="R_FACOAE140"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C12:1)" groups:idRef="R_3OAR121"/>
-          <groups:member groups:name="UDP-N-acetylglucosamine diphosphorylase" groups:idRef="R_UAGDP"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C18:1)" groups:idRef="R_EAR181x"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C10:0)" groups:idRef="R_3OAR100"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C16:1)" groups:idRef="R_3OAS161"/>
-          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C10:0)" groups:idRef="R_AACPS8"/>
-          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA80ACPHi"/>
+          <groups:member groups:name="DTDPglucose 4,6-dehydratase" groups:idRef="R_TDPGDH"/>
+          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA120ACPHi"/>
+          <groups:member groups:name="3-hydroxyacyl-[acyl-carrier-protein] dehydratase (n-C12:1)" groups:idRef="R_3HAD121"/>
+          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C18:0)" groups:idRef="R_EAR180x"/>
           <groups:member groups:name="Fatty-acid-CoA thioesterase (hexadecanoate)" groups:idRef="R_FACOAE160"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C6:0)" groups:idRef="R_3OAR60"/>
-          <groups:member groups:name="Fatty-acid-CoA ligase (tetradecanoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL140t2pp"/>
-          <groups:member groups:name="UDP-N-acetylmuramoyl-L-alanine synthetase" groups:idRef="R_UAMAS"/>
-          <groups:member groups:name="Fatty-acyl-ACP hydrolase" groups:idRef="R_FA161ACPHi"/>
-          <groups:member groups:name="UDP-N-acetyl-D-mannosaminuronic acid transferase" groups:idRef="R_ACMAMUT"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C4:0)" groups:idRef="R_EAR40y"/>
-          <groups:member groups:name="UDP-N-acetylenolpyruvoylglucosamine reductase" groups:idRef="R_UAPGR"/>
-          <groups:member groups:name="Fatty-acid-CoA thioesterase (decanoate)" groups:idRef="R_FACOAE100"/>
-          <groups:member groups:name="Fatty-acid-CoA ligase (dodecanoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL120t2pp"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C14:0)" groups:idRef="R_3OAR140"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C14:1)" groups:idRef="R_EAR141y"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADH) (n-C16:0)" groups:idRef="R_EAR160x"/>
-          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] reductase (n-C18:0)" groups:idRef="R_3OAR180"/>
-          <groups:member groups:name="Enoyl-[acyl-carrier-protein] reductase (NADPH) (n-C16:0)" groups:idRef="R_EAR160y"/>
-          <groups:member groups:name="GDP-D-mannose dehydratase" groups:idRef="R_GMAND"/>
-          <groups:member groups:name="Glucosamine-1-phosphate N-acetyltransferase" groups:idRef="R_G1PACT"/>
-          <groups:member groups:name="Fatty-acid-CoA ligase (octanoate transport via vectoral Co-A coupling)" groups:idRef="R_FACOAL80t2pp"/>
+          <groups:member groups:name="Acyl-[acyl-carrier-protein] synthetase  (n-C18:0)" groups:idRef="R_AACPS6"/>
+          <groups:member groups:name="Fatty-acid-CoA thioesterase (hexadecenoate)" groups:idRef="R_FACOAE161"/>
+          <groups:member groups:name="3-oxoacyl-[acyl-carrier-protein] synthase (n-C6:0)" groups:idRef="R_3OAS60"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group7" sboTerm="SBO:0000633" groups:id="G_group7" groups:name="Citric Acid Cycle" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="Fumarate reductase" groups:idRef="R_FRD3"/>
-          <groups:member groups:name="Aconitase (half-reaction A, Citrate hydro-lyase)" groups:idRef="R_ACONTa"/>
-          <groups:member groups:name="Malate dehydrogenase (menaquinone 8 as acceptor)" groups:idRef="R_MDH3"/>
+          <groups:member groups:name="Isocitrate dehydrogenase (NADP)" groups:idRef="R_ICDHyr"/>
           <groups:member groups:name="Aconitase (half-reaction B, Isocitrate hydro-lyase)" groups:idRef="R_ACONTb"/>
+          <groups:member groups:name="2-Oxogluterate dehydrogenase" groups:idRef="R_AKGDH"/>
+          <groups:member groups:name="Fumarate reductase" groups:idRef="R_FRD3"/>
+          <groups:member groups:name="Malate oxidase" groups:idRef="R_MOX"/>
+          <groups:member groups:name="Succinyl-CoA synthetase (ADP-forming)" groups:idRef="R_SUCOAS"/>
+          <groups:member groups:name="Citrate lyase" groups:idRef="R_CITL"/>
           <groups:member groups:name="Malate dehydrogenase" groups:idRef="R_MDH"/>
+          <groups:member groups:name="Fumarase" groups:idRef="R_FUM"/>
           <groups:member groups:name="Fumarate reductase" groups:idRef="R_FRD2"/>
-          <groups:member groups:name="Isocitrate dehydrogenase (NADP)" groups:idRef="R_ICDHyr"/>
+          <groups:member groups:name="Aconitase (half-reaction A, Citrate hydro-lyase)" groups:idRef="R_ACONTa"/>
           <groups:member groups:name="Malate dehydrogenase (ubiquinone 8 as acceptor)" groups:idRef="R_MDH2"/>
-          <groups:member groups:name="Malate oxidase" groups:idRef="R_MOX"/>
-          <groups:member groups:name="Succinyl-CoA synthetase (ADP-forming)" groups:idRef="R_SUCOAS"/>
           <groups:member groups:name="Citrate synthase" groups:idRef="R_CS"/>
-          <groups:member groups:name="2-Oxogluterate dehydrogenase" groups:idRef="R_AKGDH"/>
-          <groups:member groups:name="Fumarase" groups:idRef="R_FUM"/>
-          <groups:member groups:name="Citrate lyase" groups:idRef="R_CITL"/>
+          <groups:member groups:name="Malate dehydrogenase (menaquinone 8 as acceptor)" groups:idRef="R_MDH3"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group8" sboTerm="SBO:0000633" groups:id="G_group8" groups:name="Cofactor and Prosthetic Group Biosynthesis" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="FMN adenylyltransferase" groups:idRef="R_FMNAT"/>
-          <groups:member groups:name="Uroporphyrinogen methyltransferase" groups:idRef="R_UPP3MT"/>
-          <groups:member groups:name="Erythronate 4-phosphate (4per) dehydrogenase" groups:idRef="R_PERD"/>
-          <groups:member groups:name="Diaminohydroxyphosphoribosylaminopryrimidine deaminase (25drapp)" groups:idRef="R_DHPPDA2"/>
-          <groups:member groups:name="ThDP adenylyl transferase" groups:idRef="R_ThDPAT"/>
           <groups:member groups:name="Uroporphyrinogen decarboxylase (uroporphyrinogen III)" groups:idRef="R_UPPDC1"/>
-          <groups:member groups:name="7-cyano-7-deazaguanine reductase" groups:idRef="R_CDGR"/>
+          <groups:member groups:name="Pimeloyl-[ACP] methyl ester esterase" groups:idRef="R_PMEACPE"/>
+          <groups:member groups:name="Diaminohydroxyphosphoribosylaminopryrimidine deaminase (25drapp)" groups:idRef="R_DHPPDA2"/>
+          <groups:member groups:name="Molybdopterin guanine dinucleotide synthase" groups:idRef="R_MOGDS"/>
+          <groups:member groups:name="5-amino-6-(5-phosphoribosylamino)uracil reductase" groups:idRef="R_APRAUR"/>
+          <groups:member groups:name="Molybdopterin cytidine dinucleotide synthase" groups:idRef="R_MOCDS"/>
+          <groups:member groups:name="Nicotinate-nucleotide diphosphorylase (carboxylating)" groups:idRef="R_NNDPR"/>
+          <groups:member groups:name="O-succinylbenzoate-CoA synthase" groups:idRef="R_SUCBZS"/>
+          <groups:member groups:name="Triphosphoribosyl-dephospho-CoA synthase" groups:idRef="R_TPRDCOAS"/>
+          <groups:member groups:name="5&apos;-deoxyadenosine nuclosidase" groups:idRef="R_5DOAN"/>
+          <groups:member groups:name="Guanosine-5&apos;-triphosphate,3&apos;-diphosphate diphosphatase" groups:idRef="R_GTPDPDP"/>
+          <groups:member groups:name="Riboflavin kinase" groups:idRef="R_RBFK"/>
+          <groups:member groups:name="SUF [2Fe-2S] Synthesis II" groups:idRef="R_S2FE2SS2"/>
           <groups:member groups:name="2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase" groups:idRef="R_DHBD"/>
-          <groups:member groups:name="3-methyl-2-oxobutanoate hydroxymethyltransferase" groups:idRef="R_MOHMT"/>
-          <groups:member groups:name="Biotin sulfoxide reductase" groups:idRef="R_BSORx"/>
-          <groups:member groups:name="4-amino-2-methyl-5-phosphomethylpyrimidine synthetase" groups:idRef="R_AMPMS2"/>
+          <groups:member groups:name="2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase" groups:idRef="R_SEPHCHCS"/>
+          <groups:member groups:name="NAD diphosphatase" groups:idRef="R_NADDP"/>
+          <groups:member groups:name="Alpha-ribazole 5-phosphate phosphatase" groups:idRef="R_RZ5PP"/>
           <groups:member groups:name="Dephospho-CoA kinase" groups:idRef="R_DPCOAK"/>
-          <groups:member groups:name="Tungsten bispterin guanine dinucleotide synthase" groups:idRef="R_BWCOGDS2"/>
-          <groups:member groups:name="Pyridoxine kinase" groups:idRef="R_PYDXNK"/>
-          <groups:member groups:name="Octanoate non-lipoylated apo domain ligase" groups:idRef="R_OCTNLL"/>
-          <groups:member groups:name="Tyrosine lyase" groups:idRef="R_TYRL"/>
-          <groups:member groups:name="Hydroxymethylpyrimidine kinase (ATP)" groups:idRef="R_HMPK1"/>
-          <groups:member groups:name="NAD synthase (nh3)" groups:idRef="R_NADS1"/>
-          <groups:member groups:name="Thiamin pyrophosphatase" groups:idRef="R_TDP"/>
+          <groups:member groups:name="Phosphopantothenoylcysteine decarboxylase" groups:idRef="R_PPCDC"/>
+          <groups:member groups:name="D-alanine transaminase" groups:idRef="R_ALATA_D2"/>
+          <groups:member groups:name="2-succinyl-6-hydroxy-2,4-cyclohexadiene 1-carboxylate synthase" groups:idRef="R_SHCHCS3"/>
+          <groups:member groups:name="ThDP adenylyl transferase" groups:idRef="R_ThDPAT"/>
+          <groups:member groups:name="S-Formylglutathione hydralase" groups:idRef="R_SFGTHi"/>
+          <groups:member groups:name="Adenosyl cobinamide phosphate guanyltransferase" groups:idRef="R_ACBIPGT"/>
+          <groups:member groups:name="Alanine transaminase" groups:idRef="R_ALATA_L2"/>
+          <groups:member groups:name="7-cyano-7-deazaguanine reductase" groups:idRef="R_CDGR"/>
           <groups:member groups:name="2,3-dihydroxybenzoate adenylate synthase" groups:idRef="R_DHBS"/>
-          <groups:member groups:name="Riboflavin kinase" groups:idRef="R_RBFK"/>
+          <groups:member groups:name="Molybdopterin adenylyltransferase" groups:idRef="R_MPTAT"/>
+          <groups:member groups:name="Pantothenate kinase" groups:idRef="R_PNTK"/>
+          <groups:member groups:name="Undecaprenyl diphosphate synthase" groups:idRef="R_UDCPDPS"/>
+          <groups:member groups:name="Thiamin pyrophosphatase" groups:idRef="R_TDP"/>
           <groups:member groups:name="Carboxy-S-adenosyl-L-methionine synthase" groups:idRef="R_CXSAMS"/>
-          <groups:member groups:name="6-hydroxymethyl-dihydropterin pyrophosphokinase" groups:idRef="R_HPPK2"/>
+          <groups:member groups:name="NAD kinase" groups:idRef="R_NADK"/>
+          <groups:member groups:name="1,4-dihydroxy-2-naphthoate octaprenyltransferase" groups:idRef="R_DHNAOT4"/>
+          <groups:member groups:name="3,4-Dihydroxy-2-butanone-4-phosphate synthase" groups:idRef="R_DB4PS"/>
+          <groups:member groups:name="Dimethylallyltranstransferase" groups:idRef="R_DMATT"/>
           <groups:member groups:name="2-dehydropantoate 2-reductase" groups:idRef="R_DPR"/>
-          <groups:member groups:name="NAD nucleosidase" groups:idRef="R_NADN"/>
+          <groups:member groups:name="Hydroxymethylpyrimidine kinase (ATP)" groups:idRef="R_HMPK1"/>
           <groups:member groups:name="Octaprenyl pyrophosphate synthase" groups:idRef="R_OCTDPS"/>
-          <groups:member groups:name="2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase" groups:idRef="R_MEPCT"/>
+          <groups:member groups:name="Acid phosphatase (FMN)" groups:idRef="R_ACP1_FMN"/>
+          <groups:member groups:name="Hydroxymethylbilane synthase" groups:idRef="R_HMBS"/>
+          <groups:member groups:name="Molybdenum cofactor synthase" groups:idRef="R_MOCOS"/>
           <groups:member groups:name="2-Octaprenyl-6-methoxy-benzoquinol methylase" groups:idRef="R_OMBZLM"/>
-          <groups:member groups:name="Dihydroneopterin triphosphate 2&apos;-epimerase" groups:idRef="R_DHPTPE"/>
-          <groups:member groups:name="Thiamine-phosphate kinase" groups:idRef="R_TMPK"/>
-          <groups:member groups:name="Iron-sulfur cluster repair" groups:idRef="R_FESR"/>
-          <groups:member groups:name="Uroporphyrinogen-III synthase" groups:idRef="R_UPP3S"/>
-          <groups:member groups:name="Isochorismate synthase" groups:idRef="R_ICHORS_copy1"/>
-          <groups:member groups:name="Sirohydrochlorin dehydrogenase (NAD)" groups:idRef="R_SHCHD2"/>
-          <groups:member groups:name="Thiamine kinase" groups:idRef="R_TMK"/>
-          <groups:member groups:name="Gamma-glutamylcysteine synthetase" groups:idRef="R_GLUCYS"/>
-          <groups:member groups:name="Adenosyl cobinamide phosphate guanyltransferase" groups:idRef="R_ACBIPGT"/>
-          <groups:member groups:name="Adenosylcobalamin 5&apos;-phosphate synthase" groups:idRef="R_ADOCBLS"/>
-          <groups:member groups:name="1,4-dihydroxy-2-napthoyl-CoA thioesterase" groups:idRef="R_DHNCOAT"/>
-          <groups:member groups:name="Acid phosphatase (FMN)" groups:idRef="R_ACP1p"/>
-          <groups:member groups:name="Enoylpimeloyl-[ACP] methyl ester reductase" groups:idRef="R_EPMEACPR"/>
-          <groups:member groups:name="Isochorismatase" groups:idRef="R_ICHORT"/>
-          <groups:member groups:name="Tungsten bispterin cofactor synthase" groups:idRef="R_BWCOS"/>
-          <groups:member groups:name="Coproporphyrinogen oxidase (O2 required)" groups:idRef="R_CPPPGO"/>
-          <groups:member groups:name="Dihydrofolate synthase" groups:idRef="R_DHFS"/>
-          <groups:member groups:name="Acyl-carrier protein synthase" groups:idRef="R_ACPS1"/>
-          <groups:member groups:name="Octaprenyl-hydroxybenzoate decarboxylase" groups:idRef="R_OPHBDC"/>
           <groups:member groups:name="Quinolinate synthase" groups:idRef="R_QULNS"/>
-          <groups:member groups:name="Alanine transaminase" groups:idRef="R_ALATA_L2"/>
-          <groups:member groups:name="Nicotinamide-nucleotide amidase" groups:idRef="R_NMNDA"/>
-          <groups:member groups:name="O-succinylbenzoate-CoA ligase" groups:idRef="R_SUCBZL"/>
-          <groups:member groups:name="Thiamine-phosphate diphosphorylase" groups:idRef="R_TMPPP"/>
+          <groups:member groups:name="SUF [4Fe-4S] Transfer" groups:idRef="R_S4FE4ST"/>
+          <groups:member groups:name="ISC [2Fe-2S] regeneration" groups:idRef="R_I2FE2SR"/>
+          <groups:member groups:name="MoaD sulfuration (nadh, assumed)" groups:idRef="R_MOADSUx"/>
+          <groups:member groups:name="Biotin sulfoxide reductase" groups:idRef="R_BSORy"/>
+          <groups:member groups:name="3-Oxo-pimeloyl-[ACP] methyl ester reductase" groups:idRef="R_OPMEACPR"/>
+          <groups:member groups:name="SUF [4Fe-4S] Reduction" groups:idRef="R_S4FE4SR"/>
+          <groups:member groups:name="Acyl-carrier protein synthase" groups:idRef="R_ACPS1"/>
+          <groups:member groups:name="Glutathione oxidoreductase" groups:idRef="R_GTHOr"/>
+          <groups:member groups:name="6-hydroxymethyl-dihydropterin pyrophosphokinase" groups:idRef="R_HPPK2"/>
+          <groups:member groups:name="Flavin reductase (NAD)" groups:idRef="R_FLVRx"/>
           <groups:member groups:name="Tungsten pterin cofactor synthase" groups:idRef="R_WCOS"/>
-          <groups:member groups:name="5-amino-6-(5-phosphoribosylamino)uracil reductase" groups:idRef="R_APRAUR"/>
-          <groups:member groups:name="Cobinamide adenyltransferase" groups:idRef="R_CBIAT"/>
-          <groups:member groups:name="Pyridoxal kinase" groups:idRef="R_PYDXK"/>
+          <groups:member groups:name="Aspartate 1-decarboxylase" groups:idRef="R_ASP1DC"/>
+          <groups:member groups:name="Formaldehyde dehydrogenase" groups:idRef="R_FALDH2"/>
+          <groups:member groups:name="3-Oxo-pimeloyl-[ACP] methyl ester synthase" groups:idRef="R_OPMEACPS"/>
+          <groups:member groups:name="FMN adenylyltransferase" groups:idRef="R_FMNAT"/>
+          <groups:member groups:name="Sirohydrochlorin ferrochelatase" groups:idRef="R_SHCHF"/>
+          <groups:member groups:name="Uroporphyrinogen-III synthase" groups:idRef="R_UPP3S"/>
+          <groups:member groups:name="SUF [2Fe-2S] Synthesis" groups:idRef="R_S2FE2SS"/>
+          <groups:member groups:name="FAD reductase" groups:idRef="R_FADRx2"/>
+          <groups:member groups:name="Acid phosphatase (FMN)" groups:idRef="R_ACP1p"/>
           <groups:member groups:name="4-(cytidine 5&apos;-diphospho)-2-C-methyl-D-erythritol kinase" groups:idRef="R_CDPMEK"/>
-          <groups:member groups:name="SUF [2Fe-2S] Transfer" groups:idRef="R_S2FE2ST"/>
-          <groups:member groups:name="GTP cyclohydrolase I" groups:idRef="R_GTPCI"/>
-          <groups:member groups:name="Hydroxymethylbilane synthase" groups:idRef="R_HMBS"/>
+          <groups:member groups:name="Flavin reductase" groups:idRef="R_FLVR"/>
+          <groups:member groups:name="ISC [2Fe-2S] Synthesis II" groups:idRef="R_I2FE2SS2"/>
+          <groups:member groups:name="Pyridoxine 5&apos;-phosphate oxidase (anaerboic" groups:idRef="R_PDX5PO2"/>
           <groups:member groups:name="2,3-dihydroxybenzoylserine hydrolase" groups:idRef="R_DHBSH"/>
           <groups:member groups:name="Dihydroneopterin aldolase reversible" groups:idRef="R_DHNPA2r"/>
-          <groups:member groups:name="Flavin reductase (NAD)" groups:idRef="R_FLVRx"/>
-          <groups:member groups:name="GDP diphosphokinase" groups:idRef="R_GDPDPK"/>
-          <groups:member groups:name="Guanosine 3&apos;-diphosphate 5&apos;-triphosphate 3&apos;-diphosphatase" groups:idRef="R_GDPTPDP"/>
-          <groups:member groups:name="Pyridoxamine kinase" groups:idRef="R_PYDAMK"/>
-          <groups:member groups:name="ISC [2Fe-2S] regeneration" groups:idRef="R_I2FE2SR"/>
-          <groups:member groups:name="2-octaprenyl-6-methoxyphenol hydroxylase (NADPH)" groups:idRef="R_OMPHHXy"/>
-          <groups:member groups:name="Cyclic pyranopterin monophosphate synthase" groups:idRef="R_CPMPS"/>
-          <groups:member groups:name="FAD reductase" groups:idRef="R_FADRx"/>
-          <groups:member groups:name="GTP cyclohydrolase II (25drapp)" groups:idRef="R_GTPCII2"/>
-          <groups:member groups:name="P-aminobenzoyl-glutamate hydrolase" groups:idRef="R_4ABZGLUH"/>
-          <groups:member groups:name="Flavin reductase" groups:idRef="R_FLVR"/>
-          <groups:member groups:name="2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphatase" groups:idRef="R_2MAHMP"/>
-          <groups:member groups:name="Guanosine-5&apos;-triphosphate,3&apos;-diphosphate diphosphatase" groups:idRef="R_GTPDPDP"/>
-          <groups:member groups:name="ISC [4Fe-4S] Reduction" groups:idRef="R_I4FE4SR"/>
-          <groups:member groups:name="Protoporphyrinogen oxidase (anaerobic)" groups:idRef="R_PPPGO3"/>
-          <groups:member groups:name="7-cyano-7-carbaguanine synthase" groups:idRef="R_CCGS"/>
-          <groups:member groups:name="FAD reductase" groups:idRef="R_FADRx2"/>
-          <groups:member groups:name="Acid phosphatase (FMN)" groups:idRef="R_ACP1_FMN"/>
-          <groups:member groups:name="Fe(III) reduction" groups:idRef="R_FE3Ri"/>
-          <groups:member groups:name="Hydroxybenzoate octaprenyltransferase" groups:idRef="R_HBZOPT"/>
-          <groups:member groups:name="Lipoyl(octanoyl) transferase" groups:idRef="R_LIPOCT"/>
-          <groups:member groups:name="2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase" groups:idRef="R_MECDPS"/>
-          <groups:member groups:name="2-succinyl-6-hydroxy-2,4-cyclohexadiene 1-carboxylate synthase" groups:idRef="R_SHCHCS3"/>
-          <groups:member groups:name="Dihydroneopterin triphosphate pyrophosphatase" groups:idRef="R_DNTPPA"/>
-          <groups:member groups:name="NAD diphosphatase" groups:idRef="R_NADDP"/>
-          <groups:member groups:name="Nicotinamidase" groups:idRef="R_NNAM"/>
-          <groups:member groups:name="Dihydromonapterin reductase" groups:idRef="R_DHMPTR"/>
+          <groups:member groups:name="7-deaza-7-carboxyguanine synthase" groups:idRef="R_CDGS"/>
+          <groups:member groups:name="ISC [2Fe-2S] Synthesis" groups:idRef="R_I2FE2SS"/>
           <groups:member groups:name="Pyridoxine 5-phosphate phosphatase" groups:idRef="R_PDXPP"/>
-          <groups:member groups:name="Pyridoxal 5-phosphate phosphatase" groups:idRef="R_PYDXPP"/>
-          <groups:member groups:name="Bis-molybdopterin guanine dinucleotide synthase (single GDP)" groups:idRef="R_BMOGDS1"/>
-          <groups:member groups:name="Oxygen Independent coproporphyrinogen-III oxidase" groups:idRef="R_CPPPGO2"/>
-          <groups:member groups:name="Guanosine-3&apos;,5&apos;-bis(diphosphate) 3&apos;-diphosphatase" groups:idRef="R_PPGPPDP"/>
-          <groups:member groups:name="Aspartate 1-decarboxylase" groups:idRef="R_ASP1DC"/>
-          <groups:member groups:name="Bis-molybdenum cofactor synthase" groups:idRef="R_BMOCOS"/>
-          <groups:member groups:name="2-Octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase (NADPHl)" groups:idRef="R_OMMBLHXy"/>
-          <groups:member groups:name="Enterochelin synthase" groups:idRef="R_ENTCS"/>
-          <groups:member groups:name="Ferrochelatase" groups:idRef="R_FCLT"/>
-          <groups:member groups:name="Geranyltranstransferase" groups:idRef="R_GRTT"/>
-          <groups:member groups:name="Dihydropteroate synthase" groups:idRef="R_DHPS2"/>
-          <groups:member groups:name="Enoylglutaryl-[ACP] methyl ester reductase" groups:idRef="R_EGMEACPR"/>
-          <groups:member groups:name="Dihydroneopterin monophosphate dephosphorylase" groups:idRef="R_DNMPPA"/>
-          <groups:member groups:name="6-carboxy-5,6,7,8-tetrahydropterin synthase" groups:idRef="R_CPH4S"/>
-          <groups:member groups:name="D-alanine transaminase" groups:idRef="R_ALATA_D2"/>
-          <groups:member groups:name="Biotin sulfoxide reductase" groups:idRef="R_BSORy"/>
-          <groups:member groups:name="GTP diphosphokinase" groups:idRef="R_GTPDPK"/>
+          <groups:member groups:name="Pyridoxal kinase" groups:idRef="R_PYDXK"/>
+          <groups:member groups:name="Dihydrofolate reductase" groups:idRef="R_DHFR"/>
           <groups:member groups:name="ISC [4Fe-4S] Transfer" groups:idRef="R_I4FE4ST"/>
-          <groups:member groups:name="Isochorismate synthase" groups:idRef="R_ICHORS_copy2"/>
-          <groups:member groups:name="NMN nucleosidase" groups:idRef="R_NMNN"/>
-          <groups:member groups:name="2-Octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase (anaerobic)" groups:idRef="R_OMMBLHX3"/>
-          <groups:member groups:name="Porphobilinogen synthase" groups:idRef="R_PPBNGS"/>
-          <groups:member groups:name="Pyridoxine 5&apos;-phosphate oxidase" groups:idRef="R_PDX5POi"/>
-          <groups:member groups:name="2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase" groups:idRef="R_SEPHCHCS"/>
-          <groups:member groups:name="Pimeloyl-[ACP] methyl ester esterase" groups:idRef="R_PMEACPE"/>
-          <groups:member groups:name="SUF [2Fe-2S] Synthesis II" groups:idRef="R_S2FE2SS2"/>
-          <groups:member groups:name="Protoporphyrinogen oxidase (aerobic)" groups:idRef="R_PPPGO"/>
-          <groups:member groups:name="L-aspartate oxidase" groups:idRef="R_ASPO5"/>
+          <groups:member groups:name="2-Octaprenylphenol hydroxylase (anaerobic)" groups:idRef="R_OPHHX3"/>
+          <groups:member groups:name="L-aspartate oxidase" groups:idRef="R_ASPO3"/>
+          <groups:member groups:name="Tungsten bispterin guanine dinucleotide synthase (single GDP)" groups:idRef="R_BWCOGDS1"/>
+          <groups:member groups:name="Formaldehyde glutathione ligase (spontaneous)" groups:idRef="R_FALGTHLs"/>
+          <groups:member groups:name="Hypothetical enyme" groups:idRef="R_HYPOE"/>
+          <groups:member groups:name="Lipoyl(octanoyl) transferase" groups:idRef="R_LIPOCT"/>
+          <groups:member groups:name="2-octaprenyl-6-methoxyphenol hydroxylase (NADPH)" groups:idRef="R_OMPHHXy"/>
+          <groups:member groups:name="Dethiobiotin synthase" groups:idRef="R_DBTS"/>
+          <groups:member groups:name="2C-methyl-D-erythritol 2,4 cyclodiphosphate dehydratase" groups:idRef="R_MECDPDH5"/>
+          <groups:member groups:name="NADP phosphatase" groups:idRef="R_NADPPPS"/>
+          <groups:member groups:name="Nicotinamidase" groups:idRef="R_NNAM"/>
+          <groups:member groups:name="3-Oxo-glutaryl-[ACP] methyl ester dehydratase" groups:idRef="R_OGMEACPD"/>
+          <groups:member groups:name="3-Oxo-glutaryl-[ACP] methyl ester synthase" groups:idRef="R_OGMEACPS"/>
+          <groups:member groups:name="Enoylpimeloyl-[ACP] methyl ester reductase" groups:idRef="R_EPMEACPR"/>
+          <groups:member groups:name="L-aspartate oxidase" groups:idRef="R_ASPO4"/>
+          <groups:member groups:name="2-Octaprenylphenol hydroxylase (NADPH)" groups:idRef="R_OPHHXy"/>
+          <groups:member groups:name="Adenosyl cobinamide kinase" groups:idRef="R_ADOCBIK"/>
+          <groups:member groups:name="Heme O synthase" groups:idRef="R_HEMEOS"/>
+          <groups:member groups:name="3-methyl-2-oxobutanoate hydroxymethyltransferase" groups:idRef="R_MOHMT"/>
+          <groups:member groups:name="Biotin synthase" groups:idRef="R_BTS5"/>
+          <groups:member groups:name="Chorismate pyruvate lyase" groups:idRef="R_CHRPL"/>
+          <groups:member groups:name="Enoylglutaryl-[ACP] methyl ester reductase" groups:idRef="R_EGMEACPR"/>
+          <groups:member groups:name="8-amino-7-oxononanoate synthase" groups:idRef="R_AOXSr2"/>
+          <groups:member groups:name="Iron-sulfur cluster damage (peroxide, spontaneous)" groups:idRef="R_FESD1s"/>
+          <groups:member groups:name="Octanoate non-lipoylated apo domain ligase" groups:idRef="R_OCTNLL"/>
+          <groups:member groups:name="2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase" groups:idRef="R_MECDPS"/>
+          <groups:member groups:name="NAD synthase (nh3)" groups:idRef="R_NADS1"/>
+          <groups:member groups:name="3-Oxo-glutaryl-[ACP] methyl ester reductase" groups:idRef="R_OGMEACPR"/>
+          <groups:member groups:name="FAD reductase" groups:idRef="R_FADRx"/>
+          <groups:member groups:name="6-carboxy-5,6,7,8-tetrahydropterin synthase" groups:idRef="R_CPH4S"/>
+          <groups:member groups:name="3-Oxo-pimeloyl-[ACP] methyl ester dehydratase" groups:idRef="R_OPMEACPD"/>
+          <groups:member groups:name="Guanosine-3&apos;,5&apos;-bis(diphosphate) 3&apos;-diphosphatase" groups:idRef="R_PPGPPDP"/>
+          <groups:member groups:name="Pyridoxal 5-phosphate phosphatase" groups:idRef="R_PYDXPP"/>
+          <groups:member groups:name="O-succinylbenzoate-CoA ligase" groups:idRef="R_SUCBZL"/>
+          <groups:member groups:name="Dihydropteroate synthase" groups:idRef="R_DHPS2"/>
+          <groups:member groups:name="Cyclic pyranopterin monophosphate synthase" groups:idRef="R_CPMPS"/>
+          <groups:member groups:name="Thiamine-phosphate diphosphorylase" groups:idRef="R_TMPPP"/>
+          <groups:member groups:name="Pyridoxamine kinase" groups:idRef="R_PYDAMK"/>
           <groups:member groups:name="Glutamyl-tRNA reductase" groups:idRef="R_GLUTRR"/>
-          <groups:member groups:name="Thiazole phosphate synthesis" groups:idRef="R_THZPSN3"/>
-          <groups:member groups:name="1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (ipdp)" groups:idRef="R_IPDPS"/>
-          <groups:member groups:name="SUF Cysteine desulfuration" groups:idRef="R_SCYSDS"/>
-          <groups:member groups:name="Pyrimidine phosphatase" groups:idRef="R_PMDPHT"/>
-          <groups:member groups:name="Phosphopantothenoylcysteine decarboxylase" groups:idRef="R_PPCDC"/>
-          <groups:member groups:name="O-succinylbenzoate-CoA synthase" groups:idRef="R_SUCBZS"/>
-          <groups:member groups:name="4-aminobenzoate synthase" groups:idRef="R_ADCL"/>
+          <groups:member groups:name="3-Dimethylubiquinonol 3-methyltransferase" groups:idRef="R_DMQMT"/>
+          <groups:member groups:name="O-Phospho-4-hydroxy-L-threonine:2-oxoglutarate aminotransferase" groups:idRef="R_OHPBAT"/>
+          <groups:member groups:name="Dihydroneopterin triphosphate pyrophosphatase" groups:idRef="R_DNTPPA"/>
+          <groups:member groups:name="Riboflavin synthase" groups:idRef="R_RBFSb"/>
+          <groups:member groups:name="ISC [4Fe-4S] Reduction" groups:idRef="R_I4FE4SR"/>
+          <groups:member groups:name="Erythrose 4-phosphate dehydrogenase" groups:idRef="R_E4PD"/>
           <groups:member groups:name="Cob(I)alamin adenosyltransferase" groups:idRef="R_CBLAT"/>
+          <groups:member groups:name="Iron-sulfur cluster damage (nitrous oxide, spontaneous)" groups:idRef="R_FESD2s"/>
+          <groups:member groups:name="FMN reductase" groups:idRef="R_FMNRx2"/>
+          <groups:member groups:name="L-aspartate oxidase" groups:idRef="R_ASPO6"/>
+          <groups:member groups:name="Molybdopterin synthase" groups:idRef="R_MPTS"/>
           <groups:member groups:name="1-deoxy-D-xylulose 5-phosphate synthase" groups:idRef="R_DXPS"/>
+          <groups:member groups:name="ISC [2Fe-2S] Transfer" groups:idRef="R_I2FE2ST"/>
+          <groups:member groups:name="Isochorismate synthase" groups:idRef="R_ICHORS_copy2"/>
+          <groups:member groups:name="Isochorismatase" groups:idRef="R_ICHORT"/>
+          <groups:member groups:name="Uroporphyrinogen methyltransferase" groups:idRef="R_UPP3MT"/>
+          <groups:member groups:name="Dihydroneopterin triphosphate 2&apos;-epimerase" groups:idRef="R_DHPTPE"/>
+          <groups:member groups:name="Glutathione hydralase (periplasmic)" groups:idRef="R_GTHRDHpp"/>
+          <groups:member groups:name="1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (ipdp)" groups:idRef="R_IPDPS"/>
+          <groups:member groups:name="Biotin sulfoxide reductase" groups:idRef="R_BSORx"/>
+          <groups:member groups:name="Ferrochelatase" groups:idRef="R_FCLT"/>
+          <groups:member groups:name="GTP cyclohydrolase II (25drapp)" groups:idRef="R_GTPCII2"/>
+          <groups:member groups:name="Tungsten bispterin cofactor synthase" groups:idRef="R_BWCOS"/>
+          <groups:member groups:name="Hydroxyethylthiazole kinase" groups:idRef="R_HETZK"/>
+          <groups:member groups:name="Protoporphyrinogen oxidase (anaerobic)" groups:idRef="R_PPPGO3"/>
+          <groups:member groups:name="Pyridoxine kinase" groups:idRef="R_PYDXNK"/>
+          <groups:member groups:name="Riboflavin synthase" groups:idRef="R_RBFSa"/>
           <groups:member groups:name="Pyridoxine 5&apos;-phosphate synthase" groups:idRef="R_PDX5PS"/>
+          <groups:member groups:name="SUF [2Fe-2S] Transfer" groups:idRef="R_S2FE2ST"/>
+          <groups:member groups:name="Coproporphyrinogen oxidase (O2 required)" groups:idRef="R_CPPPGO"/>
           <groups:member groups:name="Glutathione synthetase" groups:idRef="R_GTHS"/>
-          <groups:member groups:name="S-Formylglutathione hydralase" groups:idRef="R_SFGTHi"/>
-          <groups:member groups:name="4-amino-4-deoxychorismate synthase" groups:idRef="R_ADCS"/>
-          <groups:member groups:name="S-adenosylmethione:2-demthylmenaquinole methyltransferase (menaquinone 8)" groups:idRef="R_AMMQLT8"/>
-          <groups:member groups:name="Triphosphoribosyl-dephospho-CoA synthase" groups:idRef="R_TPRDCOAS"/>
           <groups:member groups:name="Nicotinamide-nucleotide adenylyltransferase" groups:idRef="R_NMNAT"/>
-          <groups:member groups:name="3-Oxo-pimeloyl-[ACP] methyl ester dehydratase" groups:idRef="R_OPMEACPD"/>
-          <groups:member groups:name="MoaD sulfuration (nadh, assumed)" groups:idRef="R_MOADSUx"/>
-          <groups:member groups:name="8-amino-7-oxononanoate synthase" groups:idRef="R_AOXSr2"/>
-          <groups:member groups:name="Glutamate-1-semialdehyde aminotransferase" groups:idRef="R_G1SAT"/>
-          <groups:member groups:name="Glutathione hydralase (periplasmic)" groups:idRef="R_GTHRDHpp"/>
-          <groups:member groups:name="Biotin synthase" groups:idRef="R_BTS5"/>
-          <groups:member groups:name="ISC [2Fe-2S] Synthesis" groups:idRef="R_I2FE2SS"/>
+          <groups:member groups:name="Dihydromonapterin reductase" groups:idRef="R_DHMPTR"/>
+          <groups:member groups:name="2-Octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase (anaerobic)" groups:idRef="R_OMMBLHX3"/>
+          <groups:member groups:name="Protoporphyrinogen oxidase (aerobic)" groups:idRef="R_PPPGO"/>
+          <groups:member groups:name="Octaprenyl-hydroxybenzoate decarboxylase" groups:idRef="R_OPHBDC"/>
+          <groups:member groups:name="1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (dmpp)" groups:idRef="R_DMPPS"/>
+          <groups:member groups:name="Gamma-glutamylcysteine synthetase" groups:idRef="R_GLUCYS"/>
+          <groups:member groups:name="Iron-sulfur cluster repair" groups:idRef="R_FESR"/>
+          <groups:member groups:name="NAD nucleosidase" groups:idRef="R_NADN"/>
           <groups:member groups:name="2-octaprenyl-6-hydroxyphenol methylase" groups:idRef="R_OHPHM"/>
-          <groups:member groups:name="Dihydroneopterin epimerase" groups:idRef="R_DHNPTE"/>
           <groups:member groups:name="SUF [2Fe-2S] regeneration" groups:idRef="R_S2FE2SR"/>
-          <groups:member groups:name="Sirohydrochlorin ferrochelatase" groups:idRef="R_SHCHF"/>
-          <groups:member groups:name="L-aspartate oxidase" groups:idRef="R_ASPO6"/>
-          <groups:member groups:name="1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase (dmpp)" groups:idRef="R_DMPPS"/>
-          <groups:member groups:name="ISC [2Fe-2S] Transfer" groups:idRef="R_I2FE2ST"/>
-          <groups:member groups:name="SUF [4Fe-4S] Reduction" groups:idRef="R_S4FE4SR"/>
-          <groups:member groups:name="ISC [2Fe-2S] Synthesis II" groups:idRef="R_I2FE2SS2"/>
-          <groups:member groups:name="Nicotinic acid mononucleotide pyrophosphorylase" groups:idRef="R_NAMNPP"/>
-          <groups:member groups:name="Phosphomethylpyrimidine kinase" groups:idRef="R_PMPK"/>
+          <groups:member groups:name="Adenosylcobalamin 5&apos;-phosphate synthase" groups:idRef="R_ADOCBLS"/>
+          <groups:member groups:name="Thiamine-phosphate kinase" groups:idRef="R_TMPK"/>
+          <groups:member groups:name="1,4-dihydroxy-2-napthoyl-CoA thioesterase" groups:idRef="R_DHNCOAT"/>
+          <groups:member groups:name="Glutamate-1-semialdehyde aminotransferase" groups:idRef="R_G1SAT"/>
+          <groups:member groups:name="Isopentenyl-diphosphate D-isomerase" groups:idRef="R_IPDDI"/>
+          <groups:member groups:name="FMN reductase" groups:idRef="R_FMNRx"/>
+          <groups:member groups:name="GDP diphosphokinase" groups:idRef="R_GDPDPK"/>
+          <groups:member groups:name="Hydroxybenzoate octaprenyltransferase" groups:idRef="R_HBZOPT"/>
           <groups:member groups:name="Nicotinate-nucleotide dimethylbenzimidazole phosphoribosyltransferase" groups:idRef="R_NNDMBRT"/>
-          <groups:member groups:name="Heme O synthase" groups:idRef="R_HEMEOS"/>
-          <groups:member groups:name="Lipoate synthase" groups:idRef="R_LIPOS"/>
-          <groups:member groups:name="Malonyl-CoA methyltransferase" groups:idRef="R_MALCOAMT"/>
-          <groups:member groups:name="Tungsten bispterin guanine dinucleotide synthase (single GDP)" groups:idRef="R_BWCOGDS1"/>
-          <groups:member groups:name="Erythrose 4-phosphate dehydrogenase" groups:idRef="R_E4PD"/>
-          <groups:member groups:name="Glutathione oxidoreductase" groups:idRef="R_GTHOr"/>
-          <groups:member groups:name="Hydroxyethylthiazole kinase" groups:idRef="R_HETZK"/>
-          <groups:member groups:name="Alpha-ribazole 5-phosphate phosphatase" groups:idRef="R_RZ5PP"/>
-          <groups:member groups:name="Pyridoxamine 5&apos;-phosphate oxidase" groups:idRef="R_PYAM5PO"/>
-          <groups:member groups:name="Dethiobiotin synthase" groups:idRef="R_DBTS"/>
-          <groups:member groups:name="2-Octaprenylphenol hydroxylase (anaerobic)" groups:idRef="R_OPHHX3"/>
+          <groups:member groups:name="Erythronate 4-phosphate (4per) dehydrogenase" groups:idRef="R_PERD"/>
+          <groups:member groups:name="Phosphomethylpyrimidine kinase" groups:idRef="R_PMPK"/>
+          <groups:member groups:name="Lipoyl-adenylate protein ligase" groups:idRef="R_LIPAMPL"/>
+          <groups:member groups:name="Sirohydrochlorin dehydrogenase (NAD)" groups:idRef="R_SHCHD2"/>
+          <groups:member groups:name="Thiamine kinase" groups:idRef="R_TMK"/>
+          <groups:member groups:name="Dihydrofolate synthase" groups:idRef="R_DHFS"/>
+          <groups:member groups:name="2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase" groups:idRef="R_MEPCT"/>
+          <groups:member groups:name="4-aminobenzoate synthase" groups:idRef="R_ADCL"/>
+          <groups:member groups:name="Lipoate-ATP adenylate transferase" groups:idRef="R_LIPATPT"/>
+          <groups:member groups:name="Pyrimidine phosphatase" groups:idRef="R_PMDPHT"/>
+          <groups:member groups:name="Guanosine 3&apos;-diphosphate 5&apos;-triphosphate 3&apos;-diphosphatase" groups:idRef="R_GDPTPDP"/>
+          <groups:member groups:name="Molybdopterin synthase sulfurylase" groups:idRef="R_MPTSS"/>
           <groups:member groups:name="Pantothenate synthase" groups:idRef="R_PANTS"/>
-          <groups:member groups:name="SUF [4Fe-4S] Transfer" groups:idRef="R_S4FE4ST"/>
-          <groups:member groups:name="Riboflavin synthase" groups:idRef="R_RBFSa"/>
-          <groups:member groups:name="7-deaza-7-carboxyguanine synthase" groups:idRef="R_CDGS"/>
-          <groups:member groups:name="O-Phospho-4-hydroxy-L-threonine:2-oxoglutarate aminotransferase" groups:idRef="R_OHPBAT"/>
-          <groups:member groups:name="3-Oxo-pimeloyl-[ACP] methyl ester reductase" groups:idRef="R_OPMEACPR"/>
-          <groups:member groups:name="3-Oxo-pimeloyl-[ACP] methyl ester synthase" groups:idRef="R_OPMEACPS"/>
-          <groups:member groups:name="NAD kinase" groups:idRef="R_NADK"/>
-          <groups:member groups:name="3-Oxo-glutaryl-[ACP] methyl ester dehydratase" groups:idRef="R_OGMEACPD"/>
+          <groups:member groups:name="Porphobilinogen synthase" groups:idRef="R_PPBNGS"/>
+          <groups:member groups:name="(L-seryl)adenylate synthase" groups:idRef="R_SERASr"/>
+          <groups:member groups:name="Tyrosine lyase" groups:idRef="R_TYRL"/>
+          <groups:member groups:name="2-Methyl-4-amino-5-hydroxymethylpyrimidine diphosphatase" groups:idRef="R_2MAHMP"/>
+          <groups:member groups:name="Pyridoxamine 5&apos;-phosphate oxidase" groups:idRef="R_PYAM5PO"/>
+          <groups:member groups:name="Thiazole phosphate synthesis" groups:idRef="R_THZPSN3"/>
+          <groups:member groups:name="4-amino-2-methyl-5-phosphomethylpyrimidine synthetase" groups:idRef="R_AMPMS2"/>
+          <groups:member groups:name="Bis-molybdopterin guanine dinucleotide synthase (single GDP)" groups:idRef="R_BMOGDS1"/>
+          <groups:member groups:name="Cobinamide adenyltransferase" groups:idRef="R_CBIAT"/>
           <groups:member groups:name="1-deoxy-D-xylulose reductoisomerase" groups:idRef="R_DXPRIi"/>
-          <groups:member groups:name="Pyridoxine 5&apos;-phosphate oxidase (anaerboic" groups:idRef="R_PDX5PO2"/>
-          <groups:member groups:name="1,4-dihydroxy-2-naphthoate octaprenyltransferase" groups:idRef="R_DHNAOT4"/>
-          <groups:member groups:name="Formaldehyde glutathione ligase (spontaneous)" groups:idRef="R_FALGTHLs"/>
-          <groups:member groups:name="Adenosyl cobinamide kinase" groups:idRef="R_ADOCBIK"/>
+          <groups:member groups:name="Adenosylmethionine-8-amino-7-oxononanoate transaminase" groups:idRef="R_AMAOTr"/>
+          <groups:member groups:name="P-aminobenzoyl-glutamate hydrolase" groups:idRef="R_4ABZGLUH"/>
           <groups:member groups:name="Bis-molybdopterin guanine dinucleotide synthase" groups:idRef="R_BMOGDS2"/>
-          <groups:member groups:name="SUF [2Fe-2S] Synthesis" groups:idRef="R_S2FE2SS"/>
-          <groups:member groups:name="Molybdopterin adenylyltransferase" groups:idRef="R_MPTAT"/>
-          <groups:member groups:name="3-Oxo-glutaryl-[ACP] methyl ester synthase" groups:idRef="R_OGMEACPS"/>
-          <groups:member groups:name="Riboflavin synthase" groups:idRef="R_RBFSb"/>
-          <groups:member groups:name="3-Dimethylubiquinonol 3-methyltransferase" groups:idRef="R_DMQMT"/>
+          <groups:member groups:name="4-amino-4-deoxychorismate synthase" groups:idRef="R_ADCS"/>
+          <groups:member groups:name="7-cyano-7-carbaguanine synthase" groups:idRef="R_CCGS"/>
+          <groups:member groups:name="Dihydroneopterin monophosphate dephosphorylase" groups:idRef="R_DNMPPA"/>
+          <groups:member groups:name="GTP diphosphokinase" groups:idRef="R_GTPDPK"/>
+          <groups:member groups:name="Isochorismate synthase" groups:idRef="R_ICHORS_copy1"/>
+          <groups:member groups:name="Geranyltranstransferase" groups:idRef="R_GRTT"/>
+          <groups:member groups:name="Lipoate synthase" groups:idRef="R_LIPOS"/>
+          <groups:member groups:name="Malonyl-CoA methyltransferase" groups:idRef="R_MALCOAMT"/>
           <groups:member groups:name="1-Deoxy-D-xylulose kinase" groups:idRef="R_DXYLK"/>
-          <groups:member groups:name="Nicotinate-nucleotide diphosphorylase (carboxylating)" groups:idRef="R_NNDPR"/>
-          <groups:member groups:name="ISC Cysteine desulfuration" groups:idRef="R_ICYSDS"/>
-          <groups:member groups:name="5&apos;-deoxyadenosine nuclosidase" groups:idRef="R_5DOAN"/>
-          <groups:member groups:name="NADP phosphatase" groups:idRef="R_NADPPPS"/>
-          <groups:member groups:name="3-Oxo-glutaryl-[ACP] methyl ester reductase" groups:idRef="R_OGMEACPR"/>
-          <groups:member groups:name="FMN reductase" groups:idRef="R_FMNRx2"/>
-          <groups:member groups:name="Lipoate-ATP adenylate transferase" groups:idRef="R_LIPATPT"/>
-          <groups:member groups:name="Pantetheine-phosphate adenylyltransferase" groups:idRef="R_PTPATi"/>
-          <groups:member groups:name="Dihydrofolate reductase" groups:idRef="R_DHFR"/>
-          <groups:member groups:name="Iron-sulfur cluster damage (peroxide, spontaneous)" groups:idRef="R_FESD1s"/>
+          <groups:member groups:name="NMN nucleosidase" groups:idRef="R_NMNN"/>
           <groups:member groups:name="Phosphopantothenate-cysteine ligase" groups:idRef="R_PPNCL2"/>
-          <groups:member groups:name="L-aspartate oxidase" groups:idRef="R_ASPO3"/>
-          <groups:member groups:name="Lipoyl-adenylate protein ligase" groups:idRef="R_LIPAMPL"/>
-          <groups:member groups:name="(L-seryl)adenylate synthase" groups:idRef="R_SERASr"/>
-          <groups:member groups:name="Chorismate pyruvate lyase" groups:idRef="R_CHRPL"/>
+          <groups:member groups:name="Tungsten bispterin guanine dinucleotide synthase" groups:idRef="R_BWCOGDS2"/>
+          <groups:member groups:name="Dihydroneopterin epimerase" groups:idRef="R_DHNPTE"/>
+          <groups:member groups:name="Nicotinic acid mononucleotide pyrophosphorylase" groups:idRef="R_NAMNPP"/>
+          <groups:member groups:name="Bis-molybdenum cofactor synthase" groups:idRef="R_BMOCOS"/>
+          <groups:member groups:name="ISC Cysteine desulfuration" groups:idRef="R_ICYSDS"/>
+          <groups:member groups:name="Nicotinamide-nucleotide amidase" groups:idRef="R_NMNDA"/>
+          <groups:member groups:name="S-adenosylmethione:2-demthylmenaquinole methyltransferase (menaquinone 8)" groups:idRef="R_AMMQLT8"/>
+          <groups:member groups:name="L-aspartate oxidase" groups:idRef="R_ASPO5"/>
+          <groups:member groups:name="2-Octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol hydroxylase (NADPHl)" groups:idRef="R_OMMBLHXy"/>
           <groups:member groups:name="1,4-dihydroxy-2-napthoyl-CoA synthase" groups:idRef="R_DHNCOAS"/>
-          <groups:member groups:name="Molybdenum cofactor synthase" groups:idRef="R_MOCOS"/>
-          <groups:member groups:name="Adenosylmethionine-8-amino-7-oxononanoate transaminase" groups:idRef="R_AMAOTr"/>
-          <groups:member groups:name="Iron-sulfur cluster damage (nitrous oxide, spontaneous)" groups:idRef="R_FESD2s"/>
-          <groups:member groups:name="2C-methyl-D-erythritol 2,4 cyclodiphosphate dehydratase" groups:idRef="R_MECDPDH5"/>
-          <groups:member groups:name="L-aspartate oxidase" groups:idRef="R_ASPO4"/>
-          <groups:member groups:name="Molybdopterin guanine dinucleotide synthase" groups:idRef="R_MOGDS"/>
-          <groups:member groups:name="Molybdopterin synthase sulfurylase" groups:idRef="R_MPTSS"/>
-          <groups:member groups:name="3,4-Dihydroxy-2-butanone-4-phosphate synthase" groups:idRef="R_DB4PS"/>
-          <groups:member groups:name="Dimethylallyltranstransferase" groups:idRef="R_DMATT"/>
-          <groups:member groups:name="FMN reductase" groups:idRef="R_FMNRx"/>
-          <groups:member groups:name="Hypothetical enyme" groups:idRef="R_HYPOE"/>
-          <groups:member groups:name="Isopentenyl-diphosphate D-isomerase" groups:idRef="R_IPDDI"/>
-          <groups:member groups:name="Molybdopterin synthase" groups:idRef="R_MPTS"/>
-          <groups:member groups:name="Molybdopterin cytidine dinucleotide synthase" groups:idRef="R_MOCDS"/>
-          <groups:member groups:name="2-Octaprenylphenol hydroxylase (NADPH)" groups:idRef="R_OPHHXy"/>
-          <groups:member groups:name="Undecaprenyl diphosphate synthase" groups:idRef="R_UDCPDPS"/>
-          <groups:member groups:name="Pantothenate kinase" groups:idRef="R_PNTK"/>
-          <groups:member groups:name="Formaldehyde dehydrogenase" groups:idRef="R_FALDH2"/>
+          <groups:member groups:name="Fe(III) reduction" groups:idRef="R_FE3Ri"/>
+          <groups:member groups:name="Pyridoxine 5&apos;-phosphate oxidase" groups:idRef="R_PDX5POi"/>
+          <groups:member groups:name="Enterochelin synthase" groups:idRef="R_ENTCS"/>
+          <groups:member groups:name="Pantetheine-phosphate adenylyltransferase" groups:idRef="R_PTPATi"/>
+          <groups:member groups:name="SUF Cysteine desulfuration" groups:idRef="R_SCYSDS"/>
+          <groups:member groups:name="GTP cyclohydrolase I" groups:idRef="R_GTPCI"/>
+          <groups:member groups:name="Oxygen Independent coproporphyrinogen-III oxidase" groups:idRef="R_CPPPGO2"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group9" sboTerm="SBO:0000633" groups:id="G_group9" groups:name="Cysteine Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="Cysteine transaminase" groups:idRef="R_CYSTA"/>
-          <groups:member groups:name="Sulfite reductase (NADPH2)" groups:idRef="R_SULR"/>
-          <groups:member groups:name="Phosphoadenylyl-sulfate reductase (thioredoxin)" groups:idRef="R_PAPSR"/>
+          <groups:member groups:name="D-cysteine desulfhydrase" groups:idRef="R_CYSDDS"/>
           <groups:member groups:name="Cysteine synthase" groups:idRef="R_CYSS"/>
           <groups:member groups:name="3-mercaptopyruvate sulfurtransferase" groups:idRef="R_MCPST"/>
-          <groups:member groups:name="Cysteine Desulfhydrase" groups:idRef="R_CYSDS"/>
-          <groups:member groups:name="D-cysteine desulfhydrase" groups:idRef="R_CYSDDS"/>
-          <groups:member groups:name="Adenylyl-sulfate kinase" groups:idRef="R_ADSK"/>
           <groups:member groups:name="Serine O-acetyltransferase" groups:idRef="R_SERAT"/>
-          <groups:member groups:name="Alanyl aminopeptidase (cys-gly)" groups:idRef="R_AMPTASECG"/>
+          <groups:member groups:name="Cysteine transaminase" groups:idRef="R_CYSTA"/>
+          <groups:member groups:name="Phosphoadenylyl-sulfate reductase (thioredoxin)" groups:idRef="R_PAPSR"/>
+          <groups:member groups:name="Sulfite reductase (NADPH2)" groups:idRef="R_SULR"/>
           <groups:member groups:name="L-cysteine sulfinic acid desulfurase" groups:idRef="R_CYSSADS"/>
-          <groups:member groups:name="3&apos;,5&apos;-bisphosphate nucleotidase" groups:idRef="R_BPNT"/>
           <groups:member groups:name="Sulfate adenyltransferase" groups:idRef="R_SADT2"/>
+          <groups:member groups:name="Alanyl aminopeptidase (cys-gly)" groups:idRef="R_AMPTASECG"/>
+          <groups:member groups:name="Adenylyl-sulfate kinase" groups:idRef="R_ADSK"/>
+          <groups:member groups:name="Cysteine Desulfhydrase" groups:idRef="R_CYSDS"/>
+          <groups:member groups:name="3&apos;,5&apos;-bisphosphate nucleotidase" groups:idRef="R_BPNT"/>
           <groups:member groups:name="Phosphoadenylyl-sulfate reductase (glutaredoxin)" groups:idRef="R_PAPSR2"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group10" sboTerm="SBO:0000633" groups:id="G_group10" groups:name="Extracellular exchange" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="Deoxyadenosine exchange" groups:idRef="R_EX_dad_2_e"/>
-          <groups:member groups:name="Cytidine exchange" groups:idRef="R_EX_cytd_e"/>
-          <groups:member groups:name="Myo-Inositol hexakisphosphate exchange" groups:idRef="R_EX_minohp_e"/>
-          <groups:member groups:name="N-Acetyl-D-galactosamine exchange" groups:idRef="R_EX_acgal_e"/>
-          <groups:member groups:name="DGMP exchange" groups:idRef="R_EX_dgmp_e"/>
-          <groups:member groups:name="Minocycline exchange" groups:idRef="R_EX_mincyc_e"/>
-          <groups:member groups:name="N-Acetyl-D-galactosamine 1-phosphate exchange" groups:idRef="R_EX_acgal1p_e"/>
-          <groups:member groups:name="Dodecanoate (n-C12:0) exchange" groups:idRef="R_EX_ddca_e"/>
-          <groups:member groups:name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate-D-alanine exchange" groups:idRef="R_EX_LalaDgluMdapDala_e"/>
-          <groups:member groups:name="Cu2+ exchange" groups:idRef="R_EX_cu2_e"/>
-          <groups:member groups:name="1-O-methyl-Beta-D-glucuronate exchange" groups:idRef="R_EX_metglcur_e"/>
-          <groups:member groups:name="DAMP exchange" groups:idRef="R_EX_damp_e"/>
-          <groups:member groups:name="Cu+ exchange" groups:idRef="R_EX_cu_e"/>
-          <groups:member groups:name="L-methionine-R-sulfoxide exchange" groups:idRef="R_EX_metsox_R__L_e"/>
-          <groups:member groups:name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate exchange" groups:idRef="R_EX_LalaDgluMdap_e"/>
-          <groups:member groups:name="Hydrogen cyanide exchange" groups:idRef="R_EX_cyan_e"/>
-          <groups:member groups:name="Mg exchange" groups:idRef="R_EX_mg2_e"/>
-          <groups:member groups:name="L-alanine-D-glutamate exchange" groups:idRef="R_EX_LalaDglu_e"/>
-          <groups:member groups:name="L-alanine-L-glutamate exchange" groups:idRef="R_EX_LalaLglu_e"/>
-          <groups:member groups:name="Decanoate (n-C10:0) exchange" groups:idRef="R_EX_dca_e"/>
-          <groups:member groups:name="Acetate exchange" groups:idRef="R_EX_ac_e"/>
-          <groups:member groups:name="Cyanate exchange" groups:idRef="R_EX_cynt_e"/>
-          <groups:member groups:name="L-Cysteine exchange" groups:idRef="R_EX_cys__L_e"/>
-          <groups:member groups:name="Deoxycytidine exchange" groups:idRef="R_EX_dcyt_e"/>
-          <groups:member groups:name="DCMP exchange" groups:idRef="R_EX_dcmp_e"/>
+          <groups:member groups:name="Trehalose exchange" groups:idRef="R_EX_tre_e"/>
+          <groups:member groups:name="L-Prolinylglycine exchange" groups:idRef="R_EX_progly_e"/>
+          <groups:member groups:name="Trimethylamine N-oxide exchange" groups:idRef="R_EX_tmao_e"/>
+          <groups:member groups:name="D-Xylose exchange" groups:idRef="R_EX_xyl__D_e"/>
+          <groups:member groups:name="Thiamin exchange" groups:idRef="R_EX_thm_e"/>
+          <groups:member groups:name="Uridine exchange" groups:idRef="R_EX_uri_e"/>
+          <groups:member groups:name="Urea exchange" groups:idRef="R_EX_urea_e"/>
+          <groups:member groups:name="Xanthosine exchange" groups:idRef="R_EX_xtsn_e"/>
+          <groups:member groups:name="L-Threonine exchange" groups:idRef="R_EX_thr__L_e"/>
+          <groups:member groups:name="UMP exchange" groups:idRef="R_EX_ump_e"/>
+          <groups:member groups:name="L-Proline exchange" groups:idRef="R_EX_pro__L_e"/>
+          <groups:member groups:name="L-Threonine O-3-phosphate exchange" groups:idRef="R_EX_thrp_e"/>
+          <groups:member groups:name="Thymine exchange" groups:idRef="R_EX_thym_e"/>
+          <groups:member groups:name="L-Valine exchange" groups:idRef="R_EX_val__L_e"/>
+          <groups:member groups:name="Trimethylamine exchange" groups:idRef="R_EX_tma_e"/>
+          <groups:member groups:name="Urate exchange" groups:idRef="R_EX_urate_e"/>
+          <groups:member groups:name="Xanthosine 5&apos;-phosphate exchange" groups:idRef="R_EX_xmp_e"/>
+          <groups:member groups:name="Uracil exchange" groups:idRef="R_EX_ura_e"/>
+          <groups:member groups:name="Xanthine exchange" groups:idRef="R_EX_xan_e"/>
+          <groups:member groups:name="Propanal exchange" groups:idRef="R_EX_ppal_e"/>
+          <groups:member groups:name="Thymidine exchange" groups:idRef="R_EX_thymd_e"/>
+          <groups:member groups:name="Phosphonate exchange" groups:idRef="R_EX_ppt_e"/>
+          <groups:member groups:name="Phenylpropanoate exchange" groups:idRef="R_EX_pppn_e"/>
+          <groups:member groups:name="Biotin exchange" groups:idRef="R_EX_btn_e"/>
+          <groups:member groups:name="L-Fucose exchange" groups:idRef="R_EX_fuc__L_e"/>
           <groups:member groups:name="Acetaldehyde exchange" groups:idRef="R_EX_acald_e"/>
-          <groups:member groups:name="L-Methionine S-oxide exchange" groups:idRef="R_EX_metsox_S__L_e"/>
+          <groups:member groups:name="Reduced glutathione exchange" groups:idRef="R_EX_gthrd_e"/>
+          <groups:member groups:name="L-Aspartate exchange" groups:idRef="R_EX_asp__L_e"/>
+          <groups:member groups:name="(R)-Glycerate exchange" groups:idRef="R_EX_glyc__R_e"/>
+          <groups:member groups:name="Pyridoxal exchange" groups:idRef="R_EX_pydx_e"/>
+          <groups:member groups:name="D-Fructuronate exchange" groups:idRef="R_EX_fruur_e"/>
+          <groups:member groups:name="Phenethylamine exchange" groups:idRef="R_EX_peamn_e"/>
+          <groups:member groups:name="Oxidized glutathione exchange" groups:idRef="R_EX_gthox_e"/>
           <groups:member groups:name="Acetoacetate exchange" groups:idRef="R_EX_acac_e"/>
-          <groups:member groups:name="D-Cysteine exchange" groups:idRef="R_EX_cys__D_e"/>
-          <groups:member groups:name="Pyridoxine exchange" groups:idRef="R_EX_pydxn_e"/>
+          <groups:member groups:name="Phenylacetaldehyde exchange" groups:idRef="R_EX_pacald_e"/>
+          <groups:member groups:name="Glycerol 3-phosphate exchange" groups:idRef="R_EX_glyc3p_e"/>
           <groups:member groups:name="5-Methylthio-D-ribose exchange" groups:idRef="R_EX_5mtr_e"/>
-          <groups:member groups:name="Butyrate (n-C4:0) exchange" groups:idRef="R_EX_but_e"/>
-          <groups:member groups:name="Pyridoxal exchange" groups:idRef="R_EX_pydx_e"/>
-          <groups:member groups:name="5-Dehydro-D-gluconate exchange" groups:idRef="R_EX_5dglcn_e"/>
-          <groups:member groups:name="Biotin exchange" groups:idRef="R_EX_btn_e"/>
-          <groups:member groups:name="(R)-Propane-1,2-diol exchange" groups:idRef="R_EX_12ppd__R_e"/>
-          <groups:member groups:name="Propanal exchange" groups:idRef="R_EX_ppal_e"/>
-          <groups:member groups:name="3-(3-hydroxy-phenyl)propionate exchange" groups:idRef="R_EX_3hpppn_e"/>
+          <groups:member groups:name="Aerobactin minus Fe3 exchange" groups:idRef="R_EX_arbtn_e"/>
+          <groups:member groups:name="Ferrichrome minus Fe(III) exchange" groups:idRef="R_EX_fecrm_un_e"/>
+          <groups:member groups:name="Pyridoxamine exchange" groups:idRef="R_EX_pydam_e"/>
+          <groups:member groups:name="Fe-enterobactin exchange" groups:idRef="R_EX_feenter_e"/>
+          <groups:member groups:name="Octadecanoate (n-C18:0) exchange" groups:idRef="R_EX_ocdca_e"/>
+          <groups:member groups:name="Aerobactin exchange" groups:idRef="R_EX_arbtn_fe3_e"/>
+          <groups:member groups:name="Glycerol exchange" groups:idRef="R_EX_glyc_e"/>
+          <groups:member groups:name="Ferroxamine exchange" groups:idRef="R_EX_feoxam_e"/>
+          <groups:member groups:name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate-D-alanine exchange" groups:idRef="R_EX_LalaDgluMdapDala_e"/>
+          <groups:member groups:name="Glycerol 2-phosphate exchange" groups:idRef="R_EX_glyc2p_e"/>
+          <groups:member groups:name="Glycolate exchange" groups:idRef="R_EX_glyclt_e"/>
+          <groups:member groups:name="Ferroxamine minus Fe(3) exchange" groups:idRef="R_EX_feoxam_un_e"/>
           <groups:member groups:name="Psicoselysine exchange" groups:idRef="R_EX_psclys_e"/>
-          <groups:member groups:name="2-Deoxy-D-glucose exchange" groups:idRef="R_EX_2dglc_e"/>
-          <groups:member groups:name="Propionate exchange" groups:idRef="R_EX_ppa_e"/>
-          <groups:member groups:name="1,5-Diaminopentane exchange" groups:idRef="R_EX_15dap_e"/>
-          <groups:member groups:name="3&apos;-UMP exchange" groups:idRef="R_EX_3ump_e"/>
-          <groups:member groups:name="2-Dehydro-3-deoxy-D-gluconate exchange" groups:idRef="R_EX_2ddglcn_e"/>
+          <groups:member groups:name="Octadecenoate (n-C18:1) exchange" groups:idRef="R_EX_ocdcea_e"/>
+          <groups:member groups:name="Putrescine exchange" groups:idRef="R_EX_ptrc_e"/>
+          <groups:member groups:name="L-alanine-D-glutamate-meso-2,6-diaminoheptanedioate exchange" groups:idRef="R_EX_LalaDgluMdap_e"/>
+          <groups:member groups:name="FMN exchange" groups:idRef="R_EX_fmn_e"/>
           <groups:member groups:name="L-Arginine exchange" groups:idRef="R_EX_arg__L_e"/>
+          <groups:member groups:name="Guanosine exchange" groups:idRef="R_EX_gsn_e"/>
           <groups:member groups:name="O-Phospho-L-serine exchange" groups:idRef="R_EX_pser__L_e"/>
           <groups:member groups:name="L-Ascorbate exchange" groups:idRef="R_EX_ascb__L_e"/>
-          <groups:member groups:name="(S)-Propane-1,2-diol exchange" groups:idRef="R_EX_12ppd__S_e"/>
-          <groups:member groups:name="Protoheme exchange" groups:idRef="R_EX_pheme_e"/>
-          <groups:member groups:name="2&apos;,3&apos;-Cyclic AMP exchange" groups:idRef="R_EX_23camp_e"/>
-          <groups:member groups:name="4-Aminobutanoate exchange" groups:idRef="R_EX_4abut_e"/>
-          <groups:member groups:name="2&apos;,3&apos;-Cyclic CMP exchange" groups:idRef="R_EX_23ccmp_e"/>
-          <groups:member groups:name="2&apos;,3&apos;-Cyclic GMP exchange" groups:idRef="R_EX_23cgmp_e"/>
-          <groups:member groups:name="L-Asparagine exchange" groups:idRef="R_EX_asn__L_e"/>
-          <groups:member groups:name="1,4-alpha-D-glucan exchange" groups:idRef="R_EX_14glucan_e"/>
-          <groups:member groups:name="(R)-Pantothenate exchange" groups:idRef="R_EX_pnto__R_e"/>
-          <groups:member groups:name="Pyridoxamine exchange" groups:idRef="R_EX_pydam_e"/>
-          <groups:member groups:name="2&apos;,3&apos;-Cyclic UMP exchange" groups:idRef="R_EX_23cump_e"/>
-          <groups:member groups:name="4-Hydroxyphenylacetaldehyde exchange" groups:idRef="R_EX_4hoxpacd_e"/>
-          <groups:member groups:name="L-Aspartate exchange" groups:idRef="R_EX_asp__L_e"/>
-          <groups:member groups:name="Meso-2,6-Diaminoheptanedioate exchange" groups:idRef="R_EX_26dap__M_e"/>
-          <groups:member groups:name="4-aminobenzoyl-glutamate exchange" groups:idRef="R_EX_4abzglu_e"/>
-          <groups:member groups:name="Phosphate exchange" groups:idRef="R_EX_pi_e"/>
-          <groups:member groups:name="2,3-diaminopropionate exchange" groups:idRef="R_EX_23dappa_e"/>
+          <groups:member groups:name="GMP exchange" groups:idRef="R_EX_gmp_e"/>
+          <groups:member groups:name="Formate exchange" groups:idRef="R_EX_for_e"/>
+          <groups:member groups:name="Octanoate (n-C8:0) exchange" groups:idRef="R_EX_octa_e"/>
           <groups:member groups:name="Arsenite exchange" groups:idRef="R_EX_aso3_e"/>
-          <groups:member groups:name="Putrescine exchange" groups:idRef="R_EX_ptrc_e"/>
-          <groups:member groups:name="Sulfoacetate exchange" groups:idRef="R_EX_sulfac_e"/>
-          <groups:member groups:name="Dopamine exchange" groups:idRef="R_EX_dopa_e"/>
-          <groups:member groups:name="Fe3+ exchange" groups:idRef="R_EX_fe3_e"/>
-          <groups:member groups:name="Aerobactin exchange" groups:idRef="R_EX_arbtn_fe3_e"/>
-          <groups:member groups:name="Sulfur dioxide exchange" groups:idRef="R_EX_so2_e"/>
+          <groups:member groups:name="Orotate exchange" groups:idRef="R_EX_orot_e"/>
+          <groups:member groups:name="L-alanine-D-glutamate exchange" groups:idRef="R_EX_LalaDglu_e"/>
+          <groups:member groups:name="Ornithine exchange" groups:idRef="R_EX_orn_e"/>
+          <groups:member groups:name="L-Asparagine exchange" groups:idRef="R_EX_asn__L_e"/>
+          <groups:member groups:name="Acetate exchange" groups:idRef="R_EX_ac_e"/>
+          <groups:member groups:name="Fructoselysine exchange" groups:idRef="R_EX_frulys_e"/>
+          <groups:member groups:name="D-Fructose exchange" groups:idRef="R_EX_fru_e"/>
+          <groups:member groups:name="L-alanine-L-glutamate exchange" groups:idRef="R_EX_LalaLglu_e"/>
+          <groups:member groups:name="Glycine betaine exchange" groups:idRef="R_EX_glyb_e"/>
+          <groups:member groups:name="D-Galactose exchange" groups:idRef="R_EX_gal_e"/>
+          <groups:member groups:name="D-Glucosamine 6-phosphate exchange" groups:idRef="R_EX_gam6p_e"/>
+          <groups:member groups:name="L-Lysine exchange" groups:idRef="R_EX_lys__L_e"/>
+          <groups:member groups:name="Beta D-Galactose exchange" groups:idRef="R_EX_gal_bD_e"/>
+          <groups:member groups:name="Agmatine exchange" groups:idRef="R_EX_agm_e"/>
+          <groups:member groups:name="D-Galacturonate exchange" groups:idRef="R_EX_galur_e"/>
+          <groups:member groups:name="Lipoate exchange" groups:idRef="R_EX_lipoate_e"/>
+          <groups:member groups:name="Silver exchange" groups:idRef="R_EX_ag_e"/>
+          <groups:member groups:name="Glycerophosphoglycerol exchange" groups:idRef="R_EX_g3pg_e"/>
+          <groups:member groups:name="D-Galactarate exchange" groups:idRef="R_EX_galct__D_e"/>
+          <groups:member groups:name="Sn-Glycero-3-phospho-1-inositol exchange" groups:idRef="R_EX_g3pi_e"/>
+          <groups:member groups:name="D-lactate exchange" groups:idRef="R_EX_lac__D_e"/>
+          <groups:member groups:name="O-Acetyl-L-serine exchange" groups:idRef="R_EX_acser_e"/>
+          <groups:member groups:name="Adenosine exchange" groups:idRef="R_EX_adn_e"/>
+          <groups:member groups:name="D-Galactonate exchange" groups:idRef="R_EX_galctn__D_e"/>
+          <groups:member groups:name="Glycerophosphoserine exchange" groups:idRef="R_EX_g3ps_e"/>
+          <groups:member groups:name="Adenine exchange" groups:idRef="R_EX_ade_e"/>
+          <groups:member groups:name="Galactitol exchange" groups:idRef="R_EX_galt_e"/>
+          <groups:member groups:name="Adenosylcobalamin exchange" groups:idRef="R_EX_adocbl_e"/>
+          <groups:member groups:name="L-Galactonate exchange" groups:idRef="R_EX_galctn__L_e"/>
+          <groups:member groups:name="L-Lactate exchange" groups:idRef="R_EX_lac__L_e"/>
+          <groups:member groups:name="D-Glucose 6-phosphate exchange" groups:idRef="R_EX_g6p_e"/>
+          <groups:member groups:name="L-Leucine exchange" groups:idRef="R_EX_leu__L_e"/>
+          <groups:member groups:name="Lactose exchange" groups:idRef="R_EX_lcts_e"/>
+          <groups:member groups:name="Alpha-D-Galactose 1-phosphate exchange" groups:idRef="R_EX_gal1p_e"/>
           <groups:member groups:name="Fe2+ exchange" groups:idRef="R_EX_fe2_e"/>
-          <groups:member groups:name="Ferrichrome minus Fe(III) exchange" groups:idRef="R_EX_fecrm_un_e"/>
-          <groups:member groups:name="Selenite exchange" groups:idRef="R_EX_slnt_e"/>
-          <groups:member groups:name="Dimethyl sulfoxide exchange" groups:idRef="R_EX_dmso_e"/>
-          <groups:member groups:name="Ethanolamine exchange" groups:idRef="R_EX_etha_e"/>
-          <groups:member groups:name="Aerobactin minus Fe3 exchange" groups:idRef="R_EX_arbtn_e"/>
-          <groups:member groups:name="Deoxyguanosine exchange" groups:idRef="R_EX_dgsn_e"/>
-          <groups:member groups:name="Thiamin exchange" groups:idRef="R_EX_thm_e"/>
+          <groups:member groups:name="Tyramine exchange" groups:idRef="R_EX_tym_e"/>
+          <groups:member groups:name="Superoxide anion exchange" groups:idRef="R_EX_o2s_e"/>
+          <groups:member groups:name="Formaldehyde exchange" groups:idRef="R_EX_fald_e"/>
           <groups:member groups:name="Ferrichrome exchange" groups:idRef="R_EX_fecrm_e"/>
+          <groups:member groups:name="CO2 exchange" groups:idRef="R_EX_co2_e"/>
+          <groups:member groups:name="Myo-Inositol hexakisphosphate exchange" groups:idRef="R_EX_minohp_e"/>
+          <groups:member groups:name="Tungstate exchange" groups:idRef="R_EX_tungs_e"/>
+          <groups:member groups:name="D-Allose exchange" groups:idRef="R_EX_all__D_e"/>
+          <groups:member groups:name="Minocycline exchange" groups:idRef="R_EX_mincyc_e"/>
+          <groups:member groups:name="CMP exchange" groups:idRef="R_EX_cmp_e"/>
+          <groups:member groups:name="Phosphoethanolamine KDO(2)-lipid (A) exchange" groups:idRef="R_EX_enlipa_e"/>
+          <groups:member groups:name="L-Methionine exchange" groups:idRef="R_EX_met__L_e"/>
+          <groups:member groups:name="L-Tryptophan exchange" groups:idRef="R_EX_trp__L_e"/>
+          <groups:member groups:name="Enterochelin exchange" groups:idRef="R_EX_enter_e"/>
+          <groups:member groups:name="Fe(III)hydoxamate, unloaded exchange" groups:idRef="R_EX_fe3hox_un_e"/>
+          <groups:member groups:name="Thiosulfate exchange" groups:idRef="R_EX_tsul_e"/>
+          <groups:member groups:name="O2 exchange" groups:idRef="R_EX_o2_e"/>
+          <groups:member groups:name="Citrate exchange" groups:idRef="R_EX_cit_e"/>
+          <groups:member groups:name="Cobinamide exchange" groups:idRef="R_EX_cbi_e"/>
+          <groups:member groups:name="Ethanolamine exchange" groups:idRef="R_EX_etha_e"/>
+          <groups:member groups:name="Tetradecanoate (n-C14:0) exchange" groups:idRef="R_EX_ttdca_e"/>
+          <groups:member groups:name="D-Alanyl-D-alanine exchange" groups:idRef="R_EX_alaala_e"/>
+          <groups:member groups:name="1-O-methyl-Beta-D-glucuronate exchange" groups:idRef="R_EX_metglcur_e"/>
+          <groups:member groups:name="Calcium exchange" groups:idRef="R_EX_ca2_e"/>
+          <groups:member groups:name="Fe3+ exchange" groups:idRef="R_EX_fe3_e"/>
+          <groups:member groups:name="2-Oxoglutarate exchange" groups:idRef="R_EX_akg_e"/>
           <groups:member groups:name="Ethanesulfonate exchange" groups:idRef="R_EX_ethso3_e"/>
-          <groups:member groups:name="Sucrose exchange" groups:idRef="R_EX_sucr_e"/>
-          <groups:member groups:name="Sulfite exchange" groups:idRef="R_EX_so3_e"/>
-          <groups:member groups:name="Thiocyanate exchange" groups:idRef="R_EX_tcynt_e"/>
-          <groups:member groups:name="Selenate exchange" groups:idRef="R_EX_sel_e"/>
-          <groups:member groups:name="Dihydroxyacetone exchange" groups:idRef="R_EX_dha_e"/>
+          <groups:member groups:name="L-methionine-R-sulfoxide exchange" groups:idRef="R_EX_metsox_R__L_e"/>
+          <groups:member groups:name="Tetracycline exchange" groups:idRef="R_EX_ttrcyc_e"/>
           <groups:member groups:name="Ethanol exchange" groups:idRef="R_EX_etoh_e"/>
-          <groups:member groups:name="D-Serine exchange" groups:idRef="R_EX_ser__D_e"/>
-          <groups:member groups:name="Sulfate exchange" groups:idRef="R_EX_so4_e"/>
-          <groups:member groups:name="Fe(III)dicitrate exchange" groups:idRef="R_EX_fe3dcit_e"/>
-          <groups:member groups:name="2,3-Dihydroxypropane-1-sulfonate exchange" groups:idRef="R_EX_dhps_e"/>
-          <groups:member groups:name="D-fructose 6-phosphate exchange" groups:idRef="R_EX_f6p_e"/>
-          <groups:member groups:name="Ferric 2,3-dihydroxybenzoylserine exchange" groups:idRef="R_EX_fe3dhbzs_e"/>
-          <groups:member groups:name="AMP exchange" groups:idRef="R_EX_amp_e"/>
-          <groups:member groups:name="D-tartrate exchange" groups:idRef="R_EX_tartr__D_e"/>
-          <groups:member groups:name="Shikimate exchange" groups:idRef="R_EX_skm_e"/>
-          <groups:member groups:name="Taurine exchange" groups:idRef="R_EX_taur_e"/>
-          <groups:member groups:name="DIMP exchange" groups:idRef="R_EX_dimp_e"/>
-          <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramic acid exchange" groups:idRef="R_EX_anhgm_e"/>
-          <groups:member groups:name="Fe(III)hydoxamate, unloaded exchange" groups:idRef="R_EX_fe3hox_un_e"/>
-          <groups:member groups:name="L-tartrate exchange" groups:idRef="R_EX_tartr__L_e"/>
-          <groups:member groups:name="Spermidine exchange" groups:idRef="R_EX_spmd_e"/>
-          <groups:member groups:name="Dimethyl sulfide exchange" groups:idRef="R_EX_dms_e"/>
-          <groups:member groups:name="Formaldehyde exchange" groups:idRef="R_EX_fald_e"/>
-          <groups:member groups:name="Succinate exchange" groups:idRef="R_EX_succ_e"/>
+          <groups:member groups:name="Nitrate exchange" groups:idRef="R_EX_no3_e"/>
+          <groups:member groups:name="Mg exchange" groups:idRef="R_EX_mg2_e"/>
+          <groups:member groups:name="Novobiocin exchange" groups:idRef="R_EX_novbcn_e"/>
+          <groups:member groups:name="Beta-Alanine exchange" groups:idRef="R_EX_ala_B_e"/>
+          <groups:member groups:name="Butanesulfonate exchange" groups:idRef="R_EX_butso3_e"/>
+          <groups:member groups:name="Nitric oxide exchange" groups:idRef="R_EX_no_e"/>
+          <groups:member groups:name="L-Alanine exchange" groups:idRef="R_EX_ala__L_e"/>
+          <groups:member groups:name="Butyrate (n-C4:0) exchange" groups:idRef="R_EX_but_e"/>
           <groups:member groups:name="Exchange of Flavin adenine dinucleotide oxidized" groups:idRef="R_EX_fad_e"/>
+          <groups:member groups:name="Fe(III)dicitrate exchange" groups:idRef="R_EX_fe3dcit_e"/>
+          <groups:member groups:name="Tetradecenoate (n-C14:1) exchange" groups:idRef="R_EX_ttdcea_e"/>
           <groups:member groups:name="Fe(III)hydroxamate exchange" groups:idRef="R_EX_fe3hox_e"/>
-          <groups:member groups:name="Sulphoquinovose exchange" groups:idRef="R_EX_sq_e"/>
-          <groups:member groups:name="L-Serine exchange" groups:idRef="R_EX_ser__L_e"/>
-          <groups:member groups:name="Arbutin exchange" groups:idRef="R_EX_arbt_e"/>
-          <groups:member groups:name="Deoxyinosine exchange" groups:idRef="R_EX_din_e"/>
-          <groups:member groups:name="L-Arabinose exchange" groups:idRef="R_EX_arab__L_e"/>
-          <groups:member groups:name="D-Glucuronate exchange" groups:idRef="R_EX_glcur_e"/>
-          <groups:member groups:name="Allantoin exchange" groups:idRef="R_EX_alltn_e"/>
-          <groups:member groups:name="GTP exchange" groups:idRef="R_EX_gtp_e"/>
-          <groups:member groups:name="L-Methionine exchange" groups:idRef="R_EX_met__L_e"/>
-          <groups:member groups:name="D-Glucuronate 1-phosphate exchange" groups:idRef="R_EX_glcur1p_e"/>
-          <groups:member groups:name="D-Methionine exchange" groups:idRef="R_EX_met__D_e"/>
-          <groups:member groups:name="D-Glucosamine exchange" groups:idRef="R_EX_gam_e"/>
-          <groups:member groups:name="Reduced glutathione exchange" groups:idRef="R_EX_gthrd_e"/>
-          <groups:member groups:name="L-Xylulose exchange" groups:idRef="R_EX_xylu__L_e"/>
-          <groups:member groups:name="2(alpha-D-Mannosyl)-D-glycerate exchange" groups:idRef="R_EX_manglyc_e"/>
-          <groups:member groups:name="D-Allose exchange" groups:idRef="R_EX_all__D_e"/>
-          <groups:member groups:name="Glycolate exchange" groups:idRef="R_EX_glyclt_e"/>
-          <groups:member groups:name="Gamma-butyrobetaine exchange" groups:idRef="R_EX_gbbtn_e"/>
-          <groups:member groups:name="2-Oxoglutarate exchange" groups:idRef="R_EX_akg_e"/>
-          <groups:member groups:name="D-Xylose exchange" groups:idRef="R_EX_xyl__D_e"/>
-          <groups:member groups:name="GMP exchange" groups:idRef="R_EX_gmp_e"/>
-          <groups:member groups:name="Methanol exchange" groups:idRef="R_EX_meoh_e"/>
-          <groups:member groups:name="Beta-Alanine exchange" groups:idRef="R_EX_ala_B_e"/>
-          <groups:member groups:name="GDP exchange" groups:idRef="R_EX_gdp_e"/>
-          <groups:member groups:name="D-Gluconate exchange" groups:idRef="R_EX_glcn_e"/>
-          <groups:member groups:name="Zinc exchange" groups:idRef="R_EX_zn2_e"/>
-          <groups:member groups:name="Melibiose exchange" groups:idRef="R_EX_melib_e"/>
           <groups:member groups:name="D-Alanine exchange" groups:idRef="R_EX_ala__D_e"/>
-          <groups:member groups:name="Oxidized glutathione exchange" groups:idRef="R_EX_gthox_e"/>
-          <groups:member groups:name="Methylphosphonic acid exchange" groups:idRef="R_EX_mepn_e"/>
-          <groups:member groups:name="D-Alanyl-D-alanine exchange" groups:idRef="R_EX_alaala_e"/>
-          <groups:member groups:name="L-Alanine exchange" groups:idRef="R_EX_ala__L_e"/>
-          <groups:member groups:name="Xanthine exchange" groups:idRef="R_EX_xan_e"/>
-          <groups:member groups:name="D-Glucose exchange" groups:idRef="R_EX_glc__D_e"/>
-          <groups:member groups:name="Guanosine exchange" groups:idRef="R_EX_gsn_e"/>
-          <groups:member groups:name="Xanthosine exchange" groups:idRef="R_EX_xtsn_e"/>
-          <groups:member groups:name="D-Glucarate exchange" groups:idRef="R_EX_glcr_e"/>
-          <groups:member groups:name="Xanthosine 5&apos;-phosphate exchange" groups:idRef="R_EX_xmp_e"/>
-          <groups:member groups:name="Nitrate exchange" groups:idRef="R_EX_no3_e"/>
-          <groups:member groups:name="Coprogen exchange" groups:idRef="R_EX_cpgn_e"/>
-          <groups:member groups:name="L-Phenylalanine exchange" groups:idRef="R_EX_phe__L_e"/>
-          <groups:member groups:name="3-Hydroxypropanoate exchange" groups:idRef="R_EX_3hpp_e"/>
-          <groups:member groups:name="Agmatine exchange" groups:idRef="R_EX_agm_e"/>
-          <groups:member groups:name="H+ exchange" groups:idRef="R_EX_h_e"/>
-          <groups:member groups:name="Phenethylamine exchange" groups:idRef="R_EX_peamn_e"/>
-          <groups:member groups:name="Octadecanoate (n-C18:0) exchange" groups:idRef="R_EX_ocdca_e"/>
-          <groups:member groups:name="Co2+ exchange" groups:idRef="R_EX_cobalt2_e"/>
-          <groups:member groups:name="Hydrogen sulfide exchange" groups:idRef="R_EX_h2s_e"/>
-          <groups:member groups:name="D-Mannose exchange" groups:idRef="R_EX_man_e"/>
-          <groups:member groups:name="Nitrite exchange" groups:idRef="R_EX_no2_e"/>
-          <groups:member groups:name="D-Mannose 6-phosphate exchange" groups:idRef="R_EX_man6p_e"/>
-          <groups:member groups:name="Sn-Glycero-3-phospho-1-inositol exchange" groups:idRef="R_EX_g3pi_e"/>
-          <groups:member groups:name="3-hydroxycinnamic acid exchange" groups:idRef="R_EX_3hcinnm_e"/>
-          <groups:member groups:name="Silver exchange" groups:idRef="R_EX_ag_e"/>
-          <groups:member groups:name="Octadecenoate (n-C18:1) exchange" groups:idRef="R_EX_ocdcea_e"/>
-          <groups:member groups:name="Maltohexaose exchange" groups:idRef="R_EX_malthx_e"/>
-          <groups:member groups:name="Sodium exchange" groups:idRef="R_EX_na1_e"/>
-          <groups:member groups:name="Adenine exchange" groups:idRef="R_EX_ade_e"/>
-          <groups:member groups:name="Glycerophosphoglycerol exchange" groups:idRef="R_EX_g3pg_e"/>
-          <groups:member groups:name="Nicotinate exchange" groups:idRef="R_EX_nac_e"/>
-          <groups:member groups:name="3,4-Dihydroxyphenylacetaldehyde exchange" groups:idRef="R_EX_34dhpac_e"/>
-          <groups:member groups:name="Guanine exchange" groups:idRef="R_EX_gua_e"/>
-          <groups:member groups:name="Maltose exchange" groups:idRef="R_EX_malt_e"/>
-          <groups:member groups:name="Superoxide anion exchange" groups:idRef="R_EX_o2s_e"/>
-          <groups:member groups:name="3&apos;-AMP exchange" groups:idRef="R_EX_3amp_e"/>
-          <groups:member groups:name="Adenosylcobalamin exchange" groups:idRef="R_EX_adocbl_e"/>
-          <groups:member groups:name="Maltopentaose exchange" groups:idRef="R_EX_maltpt_e"/>
-          <groups:member groups:name="Octanoate (n-C8:0) exchange" groups:idRef="R_EX_octa_e"/>
-          <groups:member groups:name="Fusidic acid exchange" groups:idRef="R_EX_fusa_e"/>
-          <groups:member groups:name="Ammonia exchange" groups:idRef="R_EX_nh4_e"/>
-          <groups:member groups:name="Adenosine exchange" groups:idRef="R_EX_adn_e"/>
-          <groups:member groups:name="Maltotetraose exchange" groups:idRef="R_EX_maltttr_e"/>
-          <groups:member groups:name="Ornithine exchange" groups:idRef="R_EX_orn_e"/>
-          <groups:member groups:name="H2 exchange" groups:idRef="R_EX_h2_e"/>
+          <groups:member groups:name="L-Methionine S-oxide exchange" groups:idRef="R_EX_metsox_S__L_e"/>
+          <groups:member groups:name="Ferric 2,3-dihydroxybenzoylserine exchange" groups:idRef="R_EX_fe3dhbzs_e"/>
           <groups:member groups:name="Chloride exchange" groups:idRef="R_EX_cl_e"/>
-          <groups:member groups:name="Maltotriose exchange" groups:idRef="R_EX_malttr_e"/>
-          <groups:member groups:name="3&apos;-GMP exchange" groups:idRef="R_EX_3gmp_e"/>
-          <groups:member groups:name="NMN exchange" groups:idRef="R_EX_nmn_e"/>
-          <groups:member groups:name="3&apos;-cmp exchange" groups:idRef="R_EX_3cmp_e"/>
+          <groups:member groups:name="D-fructose 6-phosphate exchange" groups:idRef="R_EX_f6p_e"/>
           <groups:member groups:name="Chloramphenicol exchange" groups:idRef="R_EX_cm_e"/>
-          <groups:member groups:name="D-Glucose 1-phosphate exchange" groups:idRef="R_EX_g1p_e"/>
-          <groups:member groups:name="H2O exchange" groups:idRef="R_EX_h2o_e"/>
-          <groups:member groups:name="Nitric oxide exchange" groups:idRef="R_EX_no_e"/>
-          <groups:member groups:name="Hydrogen peroxide exchange" groups:idRef="R_EX_h2o2_e"/>
-          <groups:member groups:name="L-Malate exchange" groups:idRef="R_EX_mal__L_e"/>
-          <groups:member groups:name="O2 exchange" groups:idRef="R_EX_o2_e"/>
-          <groups:member groups:name="Phenylacetaldehyde exchange" groups:idRef="R_EX_pacald_e"/>
-          <groups:member groups:name="Ni2+ exchange" groups:idRef="R_EX_ni2_e"/>
-          <groups:member groups:name="CO2 exchange" groups:idRef="R_EX_co2_e"/>
-          <groups:member groups:name="Novobiocin exchange" groups:idRef="R_EX_novbcn_e"/>
-          <groups:member groups:name="Sn-Glycero-3-phosphoethanolamine exchange" groups:idRef="R_EX_g3pe_e"/>
-          <groups:member groups:name="Orotate exchange" groups:idRef="R_EX_orot_e"/>
-          <groups:member groups:name="D-Malate exchange" groups:idRef="R_EX_mal__D_e"/>
-          <groups:member groups:name="CMP exchange" groups:idRef="R_EX_cmp_e"/>
-          <groups:member groups:name="Sn-Glycero-3-phosphocholine exchange" groups:idRef="R_EX_g3pc_e"/>
-          <groups:member groups:name="D-Sorbitol exchange" groups:idRef="R_EX_sbt__D_e"/>
-          <groups:member groups:name="Enterochelin exchange" groups:idRef="R_EX_enter_e"/>
-          <groups:member groups:name="Phosphoethanolamine KDO(2)-lipid (A) exchange" groups:idRef="R_EX_enlipa_e"/>
+          <groups:member groups:name="Cytidine exchange" groups:idRef="R_EX_cytd_e"/>
+          <groups:member groups:name="3-hydroxycinnamic acid exchange" groups:idRef="R_EX_3hcinnm_e"/>
           <groups:member groups:name="L-Rhamnose exchange" groups:idRef="R_EX_rmn_e"/>
-          <groups:member groups:name="IMP exchange" groups:idRef="R_EX_imp_e"/>
-          <groups:member groups:name="O-Acetyl-L-serine exchange" groups:idRef="R_EX_acser_e"/>
-          <groups:member groups:name="Citrate exchange" groups:idRef="R_EX_cit_e"/>
-          <groups:member groups:name="L-Isoleucine exchange" groups:idRef="R_EX_ile__L_e"/>
-          <groups:member groups:name="D-lactate exchange" groups:idRef="R_EX_lac__D_e"/>
+          <groups:member groups:name="(enterobacterial common antigen)x4 core oligosaccharide lipid A exchange" groups:idRef="R_EX_eca4colipa_e"/>
+          <groups:member groups:name="L-Cysteine exchange" groups:idRef="R_EX_cys__L_e"/>
+          <groups:member groups:name="3&apos;-GMP exchange" groups:idRef="R_EX_3gmp_e"/>
+          <groups:member groups:name="D-Ribose exchange" groups:idRef="R_EX_rib__D_e"/>
+          <groups:member groups:name="Dimethyl sulfoxide exchange" groups:idRef="R_EX_dmso_e"/>
+          <groups:member groups:name="D-Xylonate exchange" groups:idRef="R_EX_dxylnt_e"/>
           <groups:member groups:name="Cytosine exchange" groups:idRef="R_EX_csn_e"/>
-          <groups:member groups:name="Chitobiose exchange" groups:idRef="R_EX_chtbs_e"/>
-          <groups:member groups:name="N-Acetylneuraminate exchange" groups:idRef="R_EX_acnam_e"/>
+          <groups:member groups:name="Propionate exchange" groups:idRef="R_EX_ppa_e"/>
+          <groups:member groups:name="Thiocyanate exchange" groups:idRef="R_EX_tcynt_e"/>
+          <groups:member groups:name="Dimethyl sulfide exchange" groups:idRef="R_EX_dms_e"/>
+          <groups:member groups:name="2-Dehydro-3-deoxy-D-gluconate exchange" groups:idRef="R_EX_2ddglcn_e"/>
+          <groups:member groups:name="Dopamine exchange" groups:idRef="R_EX_dopa_e"/>
+          <groups:member groups:name="Pyridoxine exchange" groups:idRef="R_EX_pydxn_e"/>
+          <groups:member groups:name="DGMP exchange" groups:idRef="R_EX_dgmp_e"/>
+          <groups:member groups:name="Meso-2,6-Diaminoheptanedioate exchange" groups:idRef="R_EX_26dap__M_e"/>
           <groups:member groups:name="Doxorubicin exchange" groups:idRef="R_EX_doxrbcn_e"/>
-          <groups:member groups:name="K+ exchange" groups:idRef="R_EX_k_e"/>
-          <groups:member groups:name="Cob(I)alamin exchange" groups:idRef="R_EX_cbl1_e"/>
+          <groups:member groups:name="Cu2+ exchange" groups:idRef="R_EX_cu2_e"/>
+          <groups:member groups:name="Deoxyguanosine exchange" groups:idRef="R_EX_dgsn_e"/>
+          <groups:member groups:name="(R)-Pantothenate exchange" groups:idRef="R_EX_pnto__R_e"/>
+          <groups:member groups:name="Taurine exchange" groups:idRef="R_EX_taur_e"/>
+          <groups:member groups:name="2-Deoxy-D-glucose exchange" groups:idRef="R_EX_2dglc_e"/>
           <groups:member groups:name="Pyruvate exchange" groups:idRef="R_EX_pyr_e"/>
+          <groups:member groups:name="L-Xylulose exchange" groups:idRef="R_EX_xylu__L_e"/>
+          <groups:member groups:name="2,3-diaminopropionate exchange" groups:idRef="R_EX_23dappa_e"/>
+          <groups:member groups:name="Cu+ exchange" groups:idRef="R_EX_cu_e"/>
+          <groups:member groups:name="L-Phenylalanine exchange" groups:idRef="R_EX_phe__L_e"/>
           <groups:member groups:name="DTMP exchange" groups:idRef="R_EX_dtmp_e"/>
-          <groups:member groups:name="Indole exchange" groups:idRef="R_EX_indole_e"/>
-          <groups:member groups:name="Cadmium exchange" groups:idRef="R_EX_cd2_e"/>
-          <groups:member groups:name="L-Histidine exchange" groups:idRef="R_EX_his__L_e"/>
-          <groups:member groups:name="Cesium ion exchange" groups:idRef="R_EX_cs1_e"/>
+          <groups:member groups:name="Sulfoacetate exchange" groups:idRef="R_EX_sulfac_e"/>
+          <groups:member groups:name="Dihydroxyacetone exchange" groups:idRef="R_EX_dha_e"/>
+          <groups:member groups:name="Deoxyuridine exchange" groups:idRef="R_EX_duri_e"/>
+          <groups:member groups:name="2&apos;,3&apos;-Cyclic CMP exchange" groups:idRef="R_EX_23ccmp_e"/>
+          <groups:member groups:name="L-tartrate exchange" groups:idRef="R_EX_tartr__L_e"/>
+          <groups:member groups:name="3,4-Dihydroxyphenylacetaldehyde exchange" groups:idRef="R_EX_34dhpac_e"/>
+          <groups:member groups:name="DCMP exchange" groups:idRef="R_EX_dcmp_e"/>
           <groups:member groups:name="Quinate exchange" groups:idRef="R_EX_quin_e"/>
-          <groups:member groups:name="Cellobiose exchange" groups:idRef="R_EX_cellb_e"/>
-          <groups:member groups:name="L-Homoserine exchange" groups:idRef="R_EX_hom__L_e"/>
-          <groups:member groups:name="Butanesulfonate exchange" groups:idRef="R_EX_butso3_e"/>
-          <groups:member groups:name="N-Acetyl-D-glucosamine 1-phosphate exchange" groups:idRef="R_EX_acgam1p_e"/>
+          <groups:member groups:name="Phosphate exchange" groups:idRef="R_EX_pi_e"/>
+          <groups:member groups:name="3&apos;-AMP exchange" groups:idRef="R_EX_3amp_e"/>
+          <groups:member groups:name="2&apos;,3&apos;-Cyclic UMP exchange" groups:idRef="R_EX_23cump_e"/>
+          <groups:member groups:name="Hydrogen cyanide exchange" groups:idRef="R_EX_cyan_e"/>
+          <groups:member groups:name="Protoheme exchange" groups:idRef="R_EX_pheme_e"/>
+          <groups:member groups:name="Rifampin exchange" groups:idRef="R_EX_rfamp_e"/>
           <groups:member groups:name="Alpha-D-Ribose 5-phosphate exchange" groups:idRef="R_EX_r5p_e"/>
           <groups:member groups:name="DUMP exchange" groups:idRef="R_EX_dump_e"/>
-          <groups:member groups:name="N-Acetyl-D-mannosamine exchange" groups:idRef="R_EX_acmana_e"/>
-          <groups:member groups:name="Coprogen unloaded (no Fe(III)) exchange" groups:idRef="R_EX_cpgn_un_e"/>
-          <groups:member groups:name="N-Acetyl-D-glucosamine exchange" groups:idRef="R_EX_acgam_e"/>
-          <groups:member groups:name="Cys-Gly exchange" groups:idRef="R_EX_cgly_e"/>
-          <groups:member groups:name="Myo-Inositol exchange" groups:idRef="R_EX_inost_e"/>
-          <groups:member groups:name="Cobinamide exchange" groups:idRef="R_EX_cbi_e"/>
-          <groups:member groups:name="Hexanoate (n-C6:0) exchange" groups:idRef="R_EX_hxa_e"/>
-          <groups:member groups:name="L-Carnitine exchange" groups:idRef="R_EX_crn_e"/>
-          <groups:member groups:name="Deoxyuridine exchange" groups:idRef="R_EX_duri_e"/>
-          <groups:member groups:name="D-Ribose exchange" groups:idRef="R_EX_rib__D_e"/>
-          <groups:member groups:name="L-Idonate exchange" groups:idRef="R_EX_idon__L_e"/>
-          <groups:member groups:name="Calcium exchange" groups:idRef="R_EX_ca2_e"/>
-          <groups:member groups:name="Rifampin exchange" groups:idRef="R_EX_rfamp_e"/>
-          <groups:member groups:name="Choline exchange" groups:idRef="R_EX_chol_e"/>
-          <groups:member groups:name="Isethionic acid exchange" groups:idRef="R_EX_isetac_e"/>
-          <groups:member groups:name="EX ch4 LPAREN e RPAREN" groups:idRef="R_EX_ch4_e"/>
-          <groups:member groups:name="Inosine exchange" groups:idRef="R_EX_ins_e"/>
-          <groups:member groups:name="(enterobacterial common antigen)x4 core oligosaccharide lipid A exchange" groups:idRef="R_EX_eca4colipa_e"/>
-          <groups:member groups:name="N-Acetylmuramate exchange" groups:idRef="R_EX_acmum_e"/>
-          <groups:member groups:name="D-Xylonate exchange" groups:idRef="R_EX_dxylnt_e"/>
-          <groups:member groups:name="Hypoxanthine exchange" groups:idRef="R_EX_hxan_e"/>
-          <groups:member groups:name="D-carnitine exchange" groups:idRef="R_EX_crn__D_e"/>
-          <groups:member groups:name="Urea exchange" groups:idRef="R_EX_urea_e"/>
-          <groups:member groups:name="Urate exchange" groups:idRef="R_EX_urate_e"/>
+          <groups:member groups:name="2,3-Dihydroxypropane-1-sulfonate exchange" groups:idRef="R_EX_dhps_e"/>
+          <groups:member groups:name="Zinc exchange" groups:idRef="R_EX_zn2_e"/>
+          <groups:member groups:name="D-Cysteine exchange" groups:idRef="R_EX_cys__D_e"/>
+          <groups:member groups:name="2&apos;,3&apos;-Cyclic GMP exchange" groups:idRef="R_EX_23cgmp_e"/>
+          <groups:member groups:name="Deoxyinosine exchange" groups:idRef="R_EX_din_e"/>
+          <groups:member groups:name="D-tartrate exchange" groups:idRef="R_EX_tartr__D_e"/>
+          <groups:member groups:name="DIMP exchange" groups:idRef="R_EX_dimp_e"/>
+          <groups:member groups:name="3&apos;-cmp exchange" groups:idRef="R_EX_3cmp_e"/>
+          <groups:member groups:name="Cyanate exchange" groups:idRef="R_EX_cynt_e"/>
+          <groups:member groups:name="Sn-Glycero-3-phosphoethanolamine exchange" groups:idRef="R_EX_g3pe_e"/>
+          <groups:member groups:name="Selenite exchange" groups:idRef="R_EX_slnt_e"/>
+          <groups:member groups:name="Maltose exchange" groups:idRef="R_EX_malt_e"/>
+          <groups:member groups:name="Shikimate exchange" groups:idRef="R_EX_skm_e"/>
+          <groups:member groups:name="D-Sorbitol exchange" groups:idRef="R_EX_sbt__D_e"/>
+          <groups:member groups:name="Ni2+ exchange" groups:idRef="R_EX_ni2_e"/>
+          <groups:member groups:name="Sn-Glycero-3-phosphocholine exchange" groups:idRef="R_EX_g3pc_e"/>
+          <groups:member groups:name="L-Malate exchange" groups:idRef="R_EX_mal__L_e"/>
+          <groups:member groups:name="D-Malate exchange" groups:idRef="R_EX_mal__D_e"/>
+          <groups:member groups:name="Selenate exchange" groups:idRef="R_EX_sel_e"/>
+          <groups:member groups:name="L-Serine exchange" groups:idRef="R_EX_ser__L_e"/>
+          <groups:member groups:name="Fumarate exchange" groups:idRef="R_EX_fum_e"/>
+          <groups:member groups:name="D-Glucose 1-phosphate exchange" groups:idRef="R_EX_g1p_e"/>
+          <groups:member groups:name="D-Serine exchange" groups:idRef="R_EX_ser__D_e"/>
+          <groups:member groups:name="Fusidic acid exchange" groups:idRef="R_EX_fusa_e"/>
           <groups:member groups:name="L-Lyxose exchange" groups:idRef="R_EX_lyx__L_e"/>
+          <groups:member groups:name="Hexadecenoate (n-C16:1) exchange" groups:idRef="R_EX_hdcea_e"/>
+          <groups:member groups:name="5-Dehydro-D-gluconate exchange" groups:idRef="R_EX_5dglcn_e"/>
+          <groups:member groups:name="Hexadecanoate (n-C16:0) exchange" groups:idRef="R_EX_hdca_e"/>
           <groups:member groups:name="UDP-D-glucuronate exchange" groups:idRef="R_EX_udpglcur_e"/>
+          <groups:member groups:name="D-Glucuronate 1-phosphate exchange" groups:idRef="R_EX_glcur1p_e"/>
+          <groups:member groups:name="Hydrogen sulfide exchange" groups:idRef="R_EX_h2s_e"/>
+          <groups:member groups:name="4-Hydroxyphenylacetaldehyde exchange" groups:idRef="R_EX_4hoxpacd_e"/>
+          <groups:member groups:name="L-Isoleucine exchange" groups:idRef="R_EX_ile__L_e"/>
+          <groups:member groups:name="Arbutin exchange" groups:idRef="R_EX_arbt_e"/>
+          <groups:member groups:name="D-Glyceraldehyde exchange" groups:idRef="R_EX_glyald_e"/>
+          <groups:member groups:name="D-Mannose exchange" groups:idRef="R_EX_man_e"/>
+          <groups:member groups:name="D-Methionine exchange" groups:idRef="R_EX_met__D_e"/>
           <groups:member groups:name="UDPgalactose exchange" groups:idRef="R_EX_udpgal_e"/>
+          <groups:member groups:name="K+ exchange" groups:idRef="R_EX_k_e"/>
+          <groups:member groups:name="L-Arabinose exchange" groups:idRef="R_EX_arab__L_e"/>
+          <groups:member groups:name="D-Glucarate exchange" groups:idRef="R_EX_glcr_e"/>
+          <groups:member groups:name="H+ exchange" groups:idRef="R_EX_h_e"/>
+          <groups:member groups:name="L-Idonate exchange" groups:idRef="R_EX_idon__L_e"/>
+          <groups:member groups:name="Glycine exchange" groups:idRef="R_EX_gly_e"/>
+          <groups:member groups:name="3-Hydroxypropanoate exchange" groups:idRef="R_EX_3hpp_e"/>
+          <groups:member groups:name="H2O exchange" groups:idRef="R_EX_h2o_e"/>
+          <groups:member groups:name="Methylphosphonic acid exchange" groups:idRef="R_EX_mepn_e"/>
+          <groups:member groups:name="Hg2+ exchange" groups:idRef="R_EX_hg2_e"/>
+          <groups:member groups:name="L-Tyrosine exchange" groups:idRef="R_EX_tyr__L_e"/>
+          <groups:member groups:name="Isethionic acid exchange" groups:idRef="R_EX_isetac_e"/>
+          <groups:member groups:name="D-Glucosamine exchange" groups:idRef="R_EX_gam_e"/>
+          <groups:member groups:name="GTP exchange" groups:idRef="R_EX_gtp_e"/>
+          <groups:member groups:name="D-Mannose 6-phosphate exchange" groups:idRef="R_EX_man6p_e"/>
+          <groups:member groups:name="Allantoin exchange" groups:idRef="R_EX_alltn_e"/>
+          <groups:member groups:name="IMP exchange" groups:idRef="R_EX_imp_e"/>
+          <groups:member groups:name="2(alpha-D-Mannosyl)-D-glycerate exchange" groups:idRef="R_EX_manglyc_e"/>
           <groups:member groups:name="Phosphotyrosine exchange" groups:idRef="R_EX_tyrp_e"/>
-          <groups:member groups:name="L-Lysine exchange" groups:idRef="R_EX_lys__L_e"/>
+          <groups:member groups:name="D-Glucuronate exchange" groups:idRef="R_EX_glcur_e"/>
+          <groups:member groups:name="(S)-Propane-1,2-diol exchange" groups:idRef="R_EX_12ppd__S_e"/>
+          <groups:member groups:name="Maltohexaose exchange" groups:idRef="R_EX_malthx_e"/>
+          <groups:member groups:name="3-(3-hydroxy-phenyl)propionate exchange" groups:idRef="R_EX_3hpppn_e"/>
+          <groups:member groups:name="Gamma-butyrobetaine exchange" groups:idRef="R_EX_gbbtn_e"/>
+          <groups:member groups:name="D-Glucose exchange" groups:idRef="R_EX_glc__D_e"/>
+          <groups:member groups:name="Indole exchange" groups:idRef="R_EX_indole_e"/>
+          <groups:member groups:name="2&apos;,3&apos;-Cyclic AMP exchange" groups:idRef="R_EX_23camp_e"/>
+          <groups:member groups:name="3&apos;-UMP exchange" groups:idRef="R_EX_3ump_e"/>
+          <groups:member groups:name="L-Histidine exchange" groups:idRef="R_EX_his__L_e"/>
           <groups:member groups:name="UDP-N-acetyl-D-glucosamine exchange" groups:idRef="R_EX_uacgam_e"/>
-          <groups:member groups:name="L-Lactate exchange" groups:idRef="R_EX_lac__L_e"/>
+          <groups:member groups:name="L-Glutamate exchange" groups:idRef="R_EX_glu__L_e"/>
+          <groups:member groups:name="Guanine exchange" groups:idRef="R_EX_gua_e"/>
+          <groups:member groups:name="Hexanoate (n-C6:0) exchange" groups:idRef="R_EX_hxa_e"/>
+          <groups:member groups:name="1,4-alpha-D-glucan exchange" groups:idRef="R_EX_14glucan_e"/>
+          <groups:member groups:name="Hydrogen peroxide exchange" groups:idRef="R_EX_h2o2_e"/>
+          <groups:member groups:name="Methanol exchange" groups:idRef="R_EX_meoh_e"/>
+          <groups:member groups:name="L-Homoserine exchange" groups:idRef="R_EX_hom__L_e"/>
+          <groups:member groups:name="GDP exchange" groups:idRef="R_EX_gdp_e"/>
+          <groups:member groups:name="D-Gluconate exchange" groups:idRef="R_EX_glcn_e"/>
+          <groups:member groups:name="Inosine exchange" groups:idRef="R_EX_ins_e"/>
+          <groups:member groups:name="Maltopentaose exchange" groups:idRef="R_EX_maltpt_e"/>
           <groups:member groups:name="UDPglucose exchange" groups:idRef="R_EX_udpg_e"/>
-          <groups:member groups:name="Tungstate exchange" groups:idRef="R_EX_tungs_e"/>
-          <groups:member groups:name="Lactose exchange" groups:idRef="R_EX_lcts_e"/>
+          <groups:member groups:name="L-Glutamine exchange" groups:idRef="R_EX_gln__L_e"/>
+          <groups:member groups:name="4-aminobenzoyl-glutamate exchange" groups:idRef="R_EX_4abzglu_e"/>
+          <groups:member groups:name="Hypoxanthine exchange" groups:idRef="R_EX_hxan_e"/>
           <groups:member groups:name="UDP-N-acetyl-D-galactosamine exchange" groups:idRef="R_EX_udpacgal_e"/>
-          <groups:member groups:name="Lipoate exchange" groups:idRef="R_EX_lipoate_e"/>
-          <groups:member groups:name="L-Leucine exchange" groups:idRef="R_EX_leu__L_e"/>
-          <groups:member groups:name="L-Tryptophan exchange" groups:idRef="R_EX_trp__L_e"/>
-          <groups:member groups:name="Fumarate exchange" groups:idRef="R_EX_fum_e"/>
-          <groups:member groups:name="Hg2+ exchange" groups:idRef="R_EX_hg2_e"/>
-          <groups:member groups:name="Nitrous oxide exchange" groups:idRef="R_EX_n2o_e"/>
-          <groups:member groups:name="L-Tyrosine exchange" groups:idRef="R_EX_tyr__L_e"/>
-          <groups:member groups:name="Trehalose exchange" groups:idRef="R_EX_tre_e"/>
-          <groups:member groups:name="Glycerol exchange" groups:idRef="R_EX_glyc_e"/>
-          <groups:member groups:name="Hexadecenoate (n-C16:1) exchange" groups:idRef="R_EX_hdcea_e"/>
-          <groups:member groups:name="Tyramine exchange" groups:idRef="R_EX_tym_e"/>
-          <groups:member groups:name="L-Fucose exchange" groups:idRef="R_EX_fuc__L_e"/>
-          <groups:member groups:name="Glycine betaine exchange" groups:idRef="R_EX_glyb_e"/>
-          <groups:member groups:name="L-Valine exchange" groups:idRef="R_EX_val__L_e"/>
-          <groups:member groups:name="Fe-enterobactin exchange" groups:idRef="R_EX_feenter_e"/>
-          <groups:member groups:name="Thiosulfate exchange" groups:idRef="R_EX_tsul_e"/>
-          <groups:member groups:name="D-Galactonate exchange" groups:idRef="R_EX_galctn__D_e"/>
+          <groups:member groups:name="Melibiose exchange" groups:idRef="R_EX_melib_e"/>
+          <groups:member groups:name="Maltotetraose exchange" groups:idRef="R_EX_maltttr_e"/>
+          <groups:member groups:name="Maltotriose exchange" groups:idRef="R_EX_malttr_e"/>
+          <groups:member groups:name="AMP exchange" groups:idRef="R_EX_amp_e"/>
+          <groups:member groups:name="(R)-Propane-1,2-diol exchange" groups:idRef="R_EX_12ppd__R_e"/>
+          <groups:member groups:name="H2 exchange" groups:idRef="R_EX_h2_e"/>
+          <groups:member groups:name="Myo-Inositol exchange" groups:idRef="R_EX_inost_e"/>
+          <groups:member groups:name="4-Aminobutanoate exchange" groups:idRef="R_EX_4abut_e"/>
+          <groups:member groups:name="1,5-Diaminopentane exchange" groups:idRef="R_EX_15dap_e"/>
+          <groups:member groups:name="Hepta-acylated core oligosaccharide lipid A (E. coli) exchange" groups:idRef="R_EX_hacolipa_e"/>
+          <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramic acid exchange" groups:idRef="R_EX_anhgm_e"/>
+          <groups:member groups:name="Hepta-acylated KDO(2)-lipid (A) exchange" groups:idRef="R_EX_halipa_e"/>
+          <groups:member groups:name="N-Acetylneuraminate exchange" groups:idRef="R_EX_acnam_e"/>
+          <groups:member groups:name="Sucrose exchange" groups:idRef="R_EX_sucr_e"/>
+          <groups:member groups:name="Cesium ion exchange" groups:idRef="R_EX_cs1_e"/>
+          <groups:member groups:name="Nitrite exchange" groups:idRef="R_EX_no2_e"/>
+          <groups:member groups:name="N-Acetylmuramate exchange" groups:idRef="R_EX_acmum_e"/>
+          <groups:member groups:name="Dodecanoate (n-C12:0) exchange" groups:idRef="R_EX_ddca_e"/>
           <groups:member groups:name="(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran exchange" groups:idRef="R_EX_mththf_e"/>
-          <groups:member groups:name="Uridine exchange" groups:idRef="R_EX_uri_e"/>
-          <groups:member groups:name="Ferroxamine exchange" groups:idRef="R_EX_feoxam_e"/>
-          <groups:member groups:name="L-Threonine exchange" groups:idRef="R_EX_thr__L_e"/>
-          <groups:member groups:name="Tetradecanoate (n-C14:0) exchange" groups:idRef="R_EX_ttdca_e"/>
-          <groups:member groups:name="UMP exchange" groups:idRef="R_EX_ump_e"/>
-          <groups:member groups:name="D-Glucosamine 6-phosphate exchange" groups:idRef="R_EX_gam6p_e"/>
-          <groups:member groups:name="L-Prolinylglycine exchange" groups:idRef="R_EX_progly_e"/>
-          <groups:member groups:name="D-Glyceraldehyde exchange" groups:idRef="R_EX_glyald_e"/>
-          <groups:member groups:name="Ferroxamine minus Fe(3) exchange" groups:idRef="R_EX_feoxam_un_e"/>
-          <groups:member groups:name="L-Threonine O-3-phosphate exchange" groups:idRef="R_EX_thrp_e"/>
-          <groups:member groups:name="D-Galactarate exchange" groups:idRef="R_EX_galct__D_e"/>
-          <groups:member groups:name="D-Galactose exchange" groups:idRef="R_EX_gal_e"/>
+          <groups:member groups:name="Succinate exchange" groups:idRef="R_EX_succ_e"/>
+          <groups:member groups:name="NMN exchange" groups:idRef="R_EX_nmn_e"/>
+          <groups:member groups:name="Deoxycytidine exchange" groups:idRef="R_EX_dcyt_e"/>
+          <groups:member groups:name="Chitobiose exchange" groups:idRef="R_EX_chtbs_e"/>
+          <groups:member groups:name="N-Acetyl-D-galactosamine 1-phosphate exchange" groups:idRef="R_EX_acgal1p_e"/>
+          <groups:member groups:name="Choline exchange" groups:idRef="R_EX_chol_e"/>
+          <groups:member groups:name="L-Carnitine exchange" groups:idRef="R_EX_crn_e"/>
+          <groups:member groups:name="Co2+ exchange" groups:idRef="R_EX_cobalt2_e"/>
+          <groups:member groups:name="Methanesulfonate exchange" groups:idRef="R_EX_mso3_e"/>
+          <groups:member groups:name="Cob(I)alamin exchange" groups:idRef="R_EX_cbl1_e"/>
+          <groups:member groups:name="Nitrous oxide exchange" groups:idRef="R_EX_n2o_e"/>
+          <groups:member groups:name="Deoxyadenosine exchange" groups:idRef="R_EX_dad_2_e"/>
+          <groups:member groups:name="N-Acetyl-D-galactosamine exchange" groups:idRef="R_EX_acgal_e"/>
+          <groups:member groups:name="DAMP exchange" groups:idRef="R_EX_damp_e"/>
           <groups:member groups:name="S-Methyl-L-methionine exchange" groups:idRef="R_EX_mmet_e"/>
-          <groups:member groups:name="D-Galacturonate exchange" groups:idRef="R_EX_galur_e"/>
-          <groups:member groups:name="Thymine exchange" groups:idRef="R_EX_thym_e"/>
-          <groups:member groups:name="FMN exchange" groups:idRef="R_EX_fmn_e"/>
+          <groups:member groups:name="Sulfur dioxide exchange" groups:idRef="R_EX_so2_e"/>
+          <groups:member groups:name="Sulfite exchange" groups:idRef="R_EX_so3_e"/>
+          <groups:member groups:name="Sodium exchange" groups:idRef="R_EX_na1_e"/>
+          <groups:member groups:name="Cadmium exchange" groups:idRef="R_EX_cd2_e"/>
           <groups:member groups:name="Mn2+ exchange" groups:idRef="R_EX_mn2_e"/>
-          <groups:member groups:name="Glycerophosphoserine exchange" groups:idRef="R_EX_g3ps_e"/>
-          <groups:member groups:name="Tetracycline exchange" groups:idRef="R_EX_ttrcyc_e"/>
-          <groups:member groups:name="Tetradecenoate (n-C14:1) exchange" groups:idRef="R_EX_ttdcea_e"/>
-          <groups:member groups:name="Formate exchange" groups:idRef="R_EX_for_e"/>
-          <groups:member groups:name="L-Proline exchange" groups:idRef="R_EX_pro__L_e"/>
-          <groups:member groups:name="D-Glucose 6-phosphate exchange" groups:idRef="R_EX_g6p_e"/>
-          <groups:member groups:name="Uracil exchange" groups:idRef="R_EX_ura_e"/>
-          <groups:member groups:name="Thymidine exchange" groups:idRef="R_EX_thymd_e"/>
-          <groups:member groups:name="Phosphonate exchange" groups:idRef="R_EX_ppt_e"/>
-          <groups:member groups:name="D-Fructose exchange" groups:idRef="R_EX_fru_e"/>
-          <groups:member groups:name="Hepta-acylated core oligosaccharide lipid A (E. coli) exchange" groups:idRef="R_EX_hacolipa_e"/>
-          <groups:member groups:name="Phenylpropanoate exchange" groups:idRef="R_EX_pppn_e"/>
-          <groups:member groups:name="(R)-Glycerate exchange" groups:idRef="R_EX_glyc__R_e"/>
-          <groups:member groups:name="Hexadecanoate (n-C16:0) exchange" groups:idRef="R_EX_hdca_e"/>
-          <groups:member groups:name="Glycerol 3-phosphate exchange" groups:idRef="R_EX_glyc3p_e"/>
-          <groups:member groups:name="Trimethylamine N-oxide exchange" groups:idRef="R_EX_tmao_e"/>
-          <groups:member groups:name="D-Fructuronate exchange" groups:idRef="R_EX_fruur_e"/>
-          <groups:member groups:name="D-Mannitol exchange" groups:idRef="R_EX_mnl_e"/>
-          <groups:member groups:name="L-Glutamine exchange" groups:idRef="R_EX_gln__L_e"/>
-          <groups:member groups:name="Glycerol 2-phosphate exchange" groups:idRef="R_EX_glyc2p_e"/>
-          <groups:member groups:name="Methanesulfonate exchange" groups:idRef="R_EX_mso3_e"/>
-          <groups:member groups:name="L-Galactonate exchange" groups:idRef="R_EX_galctn__L_e"/>
-          <groups:member groups:name="Glycine exchange" groups:idRef="R_EX_gly_e"/>
+          <groups:member groups:name="Nicotinate exchange" groups:idRef="R_EX_nac_e"/>
+          <groups:member groups:name="Coprogen exchange" groups:idRef="R_EX_cpgn_e"/>
+          <groups:member groups:name="D-carnitine exchange" groups:idRef="R_EX_crn__D_e"/>
+          <groups:member groups:name="Cellobiose exchange" groups:idRef="R_EX_cellb_e"/>
           <groups:member groups:name="Molybdate exchange" groups:idRef="R_EX_mobd_e"/>
-          <groups:member groups:name="Trimethylamine exchange" groups:idRef="R_EX_tma_e"/>
-          <groups:member groups:name="Alpha-D-Galactose 1-phosphate exchange" groups:idRef="R_EX_gal1p_e"/>
-          <groups:member groups:name="L-Glutamate exchange" groups:idRef="R_EX_glu__L_e"/>
-          <groups:member groups:name="Hepta-acylated KDO(2)-lipid (A) exchange" groups:idRef="R_EX_halipa_e"/>
-          <groups:member groups:name="Fructoselysine exchange" groups:idRef="R_EX_frulys_e"/>
-          <groups:member groups:name="Beta D-Galactose exchange" groups:idRef="R_EX_gal_bD_e"/>
-          <groups:member groups:name="Galactitol exchange" groups:idRef="R_EX_galt_e"/>
+          <groups:member groups:name="Sulfate exchange" groups:idRef="R_EX_so4_e"/>
+          <groups:member groups:name="N-Acetyl-D-glucosamine 1-phosphate exchange" groups:idRef="R_EX_acgam1p_e"/>
+          <groups:member groups:name="Ammonia exchange" groups:idRef="R_EX_nh4_e"/>
+          <groups:member groups:name="N-Acetyl-D-mannosamine exchange" groups:idRef="R_EX_acmana_e"/>
+          <groups:member groups:name="EX ch4 LPAREN e RPAREN" groups:idRef="R_EX_ch4_e"/>
+          <groups:member groups:name="Coprogen unloaded (no Fe(III)) exchange" groups:idRef="R_EX_cpgn_un_e"/>
+          <groups:member groups:name="D-Mannitol exchange" groups:idRef="R_EX_mnl_e"/>
+          <groups:member groups:name="N-Acetyl-D-glucosamine exchange" groups:idRef="R_EX_acgam_e"/>
+          <groups:member groups:name="Cys-Gly exchange" groups:idRef="R_EX_cgly_e"/>
+          <groups:member groups:name="Sulphoquinovose exchange" groups:idRef="R_EX_sq_e"/>
+          <groups:member groups:name="Spermidine exchange" groups:idRef="R_EX_spmd_e"/>
+          <groups:member groups:name="Decanoate (n-C10:0) exchange" groups:idRef="R_EX_dca_e"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group11" sboTerm="SBO:0000633" groups:id="G_group11" groups:name="Folate Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
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           <groups:member groups:name="Tetrahydrofolate aminomethyltransferase" groups:idRef="R_THFAT"/>
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-          <groups:member groups:name="5,10-methylenetetrahydrofolate reductase (NADH)" groups:idRef="R_MTHFR2"/>
+          <groups:member groups:name="Methylenetetrahydrofolate dehydrogenase (NADP)" groups:idRef="R_MTHFD"/>
+          <groups:member groups:name="Formate-tetrahydrofolate ligase" groups:idRef="R_FTHFLi"/>
+          <groups:member groups:name="Methenyltetrahydrofolate cyclohydrolase" groups:idRef="R_MTHFC"/>
           <groups:member groups:name="Glycolaldehyde dehydrogenase" groups:idRef="R_GCALDD"/>
-          <groups:member groups:name="Glycine Cleavage System" groups:idRef="R_GLYCL"/>
           <groups:member groups:name="Aminomethyltransferase" groups:idRef="R_FOMETRi"/>
-          <groups:member groups:name="Methenyltetrahydrofolate cyclohydrolase" groups:idRef="R_MTHFC"/>
-          <groups:member groups:name="Methylenetetrahydrofolate dehydrogenase (NADP)" groups:idRef="R_MTHFD"/>
+          <groups:member groups:name="Glycine Cleavage System" groups:idRef="R_GLYCL"/>
+          <groups:member groups:name="Formyltetrahydrofolate deformylase" groups:idRef="R_FTHFD"/>
+          <groups:member groups:name="5,10-methylenetetrahydrofolate reductase (NADH)" groups:idRef="R_MTHFR2"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group12" sboTerm="SBO:0000633" groups:id="G_group12" groups:name="Glutamate Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
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-          <groups:member groups:name="Glutaminase" groups:idRef="R_GLUN"/>
           <groups:member groups:name="Glutamate Decarboxylase" groups:idRef="R_GLUDC"/>
-          <groups:member groups:name="Glutamine synthetase" groups:idRef="R_GLNS"/>
+          <groups:member groups:name="Glutamate dehydrogenase (NADP)" groups:idRef="R_GLUDy"/>
           <groups:member groups:name="Glutaminase" groups:idRef="R_GLUNpp"/>
+          <groups:member groups:name="Glutamine synthetase" groups:idRef="R_GLNS"/>
           <groups:member groups:name="Glutamate synthase (NADPH)" groups:idRef="R_GLUSy"/>
+          <groups:member groups:name="Glutaminase" groups:idRef="R_GLUN"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group13" sboTerm="SBO:0000633" groups:id="G_group13" groups:name="Glycerophospholipid Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
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           <groups:member groups:name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C18:1)" groups:idRef="R_LPLIPAL2E181"/>
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+          <groups:member groups:name="Lysophospholipase L1 (2-acylglycerophosphotidate, n-C18:0) (periplasm)" groups:idRef="R_LPLIPAL1A180pp"/>
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           <groups:member groups:name="Phospholipase A1 (phosphatidate, n-C12:0) (periplasm)" groups:idRef="R_PLIPA1A120pp"/>
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-          <groups:member groups:name="2-acyl-glycerophospho-ethanolamine acyltransferase (n-C12:0)" groups:idRef="R_2AGPEAT120"/>
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+          <groups:member groups:name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C16:1)" groups:idRef="R_LPLIPAL2ATG161"/>
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           <groups:member groups:name="Phospholipase A2 (phosphatidate, n-C12:0) (periplasm)" groups:idRef="R_PLIPA2A120pp"/>
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-          <groups:member groups:name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C18:0)" groups:idRef="R_LPLIPAL2E180"/>
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+          <groups:member groups:name="Phospholipase A1 (phosphatidylglycerol, n-C16:0) (periplasm)" groups:idRef="R_PLIPA1G160pp"/>
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+          <groups:member groups:name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C14:1)" groups:idRef="R_LPLIPAL2G141"/>
+          <groups:member groups:name="Lysophospholipase L2 (2-acylglycerophosphoethanolamine, n-C16:0)" groups:idRef="R_LPLIPAL2E160"/>
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           <groups:member groups:name="Diacylglycerol kinase (n-C16:0)" groups:idRef="R_DAGK160"/>
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-          <groups:member groups:name="Phosphatidylglycerol synthase (n-C16:1)" groups:idRef="R_PGSA161"/>
+          <groups:member groups:name="Lysophospholipase L2 (2-acylglycerophosphoglycerol, n-C12:0)" groups:idRef="R_LPLIPAL2G120"/>
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           <groups:member groups:name="Cardiolipin synthase (periplasmic, n-C18:0)" groups:idRef="R_CLPNS180pp"/>
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-          <groups:member groups:name="Phospholipase A2 (phosphatidylglycerol, n-C16:1) (periplasm)" groups:idRef="R_PLIPA2G161pp"/>
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+          <groups:member groups:name="Lysophospholipase L2 (acyltransferase, 2-acyl-glycerophosphoglycerol, n-C18:1)" groups:idRef="R_LPLIPAL2ATG181"/>
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+          <groups:member groups:name="Glycerophosphodiester phosphodiesterase (Glycerophosphoethanolamine)" groups:idRef="R_GPDDA2"/>
+          <groups:member groups:name="Phospholipase A1 (phosphatidate, n-C16:1) (periplasm)" groups:idRef="R_PLIPA1A161pp"/>
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+          <groups:member groups:name="Cardiolipin hydrolase (periplasm, n-C14:0)" groups:idRef="R_CLPNH140pp"/>
+          <groups:member groups:name="Diacylglycerol kinase (n-C18:0)" groups:idRef="R_DAGK180"/>
+          <groups:member groups:name="Glycerophosphodiester phosphodiesterase (Glycerophosphoserine)" groups:idRef="R_GPDDA3pp"/>
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+          <groups:member groups:name="Phosphatidate phosphatase (n-C12:0)" groups:idRef="R_PAPA120"/>
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         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group14" sboTerm="SBO:0000633" groups:id="G_group14" groups:name="Glycine and Serine Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
           <groups:member groups:name="Phosphoserine transaminase" groups:idRef="R_PSERT"/>
+          <groups:member groups:name="D-serine dehydrogenase" groups:idRef="R_DSERDHr"/>
+          <groups:member groups:name="L-serine dehydrogenase" groups:idRef="R_LSERDHr"/>
+          <groups:member groups:name="Phosphoserine phosphatase (L-serine)" groups:idRef="R_PSP_L"/>
           <groups:member groups:name="L-threonine dehydrogenase" groups:idRef="R_THRD"/>
           <groups:member groups:name="4-hydroxy-L-threonine aldolase" groups:idRef="R_4HTHRA"/>
           <groups:member groups:name="4-Hydroxy-L-threonine kinase" groups:idRef="R_4HTHRK"/>
           <groups:member groups:name="Glycerate kinase" groups:idRef="R_GLYCK2"/>
-          <groups:member groups:name="D-serine dehydrogenase" groups:idRef="R_DSERDHr"/>
+          <groups:member groups:name="Sarcosine oxidase" groups:idRef="R_SARCOX"/>
+          <groups:member groups:name="L-serine deaminase" groups:idRef="R_SERD_L"/>
+          <groups:member groups:name="(R)-alpha-hydroxyglutarate dehydrogenase" groups:idRef="R_ARHGDx"/>
           <groups:member groups:name="Glycine hydroxymethyltransferase, reversible" groups:idRef="R_GHMT2r"/>
-          <groups:member groups:name="N-methyltryptophan oxidase" groups:idRef="R_MTRPOX"/>
+          <groups:member groups:name="S-2-hydroxyglutarate oxidase" groups:idRef="R_SHGO"/>
           <groups:member groups:name="(S)-alpha-hydroxyglutarate dehydrogenase" groups:idRef="R_AHGDx"/>
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-          <groups:member groups:name="Sarcosine oxidase" groups:idRef="R_SARCOX"/>
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           <groups:member groups:name="D-serine deaminase" groups:idRef="R_SERD_D"/>
-          <groups:member groups:name="L-serine dehydrogenase" groups:idRef="R_LSERDHr"/>
+          <groups:member groups:name="Phospho-L-serine phosphatase (periplasmic)" groups:idRef="R_PSP_Lpp"/>
           <groups:member groups:name="Glycine C-acetyltransferase" groups:idRef="R_GLYAT"/>
-          <groups:member groups:name="(R)-alpha-hydroxyglutarate dehydrogenase" groups:idRef="R_ARHGDx"/>
-          <groups:member groups:name="S-2-hydroxyglutarate oxidase" groups:idRef="R_SHGO"/>
-          <groups:member groups:name="L-serine deaminase" groups:idRef="R_SERD_L"/>
-          <groups:member groups:name="Phosphoserine phosphatase (L-serine)" groups:idRef="R_PSP_L"/>
           <groups:member groups:name="Phosphoglycerate dehydrogenase" groups:idRef="R_PGCD"/>
         </groups:listOfMembers>
       </groups:group>
@@ -169544,1521 +169434,1520 @@
         <groups:listOfMembers>
           <groups:member groups:name="1,4-alpha-glucan branching enzyme (glycogen -&gt; bglycogen)" groups:idRef="R_GLBRAN2"/>
           <groups:member groups:name="Glyceraldehyde-3-phosphate dehydrogenase" groups:idRef="R_GAPD"/>
-          <groups:member groups:name="Glucose-6-phosphate phosphatase" groups:idRef="R_G6PP"/>
-          <groups:member groups:name="Glycogen synthase (ADPGlc)" groups:idRef="R_GLCS1"/>
-          <groups:member groups:name="Pyruvate dehydrogenase" groups:idRef="R_PDH"/>
+          <groups:member groups:name="Glucose-6-phosphate isomerase" groups:idRef="R_PGI"/>
           <groups:member groups:name="Glycogen phosphorylase" groups:idRef="R_GLCP"/>
-          <groups:member groups:name="Phosphoglycerate kinase" groups:idRef="R_PGK"/>
+          <groups:member groups:name="Glycogen debranching enzyme (bglycogen -&gt; glycogen)" groups:idRef="R_GLDBRAN2"/>
           <groups:member groups:name="Hexokinase (D-glucose:ATP)" groups:idRef="R_HEX1"/>
-          <groups:member groups:name="Glycogen phosphorylase" groups:idRef="R_GLCP2"/>
-          <groups:member groups:name="Glucose-1-phosphate adenylyltransferase" groups:idRef="R_GLGC"/>
+          <groups:member groups:name="Pyruvate kinase" groups:idRef="R_PYK"/>
+          <groups:member groups:name="Glucose-6-phosphate phosphatase" groups:idRef="R_G6PP"/>
           <groups:member groups:name="Enolase" groups:idRef="R_ENO"/>
-          <groups:member groups:name="Glycogen debranching enzyme (bglycogen -&gt; glycogen)" groups:idRef="R_GLDBRAN2"/>
+          <groups:member groups:name="Glycogen synthase (ADPGlc)" groups:idRef="R_GLCS1"/>
+          <groups:member groups:name="Pyruvate dehydrogenase" groups:idRef="R_PDH"/>
           <groups:member groups:name="Phosphoenolpyruvate synthase" groups:idRef="R_PPS"/>
+          <groups:member groups:name="Glycogen phosphorylase" groups:idRef="R_GLCP2"/>
+          <groups:member groups:name="Phosphofructokinase" groups:idRef="R_PFK"/>
+          <groups:member groups:name="Phosphoglycerate kinase" groups:idRef="R_PGK"/>
           <groups:member groups:name="Glucose-1-phosphatase" groups:idRef="R_G1PPpp"/>
+          <groups:member groups:name="Fructose 6-phosphate aldolase" groups:idRef="R_F6PA"/>
           <groups:member groups:name="Phosphoglycerate mutase" groups:idRef="R_PGM"/>
-          <groups:member groups:name="Fructose-bisphosphatase" groups:idRef="R_FBP"/>
           <groups:member groups:name="Glucose-1-phosphatase" groups:idRef="R_G1PP"/>
+          <groups:member groups:name="Glucose-1-phosphate adenylyltransferase" groups:idRef="R_GLGC"/>
           <groups:member groups:name="Triose-phosphate isomerase" groups:idRef="R_TPI"/>
-          <groups:member groups:name="Phosphofructokinase" groups:idRef="R_PFK"/>
-          <groups:member groups:name="Pyruvate kinase" groups:idRef="R_PYK"/>
-          <groups:member groups:name="Fructose 6-phosphate aldolase" groups:idRef="R_F6PA"/>
+          <groups:member groups:name="Fructose-bisphosphatase" groups:idRef="R_FBP"/>
           <groups:member groups:name="Fructose-bisphosphate aldolase" groups:idRef="R_FBA"/>
-          <groups:member groups:name="Glucose-6-phosphate isomerase" groups:idRef="R_PGI"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group16" sboTerm="SBO:0000633" groups:id="G_group16" groups:name="Glyoxylate Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="Glycolate dehydrogenase (NAD)" groups:idRef="R_GLYCLTDx"/>
-          <groups:member groups:name="Dehydroglycine Hydratase" groups:idRef="R_DHGLYH"/>
-          <groups:member groups:name="Glycerate kinase" groups:idRef="R_GLYCK"/>
           <groups:member groups:name="Glycolate dehydrogenase (NADP)" groups:idRef="R_GLYCLTDy"/>
+          <groups:member groups:name="Glycolate dehydrogenase (NAD)" groups:idRef="R_GLYCLTDx"/>
           <groups:member groups:name="Glyoxalate carboligase" groups:idRef="R_GLXCL"/>
+          <groups:member groups:name="Dehydroglycine Hydratase" groups:idRef="R_DHGLYH"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group17" sboTerm="SBO:0000633" groups:id="G_group17" groups:name="Histidine Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
+          <groups:member groups:name="Histidinol dehydrogenase" groups:idRef="R_HISTD"/>
           <groups:member groups:name="Phosphoribosylpyrophosphate synthetase" groups:idRef="R_PRPPS"/>
-          <groups:member groups:name="ATP phosphoribosyltransferase" groups:idRef="R_ATPPRT"/>
           <groups:member groups:name="Phosphoribosyl-AMP cyclohydrolase" groups:idRef="R_PRAMPC"/>
+          <groups:member groups:name="Phosphoribosyl-ATP pyrophosphatase" groups:idRef="R_PRATPP"/>
           <groups:member groups:name="1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase" groups:idRef="R_PRMICI"/>
+          <groups:member groups:name="ATP phosphoribosyltransferase" groups:idRef="R_ATPPRT"/>
           <groups:member groups:name="Imidazoleglycerol-phosphate dehydratase" groups:idRef="R_IGPDH"/>
+          <groups:member groups:name="Histidinol-phosphatase" groups:idRef="R_HISTP"/>
           <groups:member groups:name="Histidinol-phosphate transaminase" groups:idRef="R_HSTPT"/>
-          <groups:member groups:name="Histidinol dehydrogenase" groups:idRef="R_HISTD"/>
-          <groups:member groups:name="Phosphoribosyl-ATP pyrophosphatase" groups:idRef="R_PRATPP"/>
           <groups:member groups:name="Imidazole-glycerol-3-phosphate synthase" groups:idRef="R_IG3PS"/>
-          <groups:member groups:name="Histidinol-phosphatase" groups:idRef="R_HISTP"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group18" sboTerm="SBO:0000633" groups:id="G_group18" groups:name="Inorganic Ion Transport and Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="Tungstate transport via ABC system (periplasm)" groups:idRef="R_TUNGSabcpp"/>
-          <groups:member groups:name="Ferric-dicitrate reductase via nadph" groups:idRef="R_FE3DCITR5"/>
-          <groups:member groups:name="Selenate glutathione reductase" groups:idRef="R_SELGTHR"/>
+          <groups:member groups:name="Mercury (Hg+2) transport out via proton antiport (periplasm)" groups:idRef="R_HG2t3pp"/>
+          <groups:member groups:name="Sulfate transport in via proton symport (periplasm to cytoplasm)" groups:idRef="R_SO4t2pp"/>
+          <groups:member groups:name="Copper (Cu +1) ABC transporter (periplasm)" groups:idRef="R_CU1abcpp"/>
+          <groups:member groups:name="Ferroxamine (minus Fe3) secretion (to extracellular)" groups:idRef="R_FEOXAMUtex"/>
+          <groups:member groups:name="Manganese transport in via permease (no H+)" groups:idRef="R_MN2tpp"/>
+          <groups:member groups:name="Iron transport from ferric-dicitrate via ABC system (periplasm)" groups:idRef="R_FE3DCITabcpp"/>
+          <groups:member groups:name="Molybdate transport via ABC system (periplasm)" groups:idRef="R_MOBDabcpp"/>
+          <groups:member groups:name="Nitrate transport in via nitrite antiport (periplasm)" groups:idRef="R_NO3t7pp"/>
+          <groups:member groups:name="Aerobactin Fe-loading reaction (spontaneous)" groups:idRef="R_ARBTNexs"/>
+          <groups:member groups:name="SO2 transport via diffusion (periplasm)" groups:idRef="R_SO2tpp"/>
           <groups:member groups:name="FMNH2-dependent monooxygenase" groups:idRef="R_FDMO"/>
-          <groups:member groups:name="Phosphate transport via ABC system (uptake, periplasm)" groups:idRef="R_PIuabcpp"/>
-          <groups:member groups:name="FMNH2-dependent monooxygenase (ethanesulfonate)" groups:idRef="R_FDMO3"/>
-          <groups:member groups:name="FMNH2-dependent monooxygenase (sulfoacetate)" groups:idRef="R_FDMO6"/>
-          <groups:member groups:name="FMNH2-dependent monooxygenase (butanesulfonate)" groups:idRef="R_FDMO4"/>
-          <groups:member groups:name="FMNH2-dependent monooxygenase (methanesulfonate)" groups:idRef="R_FDMO2"/>
-          <groups:member groups:name="Ammonia reversible transport (periplasm)" groups:idRef="R_NH4tpp"/>
-          <groups:member groups:name="Nickle (Ni+2) transport out via proton antiport (periplasm)" groups:idRef="R_NI2t3pp"/>
-          <groups:member groups:name="Coprogen unloaded secretion" groups:idRef="R_CPGNUtpp"/>
+          <groups:member groups:name="Cobalt (Co+2) ABC transporter (periplasm)" groups:idRef="R_COBALT2abcpp"/>
           <groups:member groups:name="Potassium transport in via proton symport (periplasm)" groups:idRef="R_Kt2pp"/>
-          <groups:member groups:name="Cadmium (Cd+2) ABC transporter (periplasm)" groups:idRef="R_CD2abcpp"/>
+          <groups:member groups:name="Coprogen unloaded secretion" groups:idRef="R_CPGNUtpp"/>
+          <groups:member groups:name="FMNH2-dependent monooxygenase (methanesulfonate)" groups:idRef="R_FDMO2"/>
+          <groups:member groups:name="Ferric-dicitrate reductase via nadph" groups:idRef="R_FE3DCITR5"/>
           <groups:member groups:name="Coprogen unloaded secretion (extracellular)" groups:idRef="R_CPGNUtex"/>
+          <groups:member groups:name="Nickle (Ni+2) transport out via proton antiport (periplasm)" groups:idRef="R_NI2t3pp"/>
+          <groups:member groups:name="Iron (Fe+2) transport out via proton antiport (periplasm)" groups:idRef="R_FE2t3pp"/>
+          <groups:member groups:name="Fe-enterobactin reduction (Fe(III)-unloading)" groups:idRef="R_FEENTERR1"/>
+          <groups:member groups:name="Dicitrate Fe(III) binding (spontaneous)" groups:idRef="R_FE3DCITexs"/>
           <groups:member groups:name="Coprogen(Fe(III)) reductase" groups:idRef="R_CPGNR3"/>
-          <groups:member groups:name="Fe(III)hydroxamate unloaded secretion (extracellular)" groups:idRef="R_FE3HOXUtpp"/>
-          <groups:member groups:name="Fe-enterobactin reduction (Fe(III)-unloading)" groups:idRef="R_FEENTERR2"/>
-          <groups:member groups:name="Calcium (Ca+2) transport out via proton antiport (periplasm)" groups:idRef="R_CA2t3pp"/>
-          <groups:member groups:name="Nickle (Ni+2) ABC transporter (periplasm)" groups:idRef="R_NI2abcpp"/>
-          <groups:member groups:name="Ferroxidase" groups:idRef="R_FEROpp"/>
-          <groups:member groups:name="Magnesium (+2) transport in via diffusion" groups:idRef="R_MG2tpp"/>
-          <groups:member groups:name="Magnesium (Mg+2) ABC transporter (ubtake, periplasm)" groups:idRef="R_MG2uabcpp"/>
-          <groups:member groups:name="Ferroxamine reductase" groups:idRef="R_FEOXAMR1"/>
-          <groups:member groups:name="Manganese transport in via permease (no H+)" groups:idRef="R_MN2tpp"/>
-          <groups:member groups:name="Enterochelin Esterase (Fe containing)" groups:idRef="R_FEENTERES"/>
-          <groups:member groups:name="NO transport (diffusion)" groups:idRef="R_NOtpp"/>
-          <groups:member groups:name="Calcium / sodium antiporter (1:1)" groups:idRef="R_CAt6pp"/>
-          <groups:member groups:name="Phosphate export via facillated diffusion (periplasm)" groups:idRef="R_PItpp"/>
-          <groups:member groups:name="Potassium ABC transporter (periplasm)" groups:idRef="R_Kabcpp"/>
-          <groups:member groups:name="Molybdate transport via ABC system (periplasm)" groups:idRef="R_MOBDabcpp"/>
-          <groups:member groups:name="Nickel (+2) transport in via permease (no H+)" groups:idRef="R_NI2tpp"/>
-          <groups:member groups:name="Iron (III) transport via ABC system (periplasm to cytoplasm)" groups:idRef="R_FE3abcpp"/>
+          <groups:member groups:name="Iron (II) transport in via proton symport (periplasm)" groups:idRef="R_FE2t2pp"/>
+          <groups:member groups:name="Ferrichrome reductase" groups:idRef="R_FECRMR2"/>
+          <groups:member groups:name="Sodium proton antiporter (H:NA is 1.5) (periplasm)" groups:idRef="R_NAt3_1p5pp"/>
+          <groups:member groups:name="Aerobactin secretion (to periplasm)" groups:idRef="R_ARBTNtpp"/>
+          <groups:member groups:name="Fe(III)-(2,3-dihydroxybenzoylserine)3 reductase via NADPH" groups:idRef="R_FE3DHBZS3R"/>
           <groups:member groups:name="Ferroxamine reductase" groups:idRef="R_FEOXAMR3"/>
-          <groups:member groups:name="Selenite ABC transporter (periplasm)" groups:idRef="R_SLNTabcpp"/>
-          <groups:member groups:name="Aerobactin reductase" groups:idRef="R_ARBTNR2"/>
-          <groups:member groups:name="Ferroxamine (minus Fe3) secretion (to extracellular)" groups:idRef="R_FEOXAMUtex"/>
-          <groups:member groups:name="Hydrogen sulfide oxidation" groups:idRef="R_H2SO"/>
           <groups:member groups:name="Aerobactin reductase" groups:idRef="R_ARBTNR1"/>
-          <groups:member groups:name="Cobalt transport in via permease (no H+)" groups:idRef="R_COBALT2tpp"/>
+          <groups:member groups:name="Enterobactin Fe(III) binding (spontaneous)" groups:idRef="R_FEENTERexs"/>
+          <groups:member groups:name="Ferroxamine Fe3-loading reaction (spontaneous)" groups:idRef="R_FEOXAMexs"/>
+          <groups:member groups:name="Thiosulfate transport via ABC system (periplasm)" groups:idRef="R_TSULabcpp"/>
+          <groups:member groups:name="Silver transport out via proton antiport" groups:idRef="R_AGt3"/>
+          <groups:member groups:name="Enterochelin Esterase (Fe containing)" groups:idRef="R_FEENTERES"/>
+          <groups:member groups:name="Ferrichrome Fe(III)-loading reaction (spontaneous)" groups:idRef="R_FECRMexs"/>
+          <groups:member groups:name="Enterochelin Esterase" groups:idRef="R_ENTERES"/>
+          <groups:member groups:name="Ferroxamine reductase" groups:idRef="R_FEOXAMR1"/>
+          <groups:member groups:name="Magnesium (+2) transport in via diffusion" groups:idRef="R_MG2tpp"/>
+          <groups:member groups:name="Sodium transport out via proton antiport (cytoplasm to periplasm)" groups:idRef="R_NAt3pp"/>
+          <groups:member groups:name="Ferroxamine (minus Fe3) secretion (to periplasm)" groups:idRef="R_FEOXAMUtpp"/>
+          <groups:member groups:name="Selenatenate transport via ABC system (periplasm)" groups:idRef="R_SELabcpp"/>
+          <groups:member groups:name="Magnesium (Mg+2) ABC transporter (ubtake, periplasm)" groups:idRef="R_MG2uabcpp"/>
           <groups:member groups:name="Copper transport in via permease (no H+)" groups:idRef="R_CU2tpp"/>
-          <groups:member groups:name="Magnesium (Mg+2) transport in/out via proton antiport (periplasm)" groups:idRef="R_MG2t3_2pp"/>
-          <groups:member groups:name="Ferroxamine transport via ABC system (periplasm)" groups:idRef="R_FEOXAMabcpp"/>
-          <groups:member groups:name="23dhbsz3 Fe III transport via ABC system periplasm" groups:idRef="R_DHBSZ3FEabcpp"/>
-          <groups:member groups:name="Cobalt (Co+2) transport out via proton antiport (periplasm)" groups:idRef="R_COBALT2t3pp"/>
           <groups:member groups:name="Ferric-dicitrate transport via ABC system (periplasm)" groups:idRef="R_FE3HOXabcpp"/>
-          <groups:member groups:name="Ferrichrome reductase" groups:idRef="R_FECRMR1"/>
-          <groups:member groups:name="Enterobactin Fe(III) binding (spontaneous)" groups:idRef="R_FEENTERexs"/>
-          <groups:member groups:name="Iron (+2) transport in via permease (no H+)" groups:idRef="R_FE2tpp"/>
-          <groups:member groups:name="Fe(III)hydroxamate reductase" groups:idRef="R_FE3HOXR3"/>
-          <groups:member groups:name="Fe-enterobactin reduction (Fe(III)-unloading)" groups:idRef="R_FEENTERR1"/>
-          <groups:member groups:name="Cyanide sulfurtransferase (periplasmic)" groups:idRef="R_CYANSTpp"/>
-          <groups:member groups:name="Fe(III)hydroxamate reductase" groups:idRef="R_FE3HOXR2"/>
-          <groups:member groups:name="Fe(III)hydroxamate unloaded secretion" groups:idRef="R_FE3HOXUtex"/>
-          <groups:member groups:name="Nitrate transport in via nitrite antiport (periplasm)" groups:idRef="R_NO3t7pp"/>
-          <groups:member groups:name="Aerobactin reductase" groups:idRef="R_ARBTNR3"/>
           <groups:member groups:name="Ferroxamine reductase" groups:idRef="R_FEOXAMR2"/>
-          <groups:member groups:name="Aminoalkylphosphonate N-acetyltransferase" groups:idRef="R_AMPNTAT"/>
-          <groups:member groups:name="Fe-enterobactin reduction (Fe(III)-unloading)" groups:idRef="R_FEENTERR3"/>
-          <groups:member groups:name="Enterochelin Esterase" groups:idRef="R_ENTERES"/>
-          <groups:member groups:name="Mercury (Hg+2) ABC transporter (periplasm)" groups:idRef="R_HG2abcpp"/>
-          <groups:member groups:name="Iron (II) transport via ABC system (periplasm)" groups:idRef="R_FE2abcpp"/>
-          <groups:member groups:name="Cobalt (Co+2) ABC transporter (periplasm)" groups:idRef="R_COBALT2abcpp"/>
-          <groups:member groups:name="Aerobactin secretion (to periplasm)" groups:idRef="R_ARBTNtpp"/>
-          <groups:member groups:name="Coprogen(Fe(III)) reductase" groups:idRef="R_CPGNR1"/>
-          <groups:member groups:name="Thiosulfate transport via ABC system (periplasm)" groups:idRef="R_TSULabcpp"/>
-          <groups:member groups:name="Sulfate transport in via proton symport (periplasm to cytoplasm)" groups:idRef="R_SO4t2pp"/>
-          <groups:member groups:name="SO2 transport via diffusion (periplasm)" groups:idRef="R_SO2tpp"/>
-          <groups:member groups:name="Ferrichrome reductase" groups:idRef="R_FECRMR3"/>
-          <groups:member groups:name="Ferroxamine Fe3-loading reaction (spontaneous)" groups:idRef="R_FEOXAMexs"/>
+          <groups:member groups:name="23dhbsz3 Fe III transport via ABC system periplasm" groups:idRef="R_DHBSZ3FEabcpp"/>
+          <groups:member groups:name="Ferrichrome transport via ABC system (periplasm)" groups:idRef="R_FECRMabcpp"/>
+          <groups:member groups:name="Fe-enterobactin transport via ABC system (periplasm)" groups:idRef="R_FEENTERabcpp"/>
+          <groups:member groups:name="Ferroxamine transport via ABC system (periplasm)" groups:idRef="R_FEOXAMabcpp"/>
+          <groups:member groups:name="Selenite ABC transporter (periplasm)" groups:idRef="R_SLNTabcpp"/>
+          <groups:member groups:name="Zinc (Zn+2) transport out via proton antiport (periplasm)" groups:idRef="R_ZN2t3pp"/>
           <groups:member groups:name="Selenate glutathione reductase II" groups:idRef="R_SELGTHR2"/>
-          <groups:member groups:name="Iron transport from ferric-dicitrate via ABC system (periplasm)" groups:idRef="R_FE3DCITabcpp"/>
-          <groups:member groups:name="Fe(III)-(2,3-dihydroxybenzoylserine)3 reductase via NADPH" groups:idRef="R_FE3DHBZS3R"/>
+          <groups:member groups:name="Aerobactin reductase" groups:idRef="R_ARBTNR2"/>
+          <groups:member groups:name="Zinc transport in via permease (no H+)" groups:idRef="R_ZN2tpp"/>
+          <groups:member groups:name="Nitrious oxide transport (diffusion)" groups:idRef="R_N2Otpp"/>
+          <groups:member groups:name="Selenate glutathione reductase III" groups:idRef="R_SELGTHR3"/>
+          <groups:member groups:name="Selenate reductase" groups:idRef="R_SELR"/>
+          <groups:member groups:name="Potassium ABC transporter (periplasm)" groups:idRef="R_Kabcpp"/>
+          <groups:member groups:name="Zinc (Zn+2) ABC transporter, efflux (periplasm)" groups:idRef="R_ZN2abcpp"/>
+          <groups:member groups:name="Manganese (Mn+2) transport out via proton antiport (periplasm)" groups:idRef="R_MN2t3pp"/>
+          <groups:member groups:name="Potassium transport out via proton antiport (periplasm)" groups:idRef="R_Kt3pp"/>
+          <groups:member groups:name="Calcium (Ca+2) transport out via proton antiport (periplasm)" groups:idRef="R_CA2t3pp"/>
+          <groups:member groups:name="Fe(III)hydroxamate reductase" groups:idRef="R_FE3HOXR2"/>
+          <groups:member groups:name="Magnesium (Mg+2) transport in/out via proton antiport (periplasm)" groups:idRef="R_MG2t3_2pp"/>
           <groups:member groups:name="Fe-enterobactin reduction via nadph" groups:idRef="R_FEENTERR4"/>
-          <groups:member groups:name="Iron (Fe+2) transport out via proton antiport (periplasm)" groups:idRef="R_FE2t3pp"/>
-          <groups:member groups:name="Zinc (Zn+2) transport out via proton antiport (periplasm)" groups:idRef="R_ZN2t3pp"/>
+          <groups:member groups:name="FMNH2-dependent monooxygenase (ethanesulfonate)" groups:idRef="R_FDMO3"/>
+          <groups:member groups:name="Ferrichrome (minus Fe) secretion (to extracellular)" groups:idRef="R_FECRMUtex"/>
+          <groups:member groups:name="Cyanide sulfurtransferase (periplasmic)" groups:idRef="R_CYANSTpp"/>
+          <groups:member groups:name="Sodium proton antiporter (H:NA is 2) (periplasm)" groups:idRef="R_NAt3_2pp"/>
+          <groups:member groups:name="Fe-enterobactin reduction (Fe(III)-unloading)" groups:idRef="R_FEENTERR2"/>
           <groups:member groups:name="Sulfate transport via ABC system (periplasm)" groups:idRef="R_SULabcpp"/>
-          <groups:member groups:name="Zinc (Zn+2) transport via ABC system (periplasm)" groups:idRef="R_ZNabcpp"/>
-          <groups:member groups:name="Chloride ion transport in via diffusion (periplasm)" groups:idRef="R_CLtipp"/>
-          <groups:member groups:name="Ferrichrome transport via ABC system (periplasm)" groups:idRef="R_FECRMabcpp"/>
+          <groups:member groups:name="Phosphate reversible transport via symport (periplasm)" groups:idRef="R_PIt2rpp"/>
+          <groups:member groups:name="Copper (Cu+2) ABC transporter (periplasm)" groups:idRef="R_CU2abcpp"/>
+          <groups:member groups:name="Fe-enterobactin reduction (Fe(III)-unloading)" groups:idRef="R_FEENTERR3"/>
+          <groups:member groups:name="Tungstate transport via ABC system (periplasm)" groups:idRef="R_TUNGSabcpp"/>
+          <groups:member groups:name="Cobalt transport in via permease (no H+)" groups:idRef="R_COBALT2tpp"/>
+          <groups:member groups:name="FMNH2-dependent monooxygenase (butanesulfonate)" groups:idRef="R_FDMO4"/>
+          <groups:member groups:name="FMNH2-dependent monooxygenase (sulfoacetate)" groups:idRef="R_FDMO6"/>
+          <groups:member groups:name="Cadmium (Cd+2) transport out via proton antiport (periplasm)" groups:idRef="R_CD2t3pp"/>
+          <groups:member groups:name="Selenate glutathione reductase" groups:idRef="R_SELGTHR"/>
           <groups:member groups:name="Nitrite transport in via proton symport, reversible (periplasm)" groups:idRef="R_NO2t2rpp"/>
-          <groups:member groups:name="O2 transport via diffusion (periplasm)" groups:idRef="R_O2tpp"/>
-          <groups:member groups:name="Dicitrate Fe(III) binding (spontaneous)" groups:idRef="R_FE3DCITexs"/>
-          <groups:member groups:name="Sodium proton antiporter (H:NA is 1.5) (periplasm)" groups:idRef="R_NAt3_1p5pp"/>
+          <groups:member groups:name="Chloride ion transport in via diffusion (periplasm)" groups:idRef="R_CLtipp"/>
           <groups:member groups:name="Enterochelin transport (secretion periplasm)" groups:idRef="R_FEENTERtex"/>
+          <groups:member groups:name="Zinc (Zn+2) transport via ABC system (periplasm)" groups:idRef="R_ZNabcpp"/>
           <groups:member groups:name="Fe(III)hydroxamate reductase" groups:idRef="R_FE3HOXR1"/>
-          <groups:member groups:name="Aerobactin Fe-loading reaction (spontaneous)" groups:idRef="R_ARBTNexs"/>
-          <groups:member groups:name="Phosphate reversible transport via symport (periplasm)" groups:idRef="R_PIt2rpp"/>
-          <groups:member groups:name="Potassium transport out via proton antiport (periplasm)" groups:idRef="R_Kt3pp"/>
-          <groups:member groups:name="Sodium proton antiporter (H:NA is 2) (periplasm)" groups:idRef="R_NAt3_2pp"/>
-          <groups:member groups:name="Selenatenate transport via ABC system (periplasm)" groups:idRef="R_SELabcpp"/>
-          <groups:member groups:name="Ferroxamine (minus Fe3) secretion (to periplasm)" groups:idRef="R_FEOXAMUtpp"/>
-          <groups:member groups:name="Mercury (Hg+2) transport out via proton antiport (periplasm)" groups:idRef="R_HG2t3pp"/>
+          <groups:member groups:name="Ferrichrome (minus Fe) secretion (to periplasm)" groups:idRef="R_FECRMUtpp"/>
+          <groups:member groups:name="Arsenate reductase" groups:idRef="R_ASR"/>
+          <groups:member groups:name="Cobalt (Co+2) transport out via proton antiport (periplasm)" groups:idRef="R_COBALT2t3pp"/>
+          <groups:member groups:name="Iron (+2) transport in via permease (no H+)" groups:idRef="R_FE2tpp"/>
+          <groups:member groups:name="Ammonia reversible transport (periplasm)" groups:idRef="R_NH4tpp"/>
+          <groups:member groups:name="Ferroxidase" groups:idRef="R_FEROpp"/>
+          <groups:member groups:name="Iron (III) transport via ABC system (periplasm to cytoplasm)" groups:idRef="R_FE3abcpp"/>
+          <groups:member groups:name="Nickle (Ni+2) ABC transporter (periplasm)" groups:idRef="R_NI2abcpp"/>
+          <groups:member groups:name="Mercury (Hg+2) ABC transporter (periplasm)" groups:idRef="R_HG2abcpp"/>
+          <groups:member groups:name="Calcium / sodium antiporter (1:1)" groups:idRef="R_CAt6pp"/>
+          <groups:member groups:name="Cadmium (+2) transport in via permease (no H+)" groups:idRef="R_CD2tpp"/>
+          <groups:member groups:name="Nickel (+2) transport in via permease (no H+)" groups:idRef="R_NI2tpp"/>
           <groups:member groups:name="Nickel transport via ABC system (uptake, periplasm)" groups:idRef="R_NI2uabcpp"/>
-          <groups:member groups:name="Coprogen Fe-loading reaction (spontaneaous)" groups:idRef="R_CPGNexs"/>
-          <groups:member groups:name="Cuprous Oxidase (Cu+1)" groups:idRef="R_CU1Opp"/>
+          <groups:member groups:name="Phosphate transport via ABC system (uptake, periplasm)" groups:idRef="R_PIuabcpp"/>
+          <groups:member groups:name="Iron (II) transport via ABC system (periplasm)" groups:idRef="R_FE2abcpp"/>
+          <groups:member groups:name="Hydrogen sulfide oxidation" groups:idRef="R_H2SO"/>
+          <groups:member groups:name="Coprogen(Fe(III)) reductase" groups:idRef="R_CPGNR2"/>
           <groups:member groups:name="Fe(III) hydroxamate Fe-loading reaction (spontaneaous)" groups:idRef="R_FE3HOXexs"/>
           <groups:member groups:name="Chloride transport out via proton antiport (2:1) (periplasm)" groups:idRef="R_CLt3_2pp"/>
-          <groups:member groups:name="Iron (II) transport in via proton symport (periplasm)" groups:idRef="R_FE2t2pp"/>
-          <groups:member groups:name="Selenate reductase" groups:idRef="R_SELR"/>
-          <groups:member groups:name="Manganese (Mn+2) transport out via proton antiport (periplasm)" groups:idRef="R_MN2t3pp"/>
-          <groups:member groups:name="Zinc (Zn+2) ABC transporter, efflux (periplasm)" groups:idRef="R_ZN2abcpp"/>
-          <groups:member groups:name="Sodium transport out via proton antiport (cytoplasm to periplasm)" groups:idRef="R_NAt3pp"/>
-          <groups:member groups:name="Copper (Cu +1) ABC transporter (periplasm)" groups:idRef="R_CU1abcpp"/>
-          <groups:member groups:name="Fe-enterobactin transport via ABC system (periplasm)" groups:idRef="R_FEENTERabcpp"/>
-          <groups:member groups:name="Cadmium (Cd+2) transport out via proton antiport (periplasm)" groups:idRef="R_CD2t3pp"/>
-          <groups:member groups:name="Selenate glutathione reductase III" groups:idRef="R_SELGTHR3"/>
-          <groups:member groups:name="Cadmium (+2) transport in via permease (no H+)" groups:idRef="R_CD2tpp"/>
-          <groups:member groups:name="Nitrious oxide transport (diffusion)" groups:idRef="R_N2Otpp"/>
-          <groups:member groups:name="Ferrichrome reductase" groups:idRef="R_FECRMR2"/>
-          <groups:member groups:name="Silver transport out via proton antiport" groups:idRef="R_AGt3"/>
-          <groups:member groups:name="Zinc transport in via permease (no H+)" groups:idRef="R_ZN2tpp"/>
-          <groups:member groups:name="Arsenate reductase" groups:idRef="R_ASR"/>
-          <groups:member groups:name="Coprogen(Fe(III)) reductase" groups:idRef="R_CPGNR2"/>
-          <groups:member groups:name="Ferrichrome (minus Fe) secretion (to periplasm)" groups:idRef="R_FECRMUtpp"/>
-          <groups:member groups:name="Ferrichrome (minus Fe) secretion (to extracellular)" groups:idRef="R_FECRMUtex"/>
-          <groups:member groups:name="Ferrichrome Fe(III)-loading reaction (spontaneous)" groups:idRef="R_FECRMexs"/>
-          <groups:member groups:name="Copper (Cu+2) ABC transporter (periplasm)" groups:idRef="R_CU2abcpp"/>
+          <groups:member groups:name="Coprogen Fe-loading reaction (spontaneaous)" groups:idRef="R_CPGNexs"/>
+          <groups:member groups:name="Cuprous Oxidase (Cu+1)" groups:idRef="R_CU1Opp"/>
+          <groups:member groups:name="Phosphate export via facillated diffusion (periplasm)" groups:idRef="R_PItpp"/>
+          <groups:member groups:name="Aminoalkylphosphonate N-acetyltransferase" groups:idRef="R_AMPNTAT"/>
+          <groups:member groups:name="Cadmium (Cd+2) ABC transporter (periplasm)" groups:idRef="R_CD2abcpp"/>
+          <groups:member groups:name="Fe(III)hydroxamate unloaded secretion" groups:idRef="R_FE3HOXUtex"/>
+          <groups:member groups:name="Aerobactin reductase" groups:idRef="R_ARBTNR3"/>
+          <groups:member groups:name="O2 transport via diffusion (periplasm)" groups:idRef="R_O2tpp"/>
+          <groups:member groups:name="Ferrichrome reductase" groups:idRef="R_FECRMR3"/>
+          <groups:member groups:name="Coprogen(Fe(III)) reductase" groups:idRef="R_CPGNR1"/>
+          <groups:member groups:name="NO transport (diffusion)" groups:idRef="R_NOtpp"/>
+          <groups:member groups:name="Fe(III)hydroxamate reductase" groups:idRef="R_FE3HOXR3"/>
+          <groups:member groups:name="Ferrichrome reductase" groups:idRef="R_FECRMR1"/>
+          <groups:member groups:name="Fe(III)hydroxamate unloaded secretion (extracellular)" groups:idRef="R_FE3HOXUtpp"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group19" sboTerm="SBO:0000633" groups:id="G_group19" groups:name="Intracellular demand" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="Sink needed to allow oxamate to leave system" groups:idRef="R_DM_oxam_c"/>
+          <groups:member groups:name="Sink needed to allow S-Adenosyl-4-methylthio-2-oxobutanoate to leave system" groups:idRef="R_DM_amob_c"/>
           <groups:member groups:name="Sink needed to allow p-Cresol to leave system" groups:idRef="R_DM_4crsol_c"/>
+          <groups:member groups:name="Sink needed to allow (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran to leave system" groups:idRef="R_DM_mththf_c"/>
+          <groups:member groups:name="Sink needed to allow oxamate to leave system" groups:idRef="R_DM_oxam_c"/>
           <groups:member groups:name="Sink needed to allow aminoacetaldehyde to leave system" groups:idRef="R_DM_aacald_c"/>
           <groups:member groups:name="Sink needed to allow 5&apos;-deoxyribose to leave system" groups:idRef="R_DM_5drib_c"/>
-          <groups:member groups:name="Sink needed to allow S-Adenosyl-4-methylthio-2-oxobutanoate to leave system" groups:idRef="R_DM_amob_c"/>
-          <groups:member groups:name="Sink needed to allow (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran to leave system" groups:idRef="R_DM_mththf_c"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group20" sboTerm="SBO:0000633" groups:id="G_group20" groups:name="Lipopolysaccharide Biosynthesis / Recycling" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="3-deoxy-D-manno-octulosonic acid transferase" groups:idRef="R_MOAT"/>
-          <groups:member groups:name="LPS heptose kinase II (LPS core synthesis)" groups:idRef="R_HEPK2"/>
-          <groups:member groups:name="Undecaprenyl phosphate transport (cytoplasm to periplasm)" groups:idRef="R_UDCPPtppi"/>
-          <groups:member groups:name="Core oligosaccharide lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)" groups:idRef="R_LIPAHT2ex"/>
-          <groups:member groups:name="Enterobacterial common antigen polymerase (periplasm)" groups:idRef="R_ECAP2pp"/>
-          <groups:member groups:name="Sedoheptulose 7-phosphate isomerase" groups:idRef="R_S7PI"/>
-          <groups:member groups:name="Endotoxin Synthesis (myristoyl transferase)" groups:idRef="R_EDTXS4"/>
-          <groups:member groups:name="3-hydroxybenzoyl-CoA thioesterase" groups:idRef="R_3HBZCT"/>
-          <groups:member groups:name="Glucosyltransferase II (LPS core synthesis)" groups:idRef="R_GLCTR2"/>
-          <groups:member groups:name="3-deoxy -D-manno-octulosonic -acid 8-phosphate synthase" groups:idRef="R_KDOPS"/>
-          <groups:member groups:name="Phosphoethanolamine transferase (c-C16:1)" groups:idRef="R_PETNT161pp"/>
-          <groups:member groups:name="3-deoxy-manno-octulosonate cytidylyltransferase" groups:idRef="R_KDOCT2"/>
-          <groups:member groups:name="O16 anitgen (x4) ligase (periplasm)" groups:idRef="R_O16A4Lpp"/>
-          <groups:member groups:name="D-glycero-D-manno-heptose 7-phosphate kinase" groups:idRef="R_GMHEPK"/>
-          <groups:member groups:name="Enterobacterial common antigen (x4) core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" groups:idRef="R_ECA4COLIPAabctex"/>
-          <groups:member groups:name="O16 antigen (flippase, cytoplasm to periplasm)" groups:idRef="R_O16AUNDtpp"/>
+          <groups:member groups:name="O16 antigen polymerase (periplasm)" groups:idRef="R_O16AP3pp"/>
+          <groups:member groups:name="Rhamnosyltransferase I (LPS core biosynthesis)" groups:idRef="R_RHAT1"/>
+          <groups:member groups:name="3-deoxy-D-manno-octulosonic acid transferase" groups:idRef="R_MOAT2"/>
           <groups:member groups:name="Lipid A transport via ABC system (periplasm to extracellular)" groups:idRef="R_LIPAabctex"/>
-          <groups:member groups:name="Undecaprenyl phosphate-L-Ara4FN transferase" groups:idRef="R_UPLA4FNT"/>
-          <groups:member groups:name="UDP-sugar hydrolase" groups:idRef="R_USHD"/>
-          <groups:member groups:name="Rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate O-acetyltransferase (LPS O16 antigen biosynthesis)" groups:idRef="R_O16AT"/>
+          <groups:member groups:name="UDP-glucuronate C-4&apos;&apos; decarboxylase" groups:idRef="R_UDPGDC"/>
+          <groups:member groups:name="Undecaprenyl phosphate transport (cytoplasm to periplasm)" groups:idRef="R_UDCPPtppi"/>
           <groups:member groups:name="ADP-D-glycero-D-manno-heptose epimerase" groups:idRef="R_AGMHE"/>
-          <groups:member groups:name="4-amino-4-deoxy-L-arabinotransferase (LPS lipid A modification, periplasmic face of membrane))" groups:idRef="R_LA4NTpp"/>
-          <groups:member groups:name="Lipid A transport via ABC system (periplasm)" groups:idRef="R_LIPAabcpp"/>
-          <groups:member groups:name="Core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" groups:idRef="R_COLIPAabctex"/>
-          <groups:member groups:name="KDO(2)-lipid IV A transport via ABC system (periplasm to extracellular)" groups:idRef="R_K2L4Aabctex"/>
-          <groups:member groups:name="UDP-3-O-(3-hydroxymyristoyl)glucosamine acyltransferase" groups:idRef="R_U23GAAT"/>
-          <groups:member groups:name="D-glycero-D-manno-hepose 1-phosphate adenyltransferase" groups:idRef="R_GMHEPAT"/>
+          <groups:member groups:name="O16 antigen (x4) core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" groups:idRef="R_O16A4COLIPAabctex"/>
+          <groups:member groups:name="3-deoxy-manno-octulosonate cytidylyltransferase" groups:idRef="R_KDOCT2"/>
+          <groups:member groups:name="O16 antigen polymerase (periplasm)" groups:idRef="R_O16AP1pp"/>
+          <groups:member groups:name="Glucosyltransferase II (LPS core synthesis)" groups:idRef="R_GLCTR2"/>
           <groups:member groups:name="Endotoxin Synthesis (palmitoleoyl ACP)" groups:idRef="R_EDTXS3"/>
-          <groups:member groups:name="Heptosyltransferase I (LPS core synthesis)" groups:idRef="R_HEPT1"/>
+          <groups:member groups:name="Lipid A disaccaride synthase" groups:idRef="R_LPADSS"/>
+          <groups:member groups:name="O16 antigen (flippase, cytoplasm to periplasm)" groups:idRef="R_O16AUNDtpp"/>
+          <groups:member groups:name="3-deoxy -D-manno-octulosonic -acid 8-phosphate synthase" groups:idRef="R_KDOPS"/>
+          <groups:member groups:name="Glucosyltransferase I (LPS O16 antigen biosynthesis)" groups:idRef="R_O16GLCT1"/>
+          <groups:member groups:name="Lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)" groups:idRef="R_LIPAHTex"/>
+          <groups:member groups:name="Lipid A transport via ABC system (periplasm)" groups:idRef="R_LIPAabcpp"/>
+          <groups:member groups:name="UDP-L-Ara4N formyltransferase" groups:idRef="R_ULA4NFT"/>
+          <groups:member groups:name="Enterobacterial common antigen (x4) core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" groups:idRef="R_ECA4COLIPAabctex"/>
+          <groups:member groups:name="D-glycero-D-manno-heptose 7-phosphate kinase" groups:idRef="R_GMHEPK"/>
           <groups:member groups:name="Undecaprenyl phosphate-L-Ara4FN formylase" groups:idRef="R_UPLA4FNF"/>
+          <groups:member groups:name="Phosphoethanolamine transferase (c-C16:1)" groups:idRef="R_PETNT181pp"/>
+          <groups:member groups:name="Phosphoethanolamine lipid A transport via ABC system (periplasm to extracellular)" groups:idRef="R_ENLIPAabctex"/>
+          <groups:member groups:name="Rhamanosyl-N-acetylglucosamyl-undecaprenyl diphosphate O-acetyltransferase (LPS O16 antigen biosynthesis)" groups:idRef="R_O16AT"/>
+          <groups:member groups:name="3-deoxy-D-manno-octulosonic acid transferase III (LPS core biosynthesis)" groups:idRef="R_MOAT3C"/>
+          <groups:member groups:name="Sedoheptulose 7-phosphate isomerase" groups:idRef="R_S7PI"/>
+          <groups:member groups:name="Undecaprenyl phosphate-L-Ara4FN transferase" groups:idRef="R_UPLA4FNT"/>
+          <groups:member groups:name="Core oligosaccharide lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)" groups:idRef="R_LIPAHT2ex"/>
+          <groups:member groups:name="Cold lipid A transport via ABC system (periplasm to extracellular)" groups:idRef="R_CLIPAabctex"/>
+          <groups:member groups:name="Enterobacterial common antigen transferase (flippase, cytoplasm to periplasm)" groups:idRef="R_ECAtpp"/>
+          <groups:member groups:name="Transport (cytoplasm to periplasm)" groups:idRef="R_ULA4Ntppi"/>
+          <groups:member groups:name="O16 antigen polymerase (periplasm)" groups:idRef="R_O16AP2pp"/>
           <groups:member groups:name="Glucosyltransferase I (LPS core synthesis)" groups:idRef="R_GLCTR1"/>
-          <groups:member groups:name="UDP-glucuronate C-4&apos;&apos; decarboxylase" groups:idRef="R_UDPGDC"/>
+          <groups:member groups:name="Endotoxin Synthesis (myristoyl transferase)" groups:idRef="R_EDTXS4"/>
+          <groups:member groups:name="Heptosyltransferase IV (LPS core synthesis)" groups:idRef="R_HEPT4"/>
+          <groups:member groups:name="UDP-4&apos;&apos;-ketopentose:UDP-4-amino-4-deoxy-L-arabinose aminotransferase" groups:idRef="R_UDPKAAT"/>
           <groups:member groups:name="Lipid A core kinase (periplasm)" groups:idRef="R_COLIPAKpp"/>
-          <groups:member groups:name="Lipid A:hexadecanoate transferase (n-C16:0) (extracellular membrane)" groups:idRef="R_LIPAHTex"/>
-          <groups:member groups:name="Heptosyltransferase II (LPS core synthesis)" groups:idRef="R_HEPT2"/>
-          <groups:member groups:name="Galactofuranosyltransferase (LPS O16 antigen biosynthesis)" groups:idRef="R_O16GALFT"/>
-          <groups:member groups:name="Transport (cytoplasm to periplasm)" groups:idRef="R_ULA4Ntppi"/>
-          <groups:member groups:name="3-deoxy-D-manno-octulosonic acid transferase III (LPS core biosynthesis)" groups:idRef="R_MOAT3C"/>
-          <groups:member groups:name="Core oligosaccharide lipid A transport via ABC system (periplasm)" groups:idRef="R_COLIPAabcpp"/>
           <groups:member groups:name="Galactosyltransferase I (LPS core synthesis)" groups:idRef="R_GALT1"/>
+          <groups:member groups:name="UDP-sugar hydrolase" groups:idRef="R_USHD"/>
           <groups:member groups:name="Glucosyltransferase III (LPS core synthesis)" groups:idRef="R_GLCTR3"/>
-          <groups:member groups:name="O16 antigen polymerase (periplasm)" groups:idRef="R_O16AP2pp"/>
-          <groups:member groups:name="Core oligosaccharide lipid A diphosphate transport via ABC system (periplasm to extracellular)" groups:idRef="R_COLIPAPabctex"/>
-          <groups:member groups:name="Heptosyltransferase III (LPS core synthesis)" groups:idRef="R_HEPT3"/>
+          <groups:member groups:name="Tetraacyldisaccharide 4&apos;kinase" groups:idRef="R_TDSK"/>
+          <groups:member groups:name="Glucosyltransferase II (LPS O16 antigen biosynthesis)" groups:idRef="R_O16GLCT2"/>
           <groups:member groups:name="Lipid (cold) A transport via ABC system (periplasm)" groups:idRef="R_LIPACabcpp"/>
-          <groups:member groups:name="O16 antigen (x4) core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" groups:idRef="R_O16A4COLIPAabctex"/>
-          <groups:member groups:name="3-deoxy-D-manno-octulosonic acid transferase" groups:idRef="R_MOAT2"/>
-          <groups:member groups:name="Glucosyltransferase I (LPS O16 antigen biosynthesis)" groups:idRef="R_O16GLCT1"/>
-          <groups:member groups:name="Lipid A disaccaride synthase" groups:idRef="R_LPADSS"/>
           <groups:member groups:name="Arabinose modified core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" groups:idRef="R_ACOLIPAabctex"/>
-          <groups:member groups:name="Enterobacterial common antigen (x4) O-antigen ligase (periplasm)" groups:idRef="R_ECA4OALpp"/>
-          <groups:member groups:name="O16 antigen polymerase (periplasm)" groups:idRef="R_O16AP1pp"/>
-          <groups:member groups:name="Glucosyltransferase II (LPS O16 antigen biosynthesis)" groups:idRef="R_O16GLCT2"/>
-          <groups:member groups:name="Phosphoethanolamine transferase (c-C16:1)" groups:idRef="R_PETNT181pp"/>
-          <groups:member groups:name="UDP-N-acetylglucosamine acyltransferase" groups:idRef="R_UAGAAT"/>
-          <groups:member groups:name="UDP-L-Ara4N formyltransferase" groups:idRef="R_ULA4NFT"/>
-          <groups:member groups:name="O16 antigen polymerase (periplasm)" groups:idRef="R_O16AP3pp"/>
+          <groups:member groups:name="Core oligosaccharide lipid A transport via ABC system (periplasm)" groups:idRef="R_COLIPAabcpp"/>
+          <groups:member groups:name="Endotoxin Synthesis (myristoyl transferase)" groups:idRef="R_EDTXS2"/>
+          <groups:member groups:name="O16 anitgen (x4) ligase (periplasm)" groups:idRef="R_O16A4Lpp"/>
+          <groups:member groups:name="Phosphoethanolamine transferase (c-C16:1)" groups:idRef="R_PETNT161pp"/>
+          <groups:member groups:name="Heptosyltransferase I (LPS core synthesis)" groups:idRef="R_HEPT1"/>
+          <groups:member groups:name="Core oligosaccharide lipid A diphosphate transport via ABC system (periplasm to extracellular)" groups:idRef="R_COLIPAPabctex"/>
+          <groups:member groups:name="3-deoxy-manno-octulosonate-8-phosphatase" groups:idRef="R_KDOPP"/>
           <groups:member groups:name="UDP-3-O-acetylglucosamine deacetylase" groups:idRef="R_UHGADA"/>
-          <groups:member groups:name="Enterobacterial common antigen polymerase (periplasm)" groups:idRef="R_ECAP3pp"/>
-          <groups:member groups:name="Phosphoethanolamine lipid A transport via ABC system (periplasm to extracellular)" groups:idRef="R_ENLIPAabctex"/>
+          <groups:member groups:name="Endotoxin Synthesis (lauroyl transferase)" groups:idRef="R_EDTXS1"/>
           <groups:member groups:name="LPS heptose kinase I (LPS core synthesis)" groups:idRef="R_HEPK1"/>
-          <groups:member groups:name="Enterobacterial common antigen transferase (flippase, cytoplasm to periplasm)" groups:idRef="R_ECAtpp"/>
+          <groups:member groups:name="KDO(2)-lipid IV A transport via ABC system (periplasm to extracellular)" groups:idRef="R_K2L4Aabctex"/>
+          <groups:member groups:name="4-amino-4-deoxy-L-arabinotransferase (LPS lipid A modification, periplasmic face of membrane))" groups:idRef="R_LA4NTpp"/>
+          <groups:member groups:name="Galactofuranosyltransferase (LPS O16 antigen biosynthesis)" groups:idRef="R_O16GALFT"/>
+          <groups:member groups:name="UDP-N-acetylglucosamine acyltransferase" groups:idRef="R_UAGAAT"/>
+          <groups:member groups:name="Enterobacterial common antigen (x4) O-antigen ligase (periplasm)" groups:idRef="R_ECA4OALpp"/>
+          <groups:member groups:name="D-glycero-D-manno-hepose 1-phosphate adenyltransferase" groups:idRef="R_GMHEPAT"/>
+          <groups:member groups:name="3-hydroxybenzoyl-CoA thioesterase" groups:idRef="R_3HBZCT"/>
           <groups:member groups:name="Enterobacterial common antigen polymerase (periplasm)" groups:idRef="R_ECAP1pp"/>
-          <groups:member groups:name="Heptosyltransferase IV (LPS core synthesis)" groups:idRef="R_HEPT4"/>
+          <groups:member groups:name="3-deoxy-D-manno-octulosonic acid transferase" groups:idRef="R_MOAT"/>
           <groups:member groups:name="D-glycero-D-manno-heptose 1,7-bisphosphate phosphatase" groups:idRef="R_GMHEPPA"/>
-          <groups:member groups:name="3-deoxy-manno-octulosonate-8-phosphatase" groups:idRef="R_KDOPP"/>
-          <groups:member groups:name="Rhamnosyltransferase I (LPS core biosynthesis)" groups:idRef="R_RHAT1"/>
-          <groups:member groups:name="Tetraacyldisaccharide 4&apos;kinase" groups:idRef="R_TDSK"/>
-          <groups:member groups:name="Endotoxin Synthesis (lauroyl transferase)" groups:idRef="R_EDTXS1"/>
-          <groups:member groups:name="Cold lipid A transport via ABC system (periplasm to extracellular)" groups:idRef="R_CLIPAabctex"/>
-          <groups:member groups:name="Endotoxin Synthesis (myristoyl transferase)" groups:idRef="R_EDTXS2"/>
-          <groups:member groups:name="UDP-4&apos;&apos;-ketopentose:UDP-4-amino-4-deoxy-L-arabinose aminotransferase" groups:idRef="R_UDPKAAT"/>
+          <groups:member groups:name="LPS heptose kinase II (LPS core synthesis)" groups:idRef="R_HEPK2"/>
+          <groups:member groups:name="UDP-3-O-(3-hydroxymyristoyl)glucosamine acyltransferase" groups:idRef="R_U23GAAT"/>
+          <groups:member groups:name="Heptosyltransferase II (LPS core synthesis)" groups:idRef="R_HEPT2"/>
+          <groups:member groups:name="Core oligosaccharide lipid A transport via ABC system (periplasm to extracellular)" groups:idRef="R_COLIPAabctex"/>
+          <groups:member groups:name="Enterobacterial common antigen polymerase (periplasm)" groups:idRef="R_ECAP3pp"/>
+          <groups:member groups:name="Heptosyltransferase III (LPS core synthesis)" groups:idRef="R_HEPT3"/>
+          <groups:member groups:name="Enterobacterial common antigen polymerase (periplasm)" groups:idRef="R_ECAP2pp"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group21" sboTerm="SBO:0000633" groups:id="G_group21" groups:name="Membrane Lipid Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="3-hydroxyacyl-CoA dehydrogenase (3-oxohexadecanoyl-CoA)" groups:idRef="R_HACD7"/>
+          <groups:member groups:name="3-hydroxyacyl-CoA dehydrogenase (3-oxooctanoyl-CoA)" groups:idRef="R_HACD3"/>
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+          <groups:member groups:name="3-hydroxyacyl-CoA dehydratase (3-hydroxyhexanoyl-CoA)" groups:idRef="R_ECOAH2"/>
+          <groups:member groups:name="3-hydroxyacyl-CoA dehydrogenase (3-oxooctadecanoyl-CoA), peroxisomal" groups:idRef="R_HACD8"/>
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           <groups:member groups:name="Acyl-CoA dehydrogenase (butanoyl-CoA)" groups:idRef="R_ACOAD1f"/>
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-          <groups:member groups:name="Acyl-CoA dehydrogenase (octanoyl-CoA)" groups:idRef="R_ACOAD3f"/>
+          <groups:member groups:name="Acetyl-CoA C-acyltransferase (octanoyl-CoA) (r)" groups:idRef="R_ACACT4r"/>
+          <groups:member groups:name="Acyl-CoA dehydrogenase (butanoyl-CoA)" groups:idRef="R_ACOAD1fr"/>
+          <groups:member groups:name="Acyl-CoA dehydrogenase (hexadecanoyl-CoA)" groups:idRef="R_ACOAD7f"/>
           <groups:member groups:name="Acetyl-CoA carboxylase" groups:idRef="R_ACCOAC"/>
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-          <groups:member groups:name="Beta-ketoacyl-ACP synthase" groups:idRef="R_KAS14"/>
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-          <groups:member groups:name="3-hydroxyacyl-CoA dehydrogenase (3-oxohexanoyl-CoA)" groups:idRef="R_HACD2"/>
+          <groups:member groups:name="Acetyl-CoA C-acetyltransferase" groups:idRef="R_ACACT1r"/>
+          <groups:member groups:name="Acetyl-CoA C-acyltransferase (tetradecanoyl-CoA) (r)" groups:idRef="R_ACACT7r"/>
+          <groups:member groups:name="3-cis-2-trans-enoyl-CoA isomerase" groups:idRef="R_CTECOAI6"/>
+          <groups:member groups:name="Acetyl-CoA C-acyltransferase (dodecanoyl-CoA) (r)" groups:idRef="R_ACACT6r"/>
           <groups:member groups:name="Acetyl-CoA C-acyltransferase (hexanoyl-CoA) (r)" groups:idRef="R_ACACT3r"/>
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-          <groups:member groups:name="Acetyl-CoA acyltransferase (hexadecanoyl-CoA), (r)" groups:idRef="R_ACACT8r"/>
-          <groups:member groups:name="3-hydroxyacyl-CoA dehydratase (3-hydroxytetradecanoyl-CoA)" groups:idRef="R_ECOAH6"/>
+          <groups:member groups:name="Acyl-CoA dehydrogenase (octadecanoyl-CoA)" groups:idRef="R_ACOAD8f"/>
+          <groups:member groups:name="Acetyl-CoA C-acyltransferase (butanoyl-CoA) (r)" groups:idRef="R_ACACT2r"/>
           <groups:member groups:name="Acetyl-CoA C-acyltransferase (decanoyl-CoA) (r)" groups:idRef="R_ACACT5r"/>
-          <groups:member groups:name="Acetyl-CoA C-acyltransferase (dodecanoyl-CoA) (r)" groups:idRef="R_ACACT6r"/>
+          <groups:member groups:name="3-hydroxyacyl-CoA dehydrogenase (3-oxotetradecanoyl-CoA)" groups:idRef="R_HACD6"/>
+          <groups:member groups:name="Malonyl-CoA-ACP transacylase" groups:idRef="R_MCOATA"/>
+          <groups:member groups:name="3-cis-2-trans-enoyl-CoA isomerase" groups:idRef="R_CTECOAI7"/>
           <groups:member groups:name="3-hydroxyacyl-CoA dehydrogenase (3-oxododecanoyl-CoA)" groups:idRef="R_HACD5"/>
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-          <groups:member groups:name="3-hydroxyacyl-CoA dehydratase (3-hydroxybutanoyl-CoA)" groups:idRef="R_ECOAH1"/>
-          <groups:member groups:name="Acetyl-CoA C-acetyltransferase" groups:idRef="R_ACACT1r"/>
-          <groups:member groups:name="3-hydroxyacyl-CoA dehydratase (3-hydroxyoctanoyl-CoA)" groups:idRef="R_ECOAH3"/>
+          <groups:member groups:name="Acetyl-CoA:oxalate CoA-transferase" groups:idRef="R_ACOXT"/>
+          <groups:member groups:name="3-hydroxyacyl-CoA dehydrogenase (3-oxohexadecanoyl-CoA)" groups:idRef="R_HACD7"/>
+          <groups:member groups:name="Malonyl-ACP decarboxylase" groups:idRef="R_MACPD"/>
+          <groups:member groups:name="Acyl-CoA dehydrogenase (octanoyl-CoA)" groups:idRef="R_ACOAD3f"/>
           <groups:member groups:name="Beta-ketoacyl-ACP synthase (2)" groups:idRef="R_KAS15"/>
-          <groups:member groups:name="Acetyl-CoA C-acyltransferase (butanoyl-CoA) (r)" groups:idRef="R_ACACT2r"/>
+          <groups:member groups:name="Beta-ketoacyl-ACP synthase" groups:idRef="R_KAS14"/>
+          <groups:member groups:name="3-hydroxyacyl-CoA dehydratase (3-hydroxydodecanoyl-CoA)" groups:idRef="R_ECOAH5"/>
           <groups:member groups:name="3-hydroxyacyl-CoA dehydrogenase (acetoacetyl-CoA)" groups:idRef="R_HACD1"/>
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-          <groups:member groups:name="Acyl-CoA dehydrogenase (butanoyl-CoA)" groups:idRef="R_ACOAD1fr"/>
           <groups:member groups:name="Acyl-CoA dehydrogenase (dodecanoyl-CoA)" groups:idRef="R_ACOAD5f"/>
+          <groups:member groups:name="3-hydroxyacyl-CoA dehydrogenase (3-oxohexanoyl-CoA)" groups:idRef="R_HACD2"/>
+          <groups:member groups:name="Acyl-CoA dehydrogenase (decanoyl-CoA)" groups:idRef="R_ACOAD4f"/>
+          <groups:member groups:name="Acetyl-CoA acyltransferase (hexadecanoyl-CoA), (r)" groups:idRef="R_ACACT8r"/>
+          <groups:member groups:name="3-hydroxyacyl-CoA dehydratase (3-hydroxytetradecanoyl-CoA)" groups:idRef="R_ECOAH6"/>
           <groups:member groups:name="Acetyl-CoA ACP transacylase" groups:idRef="R_ACOATA"/>
+          <groups:member groups:name="3-cis-2-trans-enoyl-CoA isomerase" groups:idRef="R_CTECOAI8"/>
+          <groups:member groups:name="3-hydroxyacyl-CoA dehydratase (3-hydroxyhexadecanoyl-CoA)" groups:idRef="R_ECOAH7"/>
+          <groups:member groups:name="3-hydroxyacyl-CoA dehydratase (3-hydroxyoctanoyl-CoA)" groups:idRef="R_ECOAH3"/>
+          <groups:member groups:name="3-hydroxyacyl-CoA dehydratase (3-hydroxydecanoyl-CoA)" groups:idRef="R_ECOAH4"/>
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           <groups:member groups:name="3-hydroxyacyl-CoA dehydratase (3-hydroxyoctadecanoyl-CoA)" groups:idRef="R_ECOAH8"/>
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-          <groups:member groups:name="Acetyl-CoA C-acyltransferase (tetradecanoyl-CoA) (r)" groups:idRef="R_ACACT7r"/>
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-          <groups:member groups:name="3-hydroxyacyl-CoA dehydrogenase (3-oxotetradecanoyl-CoA)" groups:idRef="R_HACD6"/>
-          <groups:member groups:name="Malonyl-ACP decarboxylase" groups:idRef="R_MACPD"/>
+          <groups:member groups:name="3-hydroxyacyl-CoA dehydratase (3-hydroxybutanoyl-CoA)" groups:idRef="R_ECOAH1"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group22" sboTerm="SBO:0000633" groups:id="G_group22" groups:name="Metabolite Repair" groups:kind="partonomy">
         <groups:listOfMembers>
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           <groups:member groups:name="NADHX epimerase" groups:idRef="R_NADHXE"/>
-          <groups:member groups:name="NADH hydratase" groups:idRef="R_NADHHR"/>
+          <groups:member groups:name="NADPH hydratase" groups:idRef="R_NADPHHS"/>
+          <groups:member groups:name="NADPH hydratase" groups:idRef="R_NADPHHR"/>
           <groups:member groups:name="NADHX dehydratase" groups:idRef="R_NADHXD"/>
           <groups:member groups:name="NADPHX epimerase" groups:idRef="R_NADPHXE"/>
-          <groups:member groups:name="NADPH hydratase" groups:idRef="R_NADPHHS"/>
           <groups:member groups:name="NADPHX dehydratase" groups:idRef="R_NADPHXD"/>
-          <groups:member groups:name="NADH hydratase" groups:idRef="R_NADHHS"/>
-          <groups:member groups:name="NADPH hydratase" groups:idRef="R_NADPHHR"/>
+          <groups:member groups:name="NADH hydratase" groups:idRef="R_NADHHR"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group23" sboTerm="SBO:0000633" groups:id="G_group23" groups:name="Methionine Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
+          <groups:member groups:name="Methionine oxidation 2 (spontaneous)" groups:idRef="R_METOX2s"/>
+          <groups:member groups:name="Methionine oxidation (spontaneous)" groups:idRef="R_METOX1s"/>
+          <groups:member groups:name="Methionine adenosyltransferase" groups:idRef="R_METAT"/>
           <groups:member groups:name="S-ribosylhomocysteine cleavage enzyme" groups:idRef="R_RHCCE"/>
+          <groups:member groups:name="S-adenosylhomocysteine nucleosidase" groups:idRef="R_AHCYSNS"/>
+          <groups:member groups:name="(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran synthesis (spontaneous)" groups:idRef="R_MTHTHFSs"/>
           <groups:member groups:name="L-methionine-R-sulfoxide reductase" groups:idRef="R_METSOXR2"/>
-          <groups:member groups:name="L-methionine-S-oxide reductase" groups:idRef="R_METSOXR1"/>
+          <groups:member groups:name="O-succinylhomoserine lyase (L-cysteine)" groups:idRef="R_SHSL1"/>
           <groups:member groups:name="Homocysteine Methyltransferase" groups:idRef="R_HCYSMT2"/>
-          <groups:member groups:name="4,5-dihydroxy-2,3-pentanedione cyclization (spontaneous)" groups:idRef="R_DHPTDCs2"/>
-          <groups:member groups:name="S-adenosylhomocysteine nucleosidase" groups:idRef="R_AHCYSNS"/>
           <groups:member groups:name="Cystathionine b-lyase" groups:idRef="R_CYSTL"/>
           <groups:member groups:name="Homocysteine S-methyltransferase" groups:idRef="R_HCYSMT"/>
-          <groups:member groups:name="(2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran synthesis (spontaneous)" groups:idRef="R_MTHTHFSs"/>
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-          <groups:member groups:name="Methionine adenosyltransferase" groups:idRef="R_METAT"/>
+          <groups:member groups:name="4,5-dihydroxy-2,3-pentanedione cyclization (spontaneous)" groups:idRef="R_DHPTDCs2"/>
+          <groups:member groups:name="L-amino acid N-acyltransferase" groups:idRef="R_METNA"/>
+          <groups:member groups:name="L-methionine-S-oxide reductase" groups:idRef="R_METSOXR1"/>
+          <groups:member groups:name="Homoserine O-succinyltransferase" groups:idRef="R_HSST"/>
           <groups:member groups:name="Autoinducer-2 kinase" groups:idRef="R_AI2K"/>
+          <groups:member groups:name="Methionine synthase" groups:idRef="R_METS"/>
           <groups:member groups:name="3-hydroxy-2,4-pentadione 5-phosphate thiolase" groups:idRef="R_PAI2T"/>
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           <groups:member groups:name="Phospho-AI-2 isomerase" groups:idRef="R_PAI2I"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group24" sboTerm="SBO:0000633" groups:id="G_group24" groups:name="Methylglyoxal Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
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           <groups:member groups:name="L-Lactaldehyde:NADP+ 1-oxidoreductase" groups:idRef="R_LALDO3"/>
           <groups:member groups:name="Methylglyoxal synthase" groups:idRef="R_MGSA"/>
-          <groups:member groups:name="Lactoylglutathione lyase" groups:idRef="R_LGTHL"/>
-          <groups:member groups:name="D-Lactaldehyde:NAD+ 1-oxidoreductase" groups:idRef="R_LALDO2x"/>
+          <groups:member groups:name="Aminoacetone:oxygen oxidoreductase(deaminating)(flavin-containing)" groups:idRef="R_AACTOOR"/>
           <groups:member groups:name="Hydroxyacylglutathione hydrolase" groups:idRef="R_GLYOX"/>
+          <groups:member groups:name="Aldose reductase (methylglyoxal) (nadh)" groups:idRef="R_ALR2x"/>
           <groups:member groups:name="Aldose reductase (methylglyoxal)" groups:idRef="R_ALR2"/>
           <groups:member groups:name="Glyoxalase III" groups:idRef="R_GLYOX3"/>
+          <groups:member groups:name="D-Lactaldehyde:NAD+ 1-oxidoreductase" groups:idRef="R_LALDO2x"/>
+          <groups:member groups:name="Lactoylglutathione lyase" groups:idRef="R_LGTHL"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group25" sboTerm="SBO:0000633" groups:id="G_group25" groups:name="Murein Biosynthesis" groups:kind="partonomy">
         <groups:listOfMembers>
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-          <groups:member groups:name="Murein D,D-carboxypeptidase (murein5p4p) (periplasm)" groups:idRef="R_MDDCP4pp"/>
           <groups:member groups:name="Murein L,D-carboxypeptidase (murein4p3p) (periplasm)" groups:idRef="R_MLDCP2Bpp"/>
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-          <groups:member groups:name="Murein crosslinking transpeptidase 1B:(A2pm-&gt;A2pm) (periplasm)" groups:idRef="R_MCTP1Bpp"/>
-          <groups:member groups:name="Murein polymerizing transglycosylase 2 (three linked units)" groups:idRef="R_MPTG2"/>
-          <groups:member groups:name="Murein crosslinking transpeptidase 1A:(A2pm-&gt;D-ala) (periplasm)" groups:idRef="R_MCTP1App"/>
           <groups:member groups:name="Murein D,D-carboxypeptidase (murein5p5p) (periplasm)" groups:idRef="R_MDDCP3pp"/>
+          <groups:member groups:name="Murein polymerizing transglycosylase 2 (three linked units)" groups:idRef="R_MPTG2"/>
           <groups:member groups:name="Murein L,D-carboxypeptidase (murein5p5p) (periplasm)" groups:idRef="R_MLDCP2App"/>
+          <groups:member groups:name="Murein L,D-carboxypeptidase (murein5px4p) (periplasm)" groups:idRef="R_MLDCP1App"/>
+          <groups:member groups:name="Murein crosslinking transpeptidase 1A:(A2pm-&gt;D-ala) (periplasm)" groups:idRef="R_MCTP1App"/>
+          <groups:member groups:name="Murein polymerizing transglycosylase" groups:idRef="R_MPTG"/>
           <groups:member groups:name="Murein L,D-carboxypeptidase (murein4p4p) (periplasm)" groups:idRef="R_MLDCP1Bpp"/>
+          <groups:member groups:name="Murein D,D-carboxypeptidase (murein5px4p) (periplasm)" groups:idRef="R_MDDCP1pp"/>
+          <groups:member groups:name="Murein crosslinking transpeptidase 1B:(A2pm-&gt;A2pm) (periplasm)" groups:idRef="R_MCTP1Bpp"/>
+          <groups:member groups:name="Murein L,D-carboxypeptidase (murein5px3p) (periplasm)" groups:idRef="R_MLDCP3App"/>
+          <groups:member groups:name="Murein D,D-carboxypeptidase (murein5p4p) (periplasm)" groups:idRef="R_MDDCP4pp"/>
+          <groups:member groups:name="Murein crosslinking transpeptidase 1A:(A2pm-&gt;D-ala) (periplasm)" groups:idRef="R_MCTP2App"/>
+          <groups:member groups:name="Murein D,D-carboxypeptidase (murein5p3p) (periplasm)" groups:idRef="R_MDDCP5pp"/>
           <groups:member groups:name="Murein D,D-carboxypeptidase (murein5px4px4p) (periplasm)" groups:idRef="R_MDDCP2pp"/>
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-          <groups:member groups:name="Murein L,D-carboxypeptidase (murein5px4p) (periplasm)" groups:idRef="R_MLDCP1App"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group26" sboTerm="SBO:0000633" groups:id="G_group26" groups:name="Murein Recycling" groups:kind="partonomy">
         <groups:listOfMembers>
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-          <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide amidase (periplasm)" groups:idRef="R_AGM3PApp"/>
-          <groups:member groups:name="Murein lytic transglycosylase (murein3p3p) (periplasm)" groups:idRef="R_MLTGY3pp"/>
-          <groups:member groups:name="Murein L,D-endopeptidase (murein3px3p) (periplasm)" groups:idRef="R_MLDEP1pp"/>
+          <groups:member groups:name="Murein lytic transglycosylase (murein4p4p) (periplasm)" groups:idRef="R_MLTGY1pp"/>
+          <groups:member groups:name="Anhydrous-N-Acetylmuramyl-tetrapeptide amidase" groups:idRef="R_AM4PA"/>
+          <groups:member groups:name="Murein D,D-endopeptidase (murein4px4p) (periplasm)" groups:idRef="R_MDDEP1pp"/>
           <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide beta -1,4-N-acetylglucosaminidase" groups:idRef="R_AGM3PH"/>
-          <groups:member groups:name="GlcNAc-anhMurNAc tripeptide transport in via proton symport (periplasm)" groups:idRef="R_AGM3Pt2pp"/>
-          <groups:member groups:name="1,6-anhydrous-N-Acetylmuramate kinase" groups:idRef="R_ANHMK"/>
-          <groups:member groups:name="UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase" groups:idRef="R_UM3PL"/>
+          <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase" groups:idRef="R_AGM4PCP"/>
+          <groups:member groups:name="Tripeptide (LalaDgluMdap) transport via ABC system (periplasm)" groups:idRef="R_3PEPTabcpp"/>
+          <groups:member groups:name="Tetrapeptide L,D-carboxypeptidase" groups:idRef="R_4PCP"/>
+          <groups:member groups:name="D-alanine-D-alanine dipeptidase" groups:idRef="R_ALAALAD"/>
           <groups:member groups:name="L-alanyl-gamma-D-glutamyl-meso-diaminopimelate hydrolase" groups:idRef="R_LADGMDH"/>
+          <groups:member groups:name="Murein L,D-endopeptidase (murein3px3p) (periplasm)" groups:idRef="R_MLDEP1pp"/>
+          <groups:member groups:name="Murein lytic transglycosylase (murein4p3p) (periplasm)" groups:idRef="R_MLTGY2pp"/>
+          <groups:member groups:name="Murein lytic transglycosylase (murein4px4p4p) (periplasm)" groups:idRef="R_MLTGY4pp"/>
           <groups:member groups:name="Anhydrous-N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase" groups:idRef="R_AM4PCP"/>
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-          <groups:member groups:name="Tripeptide (LalaDgluMdap) transport via ABC system (periplasm)" groups:idRef="R_3PEPTabcpp"/>
+          <groups:member groups:name="L-alanyl-gamma-glutamate epimerase" groups:idRef="R_ALAGLUE"/>
+          <groups:member groups:name="Tetrapeptide (LalaDgluMdapDala) transport via ABC system (periplasm)" groups:idRef="R_4PEPTabcpp"/>
+          <groups:member groups:name="Tetrapeptide L,D-carboxypeptidase (periplasm)" groups:idRef="R_4PCPpp"/>
+          <groups:member groups:name="Murein D,D-endopeptidase (murein5px4p) (periplasm)" groups:idRef="R_MDDEP3pp"/>
           <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase (periplasmic)" groups:idRef="R_AGM4PCPpp"/>
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-          <groups:member groups:name="N-acetylglucosamine kinase" groups:idRef="R_ACGAMK"/>
-          <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide amidase (periplasm)" groups:idRef="R_AGM4PApp"/>
-          <groups:member groups:name="UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine L,D-carboxypeptidase" groups:idRef="R_UM4PCP"/>
+          <groups:member groups:name="Anhydrous-N-Acetylmuramyl-tripeptide amidase" groups:idRef="R_AM3PA"/>
+          <groups:member groups:name="1,6-anhydrous-N-Acetylmuramate kinase" groups:idRef="R_ANHMK"/>
+          <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide beta -1,4-N-acetylglucosaminidase" groups:idRef="R_AGM4PH"/>
+          <groups:member groups:name="Murein lytic transglycosylase (murein3p3p) (periplasm)" groups:idRef="R_MLTGY3pp"/>
           <groups:member groups:name="GlcNAc-anhMurNAc transport in via proton symport (periplasm)" groups:idRef="R_AGMt2pp"/>
-          <groups:member groups:name="Tetrapeptide L,D-carboxypeptidase" groups:idRef="R_4PCP"/>
           <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl beta -1,4-N-acetylglucosaminidase" groups:idRef="R_AGMH"/>
-          <groups:member groups:name="Murein D,D-endopeptidase (murein5px4p) (periplasm)" groups:idRef="R_MDDEP3pp"/>
-          <groups:member groups:name="Tetrapeptide L,D-carboxypeptidase (periplasm)" groups:idRef="R_4PCPpp"/>
+          <groups:member groups:name="Murein D,D-endopeptidase (murein4px4px4p) (periplasm)" groups:idRef="R_MDDEP4pp"/>
+          <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide amidase" groups:idRef="R_AGM4PA"/>
+          <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide amidase (periplasm)" groups:idRef="R_AGM3PApp"/>
           <groups:member groups:name="GlcNAc-anhMurNAc tetrapeptide transport in via proton symport (periplasm)" groups:idRef="R_AGM4Pt2pp"/>
-          <groups:member groups:name="UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate-D-alanine ligase" groups:idRef="R_UM4PL"/>
-          <groups:member groups:name="Tetrapeptide (LalaDgluMdapDala) transport via ABC system (periplasm)" groups:idRef="R_4PEPTabcpp"/>
-          <groups:member groups:name="Anhydrous-N-Acetylmuramyl-tripeptide amidase" groups:idRef="R_AM3PA"/>
-          <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide L,D-carboxypeptidase" groups:idRef="R_AGM4PCP"/>
           <groups:member groups:name="Murein L,D-endopeptidase (murein5px3p) (periplasm)" groups:idRef="R_MLDEP2pp"/>
-          <groups:member groups:name="L-alanyl-gamma-glutamate epimerase" groups:idRef="R_ALAGLUE"/>
-          <groups:member groups:name="Murein lytic transglycosylase (murein4p4p) (periplasm)" groups:idRef="R_MLTGY1pp"/>
-          <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide beta -1,4-N-acetylglucosaminidase" groups:idRef="R_AGM4PH"/>
-          <groups:member groups:name="D-alanine-D-alanine dipeptidase" groups:idRef="R_ALAALAD"/>
-          <groups:member groups:name="Anhydrous-N-Acetylmuramyl-tetrapeptide amidase" groups:idRef="R_AM4PA"/>
-          <groups:member groups:name="Murein lytic transglycosylase (murein4p3p) (periplasm)" groups:idRef="R_MLTGY2pp"/>
+          <groups:member groups:name="UDP-N-acetylmuramoyl-L-alanyl-D-gamma-glutamyl-meso-2,6-diaminopimelate-D-alanine L,D-carboxypeptidase" groups:idRef="R_UM4PCP"/>
+          <groups:member groups:name="UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate-D-alanine ligase" groups:idRef="R_UM4PL"/>
+          <groups:member groups:name="GlcNAc-anhMurNAc tripeptide transport in via proton symport (periplasm)" groups:idRef="R_AGM3Pt2pp"/>
           <groups:member groups:name="Murein D,D-endopeptidase (murein3px4p) (periplasm)" groups:idRef="R_MDDEP2pp"/>
+          <groups:member groups:name="N-acetylglucosamine kinase" groups:idRef="R_ACGAMK"/>
           <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tripeptide amidase" groups:idRef="R_AGM3PA"/>
-          <groups:member groups:name="Murein D,D-endopeptidase (murein4px4px4p) (periplasm)" groups:idRef="R_MDDEP4pp"/>
-          <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide amidase" groups:idRef="R_AGM4PA"/>
+          <groups:member groups:name="UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase" groups:idRef="R_UM3PL"/>
+          <groups:member groups:name="L-alanyl-gamma-L-glutamate peptidase" groups:idRef="R_LALGP"/>
+          <groups:member groups:name="N-Acetyl-D-glucosamine(anhydrous)N-Acetylmuramyl-tetrapeptide amidase (periplasm)" groups:idRef="R_AGM4PApp"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group27" sboTerm="SBO:0000633" groups:id="G_group27" groups:name="Nitrogen Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="Phenethylamine oxidase" groups:idRef="R_PEAMNOpp"/>
-          <groups:member groups:name="Nitric oxide dioxygenase" groups:idRef="R_NODOy"/>
-          <groups:member groups:name="Nitrite Reductase (Ubiquinole-8, periplasm)" groups:idRef="R_NTRIR3pp"/>
-          <groups:member groups:name="Allantoinase" groups:idRef="R_ALLTN"/>
-          <groups:member groups:name="Nitrite Reductase (Menaquinole-8, periplasm)" groups:idRef="R_NTRIR4pp"/>
-          <groups:member groups:name="Oxamate transcarbamoylase" groups:idRef="R_OXAMTC"/>
           <groups:member groups:name="Allantoate amidinohydrolase" groups:idRef="R_ALLTAMH2"/>
+          <groups:member groups:name="Ureidoglycolate hydrolase" groups:idRef="R_UGLYCH"/>
+          <groups:member groups:name="Cyanate aminohydrolase" groups:idRef="R_CYNTAH"/>
           <groups:member groups:name="Nitric oxide dioxygenase" groups:idRef="R_NODOx"/>
-          <groups:member groups:name="Tyramine:oxygen oxidoreductase(deaminating)(flavin-containing) (periplasm)" groups:idRef="R_TYROXDApp"/>
-          <groups:member groups:name="Nitrate reductase (Ubiquinol-8)" groups:idRef="R_NO3R1bpp"/>
-          <groups:member groups:name="4-(2-Aminoethyl)-1,2-benzenediol:oxygen oxidoreductase(deaminating)(flavin-containing)" groups:idRef="R_42A12BOOXpp"/>
           <groups:member groups:name="Ureidoglycine aminohydrolase" groups:idRef="R_UGCIAMH"/>
-          <groups:member groups:name="Carbamate kinase" groups:idRef="R_CBMKr"/>
-          <groups:member groups:name="Cyanate aminohydrolase" groups:idRef="R_CYNTAH"/>
+          <groups:member groups:name="Oxamate transcarbamoylase" groups:idRef="R_OXAMTC"/>
           <groups:member groups:name="NADH:flavorubredoxin oxidoreductase" groups:idRef="R_NHFRBO"/>
+          <groups:member groups:name="Nitric oxide dioxygenase" groups:idRef="R_NODOy"/>
+          <groups:member groups:name="Nitrate reductase (Ubiquinol-8)" groups:idRef="R_NO3R1bpp"/>
+          <groups:member groups:name="Phenethylamine oxidase" groups:idRef="R_PEAMNOpp"/>
+          <groups:member groups:name="Carbamate kinase" groups:idRef="R_CBMKr"/>
           <groups:member groups:name="Nitrate reductase (Menaquinol-8) (periplasm)" groups:idRef="R_NO3R2bpp"/>
-          <groups:member groups:name="Ureidoglycolate hydrolase" groups:idRef="R_UGLYCH"/>
+          <groups:member groups:name="Tyramine:oxygen oxidoreductase(deaminating)(flavin-containing) (periplasm)" groups:idRef="R_TYROXDApp"/>
+          <groups:member groups:name="Nitrite Reductase (Menaquinole-8, periplasm)" groups:idRef="R_NTRIR4pp"/>
+          <groups:member groups:name="4-(2-Aminoethyl)-1,2-benzenediol:oxygen oxidoreductase(deaminating)(flavin-containing)" groups:idRef="R_42A12BOOXpp"/>
+          <groups:member groups:name="Allantoinase" groups:idRef="R_ALLTN"/>
+          <groups:member groups:name="Nitrite Reductase (Ubiquinole-8, periplasm)" groups:idRef="R_NTRIR3pp"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group28" sboTerm="SBO:0000633" groups:id="G_group28" groups:name="Nucleotide Salvage Pathway" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="Ribonucleoside-diphosphate reductase (GDP) (glutaredoxin)" groups:idRef="R_RNDR2b"/>
-          <groups:member groups:name="Cytidine deaminase" groups:idRef="R_CYTD"/>
-          <groups:member groups:name="2&apos;,3&apos;-cyclic-nucleotide phosphodiesterase (UMP) (periplasm)" groups:idRef="R_23PDE2pp"/>
-          <groups:member groups:name="2&apos;,3&apos;-cyclic-nucleotide phosphodiesterase (CMP) (periplasm)" groups:idRef="R_23PDE4pp"/>
-          <groups:member groups:name="2&apos;,3&apos;-cyclic-nucleotide phosphodiesterase (GMP) (periplasm)" groups:idRef="R_23PDE9pp"/>
-          <groups:member groups:name="Xanthosine hydrolase" groups:idRef="R_XTSNH"/>
+          <groups:member groups:name="5&apos;-nucleotidase (dTMP)" groups:idRef="R_NTD5pp"/>
+          <groups:member groups:name="Ribonucleoside-triphosphate reductase (CTP) (flavodoxin)" groups:idRef="R_RNTR3c2"/>
+          <groups:member groups:name="5&apos;-nucleotidase (CMP)" groups:idRef="R_NTD4pp"/>
+          <groups:member groups:name="Xanthine phosphoribosyltransferase" groups:idRef="R_XPPT"/>
+          <groups:member groups:name="3&apos;-nucleotidase (CMP) (periplasm)" groups:idRef="R_3NTD4pp"/>
+          <groups:member groups:name="Insosine kinase" groups:idRef="R_INSK"/>
+          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (gtp)" groups:idRef="R_NTPP2"/>
+          <groups:member groups:name="Nucleoside-triphosphatase (CTP)" groups:idRef="R_NTP5"/>
+          <groups:member groups:name="Ap4A hydrolase" groups:idRef="R_AP4AH"/>
+          <groups:member groups:name="Nucleoside-diphosphate kinase (ATP:dUDP)" groups:idRef="R_NDPK6"/>
+          <groups:member groups:name="Purine-nucleoside phosphorylase (Inosine)" groups:idRef="R_PUNP5"/>
+          <groups:member groups:name="Ribonucleoside-diphosphate reductase (UDP)" groups:idRef="R_RNDR4"/>
+          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (ditp)" groups:idRef="R_NTPP10"/>
+          <groups:member groups:name="Uracil phosphoribosyltransferase" groups:idRef="R_UPPRT"/>
           <groups:member groups:name="Nicotinate-nucleotide adenylyltransferase" groups:idRef="R_NNATr"/>
+          <groups:member groups:name="5&apos;-nucleotidase (XMP)" groups:idRef="R_NTD10pp"/>
           <groups:member groups:name="Nucleoside-diphosphate kinase (ATP:dADP)" groups:idRef="R_NDPK8"/>
-          <groups:member groups:name="Thymidine phosphorylase" groups:idRef="R_TMDPP"/>
-          <groups:member groups:name="Thymidylate synthase" groups:idRef="R_TMDS"/>
+          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (dgtp)" groups:idRef="R_NTPP1"/>
+          <groups:member groups:name="Guanylate kinase (GMP:ATP)" groups:idRef="R_GK1"/>
+          <groups:member groups:name="5&apos;-nucleotidase (dCMP)" groups:idRef="R_NTD3pp"/>
+          <groups:member groups:name="Cytidylate kinase (CMP)" groups:idRef="R_CYTK1"/>
+          <groups:member groups:name="3&apos;,5&apos;-cyclic-nucleotide phosphodiesterase" groups:idRef="R_PDE1"/>
+          <groups:member groups:name="3&apos;-nucleotidase (GMP) (periplasm)" groups:idRef="R_3NTD9pp"/>
+          <groups:member groups:name="Hypoxanthine phosphoribosyltransferase (Hypoxanthine)" groups:idRef="R_HXPRT"/>
+          <groups:member groups:name="Guanine phosphoribosyltransferase" groups:idRef="R_GUAPRT"/>
+          <groups:member groups:name="5&apos;-nucleotidase (GMP)" groups:idRef="R_NTD9pp"/>
+          <groups:member groups:name="Peroxyureidoacrylate hydrolase" groups:idRef="R_URACPAH"/>
+          <groups:member groups:name="Hypoxanthine dehydrogenase" groups:idRef="R_HXAND"/>
+          <groups:member groups:name="5&apos;-nucleotidase (GMP)" groups:idRef="R_NTD9"/>
+          <groups:member groups:name="Diguanylate cyclase" groups:idRef="R_DGUNC"/>
+          <groups:member groups:name="Nucleoside-triphosphatase (XTP)" groups:idRef="R_NTP12"/>
+          <groups:member groups:name="5&apos;-nucleotidase (AMP)" groups:idRef="R_NTD7pp"/>
           <groups:member groups:name="2&apos;,3&apos;-cyclic-nucleotide phosphodiesterase (AMP) (periplasm)" groups:idRef="R_23PDE7pp"/>
-          <groups:member groups:name="DCTP deaminase" groups:idRef="R_DCTPD"/>
-          <groups:member groups:name="Purine-nucleoside phosphorylase (Inosine)" groups:idRef="R_PUNP5"/>
+          <groups:member groups:name="UMP kinase" groups:idRef="R_UMPK"/>
+          <groups:member groups:name="Nucleoside-triphosphatase (dITP)" groups:idRef="R_NTP11"/>
+          <groups:member groups:name="Adenosine kinase" groups:idRef="R_ADNK1"/>
+          <groups:member groups:name="Xanthosine hydrolase" groups:idRef="R_XTSNH"/>
+          <groups:member groups:name="Pyrimidine-nucleoside phosphorylase (uracil)" groups:idRef="R_PYNP2r"/>
+          <groups:member groups:name="Thymidine kinase (ATP:thymidine)" groups:idRef="R_TMDK1"/>
+          <groups:member groups:name="5&apos;-nucleotidase (AMP)" groups:idRef="R_NTD7"/>
+          <groups:member groups:name="Purine-nucleoside phosphorylase (Adenosine)" groups:idRef="R_PUNP1"/>
+          <groups:member groups:name="Purine-nucleoside phosphorylase (Guanosine)" groups:idRef="R_PUNP3"/>
+          <groups:member groups:name="Ribonucleoside-triphosphate reductase (GTP) (flavodoxin)" groups:idRef="R_RNTR2c2"/>
           <groups:member groups:name="Xanthine dehydrogenase" groups:idRef="R_XAND"/>
-          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (gtp)" groups:idRef="R_NTPP2"/>
-          <groups:member groups:name="Pyruvate kinase(3)" groups:idRef="R_PYK3"/>
-          <groups:member groups:name="Malonic semialdehyde reductase" groups:idRef="R_MSAR"/>
-          <groups:member groups:name="Nucleoside-triphosphatase (CTP)" groups:idRef="R_NTP5"/>
-          <groups:member groups:name="Nucleoside diphosphatase  GDP" groups:idRef="R_NDP3"/>
           <groups:member groups:name="Adenine phosphoribosyltransferase" groups:idRef="R_ADPT"/>
-          <groups:member groups:name="Pyruvate kinase(2)" groups:idRef="R_PYK2"/>
-          <groups:member groups:name="Nucleoside-diphosphate kinase (ATP:GDP)" groups:idRef="R_NDPK1"/>
-          <groups:member groups:name="Guanosine kinase" groups:idRef="R_GSNK"/>
-          <groups:member groups:name="Ribonucleoside-diphosphate reductase (UDP) (glutaredoxin)" groups:idRef="R_RNDR4b"/>
-          <groups:member groups:name="Purine-nucleoside phosphorylase (Adenosine)" groups:idRef="R_PUNP1"/>
-          <groups:member groups:name="AMP nucleosidase" groups:idRef="R_AMPN"/>
-          <groups:member groups:name="Nucleoside-triphosphatase (ITP)" groups:idRef="R_NTP10"/>
-          <groups:member groups:name="Adenosine kinase" groups:idRef="R_ADNK1"/>
-          <groups:member groups:name="Hypoxanthine dehydrogenase" groups:idRef="R_HXAND"/>
-          <groups:member groups:name="5&apos;-nucleotidase (CMP)" groups:idRef="R_NTD4pp"/>
-          <groups:member groups:name="5&apos;-nucleotidase (dGMP)" groups:idRef="R_NTD8"/>
-          <groups:member groups:name="Adenylate cyclase" groups:idRef="R_ADNCYC"/>
-          <groups:member groups:name="3&apos;-nucleotidase (UMP) (periplasm)" groups:idRef="R_3NTD2pp"/>
-          <groups:member groups:name="5&apos;-nucleotidase (dAMP)" groups:idRef="R_NTD6"/>
           <groups:member groups:name="Ap5A hydrolase" groups:idRef="R_AP5AH"/>
+          <groups:member groups:name="Adenosine deaminase" groups:idRef="R_ADA"/>
+          <groups:member groups:name="DUTP diphosphatase" groups:idRef="R_DUTPDP"/>
+          <groups:member groups:name="Linear diguanylate phosphodiesterase" groups:idRef="R_LDGUNPD"/>
+          <groups:member groups:name="Ribonucleoside-diphosphate reductase (GDP) (glutaredoxin)" groups:idRef="R_RNDR2b"/>
+          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (atp)" groups:idRef="R_NTPP6"/>
+          <groups:member groups:name="Nucleoside-diphosphate kinase (ATP:dCDP)" groups:idRef="R_NDPK7"/>
+          <groups:member groups:name="Ap4A synthetase" groups:idRef="R_AP4AS"/>
+          <groups:member groups:name="5&apos;-nucleotidase (dIMP)" groups:idRef="R_NTD12"/>
+          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (datp)" groups:idRef="R_NTPP5"/>
+          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (dttp)" groups:idRef="R_NTPP7"/>
+          <groups:member groups:name="Peroxyaminoacrylate reductase" groups:idRef="R_POAACR"/>
+          <groups:member groups:name="Purine-nucleoside phosphorylase (Deoxyadenosine)" groups:idRef="R_PUNP2"/>
+          <groups:member groups:name="Uridine kinase (GTP:Uridine)" groups:idRef="R_URIK2"/>
+          <groups:member groups:name="5&apos;-nucleotidase (UMP)" groups:idRef="R_NTD2pp"/>
           <groups:member groups:name="5&apos;-nucleotidase (dGMP)" groups:idRef="R_NTD8pp"/>
-          <groups:member groups:name="Nucleoside-triphosphatase (XTP)" groups:idRef="R_NTP12"/>
+          <groups:member groups:name="5&apos;-nucleotidase (UMP)" groups:idRef="R_NTD2"/>
           <groups:member groups:name="Adentylate kinase (ITP)" groups:idRef="R_ADK4"/>
-          <groups:member groups:name="Cytidylate kinase (CMP)" groups:idRef="R_CYTK1"/>
-          <groups:member groups:name="Adentylate kinase (GTP)" groups:idRef="R_ADK3"/>
-          <groups:member groups:name="Nucleoside-triphosphatase (GTP)" groups:idRef="R_NTP3"/>
+          <groups:member groups:name="Nucleoside triphosphate tripolyhydrolase" groups:idRef="R_NTPTP2"/>
+          <groups:member groups:name="DATP amine hydrolysis (spontaneous)" groups:idRef="R_DATPHs"/>
+          <groups:member groups:name="Nucleoside triphosphate tripolyhydrolase" groups:idRef="R_NTPTP1"/>
+          <groups:member groups:name="Ribonucleoside-diphosphate reductase (GDP)" groups:idRef="R_RNDR2"/>
+          <groups:member groups:name="3&apos;-nucleotidase (AMP) (periplasm)" groups:idRef="R_3NTD7pp"/>
+          <groups:member groups:name="5&apos;-nucleotidase (CMP)" groups:idRef="R_NTD4"/>
+          <groups:member groups:name="5&apos;-nucleotidase (dTMP)" groups:idRef="R_NTD5"/>
+          <groups:member groups:name="5&apos;-nucleotidase (IMP)" groups:idRef="R_NTD11"/>
+          <groups:member groups:name="ATP amine hydrolysis (spontaneous)" groups:idRef="R_ATPHs"/>
+          <groups:member groups:name="5&apos;-nucleotidase (dUMP)" groups:idRef="R_NTD1pp"/>
+          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (itp)" groups:idRef="R_NTPP9"/>
+          <groups:member groups:name="Pyrimidine oxygenase" groups:idRef="R_PYROX"/>
+          <groups:member groups:name="Ribonucleoside-diphosphate reductase (CDP)" groups:idRef="R_RNDR3"/>
+          <groups:member groups:name="Ribonucleoside-triphosphate reductase (ATP) (flavodoxin)" groups:idRef="R_RNTR1c2"/>
+          <groups:member groups:name="5&apos;-nucleotidase (dAMP)" groups:idRef="R_NTD6"/>
+          <groups:member groups:name="Ribonucleoside-triphosphate reductase (UTP) (flavodoxin)" groups:idRef="R_RNTR4c2"/>
+          <groups:member groups:name="Pyruvate kinase(4)" groups:idRef="R_PYK4"/>
+          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (dctp)" groups:idRef="R_NTPP3"/>
+          <groups:member groups:name="Ribonucleoside-diphosphate reductase (CDP) (glutaredoxin)" groups:idRef="R_RNDR3b"/>
           <groups:member groups:name="Purine-nucleoside phosphorylase (Deoxyinosine)" groups:idRef="R_PUNP6"/>
-          <groups:member groups:name="ADPribose diphosphatase" groups:idRef="R_ADPRDP"/>
-          <groups:member groups:name="Peroxyaminoacrylate reductase" groups:idRef="R_POAACR"/>
-          <groups:member groups:name="Uracil phosphoribosyltransferase" groups:idRef="R_UPPRT"/>
-          <groups:member groups:name="GTP amine hydrolysis (spontaneous)" groups:idRef="R_GTPHs"/>
+          <groups:member groups:name="Dihydrouracil dehydrogenase (NAD)" groups:idRef="R_DURADx"/>
           <groups:member groups:name="5&apos;-nucleotidase (dCMP)" groups:idRef="R_NTD3"/>
-          <groups:member groups:name="5&apos;-nucleotidase (dCMP)" groups:idRef="R_NTD3pp"/>
-          <groups:member groups:name="5&apos;-nucleotidase (GMP)" groups:idRef="R_NTD9"/>
-          <groups:member groups:name="5&apos;-nucleotidase (GMP)" groups:idRef="R_NTD9pp"/>
-          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (dgtp)" groups:idRef="R_NTPP1"/>
-          <groups:member groups:name="5&apos;-nucleotidase (dUMP)" groups:idRef="R_NTD1"/>
-          <groups:member groups:name="CDP phosphohydrolase" groups:idRef="R_CDPPH"/>
-          <groups:member groups:name="Pyruvate kinase(4)" groups:idRef="R_PYK4"/>
-          <groups:member groups:name="Deoxycytidine deaminase" groups:idRef="R_DCYTD"/>
-          <groups:member groups:name="Hypoxanthine phosphoribosyltransferase (Hypoxanthine)" groups:idRef="R_HXPRT"/>
-          <groups:member groups:name="Ribonucleoside-triphosphate reductase (UTP) (flavodoxin)" groups:idRef="R_RNTR4c2"/>
-          <groups:member groups:name="Thymidine kinase (ATP:thymidine)" groups:idRef="R_TMDK1"/>
-          <groups:member groups:name="5&apos;-nucleotidase (dTMP)" groups:idRef="R_NTD5pp"/>
-          <groups:member groups:name="Ribonucleoside-diphosphate reductase (UDP)" groups:idRef="R_RNDR4"/>
-          <groups:member groups:name="Adenylate kinase" groups:idRef="R_ADK1"/>
+          <groups:member groups:name="Cytidine deaminase" groups:idRef="R_CYTD"/>
+          <groups:member groups:name="3&apos;-nucleotidase (UMP) (periplasm)" groups:idRef="R_3NTD2pp"/>
+          <groups:member groups:name="Ribonucleoside-diphosphate reductase (UDP) (glutaredoxin)" groups:idRef="R_RNDR4b"/>
           <groups:member groups:name="CMP nucleosidase" groups:idRef="R_CMPN"/>
-          <groups:member groups:name="5&apos;-nucleotidase (AMP)" groups:idRef="R_NTD7"/>
-          <groups:member groups:name="3&apos;-nucleotidase (GMP) (periplasm)" groups:idRef="R_3NTD9pp"/>
-          <groups:member groups:name="Nucleoside-diphosphate kinase (ATP:CDP)" groups:idRef="R_NDPK3"/>
-          <groups:member groups:name="Ribonucleoside-triphosphate reductase (GTP) (flavodoxin)" groups:idRef="R_RNTR2c2"/>
-          <groups:member groups:name="Nucleoside diphosphatase  UDP" groups:idRef="R_NDP7"/>
-          <groups:member groups:name="5&apos;-nucleotidase (XMP)" groups:idRef="R_NTD10"/>
-          <groups:member groups:name="3&apos;,5&apos;-cyclic-nucleotide phosphodiesterase" groups:idRef="R_PDE1"/>
-          <groups:member groups:name="DTMP kinase" groups:idRef="R_DTMPK"/>
-          <groups:member groups:name="5&apos;-nucleotidase (CMP)" groups:idRef="R_NTD4"/>
-          <groups:member groups:name="5&apos;-nucleotidase (AMP)" groups:idRef="R_NTD7pp"/>
-          <groups:member groups:name="Cytosine deaminase" groups:idRef="R_CSND"/>
-          <groups:member groups:name="3&apos;,5&apos;-cyclic-nucleotide phosphodiesterase" groups:idRef="R_PDE4"/>
-          <groups:member groups:name="Ribonucleoside-diphosphate reductase (GDP)" groups:idRef="R_RNDR2"/>
           <groups:member groups:name="Gp4G hydrolase" groups:idRef="R_GP4GH"/>
-          <groups:member groups:name="Nucleoside-diphosphate kinase (ATP:UDP)" groups:idRef="R_NDPK2"/>
-          <groups:member groups:name="Ribonucleoside-diphosphate reductase (CDP) (glutaredoxin)" groups:idRef="R_RNDR3b"/>
-          <groups:member groups:name="RE2954" groups:idRef="R_PYK6"/>
-          <groups:member groups:name="Ribonucleoside-triphosphate reductase (CTP) (flavodoxin)" groups:idRef="R_RNTR3c2"/>
-          <groups:member groups:name="Dihydrouracil dehydrogenase (NAD)" groups:idRef="R_DURADx"/>
-          <groups:member groups:name="Guanine deaminase" groups:idRef="R_GUAD"/>
-          <groups:member groups:name="Purine-nucleoside phosphorylase (Deoxyadenosine)" groups:idRef="R_PUNP2"/>
-          <groups:member groups:name="5&apos;-nucleotidase (XMP)" groups:idRef="R_NTD10pp"/>
-          <groups:member groups:name="Adenine deaminase" groups:idRef="R_ADD"/>
-          <groups:member groups:name="Peroxyureidoacrylate hydrolase" groups:idRef="R_URACPAH"/>
+          <groups:member groups:name="DTMP kinase" groups:idRef="R_DTMPK"/>
+          <groups:member groups:name="Purine-nucleoside phosphorylase (Xanthosine)" groups:idRef="R_PUNP7"/>
+          <groups:member groups:name="Thymidylate synthase" groups:idRef="R_TMDS"/>
           <groups:member groups:name="Deoxyguanylate kinase (dGMP:ATP)" groups:idRef="R_DGK1"/>
-          <groups:member groups:name="Nucleoside-diphosphate kinase (ATP:dCDP)" groups:idRef="R_NDPK7"/>
-          <groups:member groups:name="Ap4A hydrolase" groups:idRef="R_AP4AH"/>
-          <groups:member groups:name="Ap4A synthetase" groups:idRef="R_AP4AS"/>
-          <groups:member groups:name="Guanylate kinase (GMP:ATP)" groups:idRef="R_GK1"/>
+          <groups:member groups:name="3-aminoacrylate hydrolase" groups:idRef="R_3AMACHYD"/>
+          <groups:member groups:name="Pyruvate kinase(2)" groups:idRef="R_PYK2"/>
+          <groups:member groups:name="Nucleoside diphosphatase  UDP" groups:idRef="R_NDP7"/>
+          <groups:member groups:name="Guanine deaminase" groups:idRef="R_GUAD"/>
+          <groups:member groups:name="2&apos;,3&apos;-cyclic-nucleotide phosphodiesterase (UMP) (periplasm)" groups:idRef="R_23PDE2pp"/>
+          <groups:member groups:name="Pyruvate kinase(3)" groups:idRef="R_PYK3"/>
+          <groups:member groups:name="Nucleoside-diphosphate kinase (ATP:UDP)" groups:idRef="R_NDPK2"/>
+          <groups:member groups:name="Ribonucleoside-diphosphate reductase (ADP) (glutaredoxin)" groups:idRef="R_RNDR1b"/>
+          <groups:member groups:name="Guanosine kinase" groups:idRef="R_GSNK"/>
+          <groups:member groups:name="Uridine kinase  ATPUridine" groups:idRef="R_URIK1"/>
+          <groups:member groups:name="Thymidine phosphorylase" groups:idRef="R_TMDPP"/>
+          <groups:member groups:name="AMP nucleosidase" groups:idRef="R_AMPN"/>
+          <groups:member groups:name="3&apos;,5&apos;-cyclic-nucleotide phosphodiesterase" groups:idRef="R_PDE4"/>
           <groups:member groups:name="Carbamate deaminase" groups:idRef="R_CBMD"/>
-          <groups:member groups:name="Nucleoside triphosphate tripolyhydrolase" groups:idRef="R_NTPTP2"/>
-          <groups:member groups:name="Inosine hydrolase" groups:idRef="R_INSH"/>
-          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (ctp)" groups:idRef="R_NTPP4"/>
-          <groups:member groups:name="3&apos;-nucleotidase (AMP) (periplasm)" groups:idRef="R_3NTD7pp"/>
-          <groups:member groups:name="ATP amine hydrolysis (spontaneous)" groups:idRef="R_ATPHs"/>
-          <groups:member groups:name="DATP amine hydrolysis (spontaneous)" groups:idRef="R_DATPHs"/>
-          <groups:member groups:name="Nucleoside-triphosphatase (GTP) (periplasm)" groups:idRef="R_NTP3pp"/>
+          <groups:member groups:name="Deoxyuridine kinase (ATP:Deoxyuridine)" groups:idRef="R_DURIK1"/>
+          <groups:member groups:name="Guanylate cyclase" groups:idRef="R_GUACYC"/>
           <groups:member groups:name="Ribonucleoside-diphosphate reductase (ADP)" groups:idRef="R_RNDR1"/>
-          <groups:member groups:name="Xanthine phosphoribosyltransferase" groups:idRef="R_XPPT"/>
+          <groups:member groups:name="Adenylate kinase" groups:idRef="R_ADK1"/>
+          <groups:member groups:name="ATP:cytidine 5&apos;-phosphotransferase" groups:idRef="R_CYTDK1"/>
+          <groups:member groups:name="Malonic semialdehyde reductase" groups:idRef="R_MSAR"/>
           <groups:member groups:name="Nucleoside-diphosphate kinase (ATP:dGDP)" groups:idRef="R_NDPK5"/>
+          <groups:member groups:name="Nucleoside-triphosphatase (GTP) (periplasm)" groups:idRef="R_NTP3pp"/>
+          <groups:member groups:name="Nucleoside-diphosphate kinase (ATP:CDP)" groups:idRef="R_NDPK3"/>
           <groups:member groups:name="Nucleoside-diphosphate kinase (ATP:dTDP)" groups:idRef="R_NDPK4"/>
+          <groups:member groups:name="Nucleoside-triphosphatase (ITP)" groups:idRef="R_NTP10"/>
+          <groups:member groups:name="Purine-nucleoside phosphorylase (Deoxyguanosine)" groups:idRef="R_PUNP4"/>
+          <groups:member groups:name="GTP amine hydrolysis (spontaneous)" groups:idRef="R_GTPHs"/>
+          <groups:member groups:name="RE2954" groups:idRef="R_PYK6"/>
+          <groups:member groups:name="CDP phosphohydrolase" groups:idRef="R_CDPPH"/>
+          <groups:member groups:name="5&apos;-nucleotidase (dGMP)" groups:idRef="R_NTD8"/>
+          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (xtp)" groups:idRef="R_NTPP11"/>
+          <groups:member groups:name="Inosine hydrolase" groups:idRef="R_INSH"/>
+          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (ctp)" groups:idRef="R_NTPP4"/>
           <groups:member groups:name="Deoxyadenylate kinase" groups:idRef="R_DADK"/>
-          <groups:member groups:name="Insosine kinase" groups:idRef="R_INSK"/>
-          <groups:member groups:name="5&apos;-nucleotidase (dIMP) (periplasm)" groups:idRef="R_NTD12pp"/>
-          <groups:member groups:name="Adenosine deaminase" groups:idRef="R_ADA"/>
-          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (dctp)" groups:idRef="R_NTPP3"/>
-          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (atp)" groups:idRef="R_NTPP6"/>
-          <groups:member groups:name="Ribonucleoside-diphosphate reductase (ADP) (glutaredoxin)" groups:idRef="R_RNDR1b"/>
           <groups:member groups:name="5&apos;-nucleotidase (dAMP)" groups:idRef="R_NTD6pp"/>
+          <groups:member groups:name="Adenine deaminase" groups:idRef="R_ADD"/>
           <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (utp)" groups:idRef="R_NTPP8"/>
-          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (datp)" groups:idRef="R_NTPP5"/>
-          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (dttp)" groups:idRef="R_NTPP7"/>
-          <groups:member groups:name="Cytidine kinase (GTP)" groups:idRef="R_CYTDK2"/>
-          <groups:member groups:name="5&apos;-nucleotidase (IMP)" groups:idRef="R_NTD11"/>
-          <groups:member groups:name="Purine-nucleoside phosphorylase (Deoxyguanosine)" groups:idRef="R_PUNP4"/>
-          <groups:member groups:name="5&apos;-nucleotidase (IMP)" groups:idRef="R_NTD11pp"/>
-          <groups:member groups:name="5&apos;-nucleotidase (UMP)" groups:idRef="R_NTD2pp"/>
-          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (xtp)" groups:idRef="R_NTPP11"/>
-          <groups:member groups:name="5&apos;-nucleotidase (UMP)" groups:idRef="R_NTD2"/>
-          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (ditp)" groups:idRef="R_NTPP10"/>
-          <groups:member groups:name="Nucleoside triphosphate tripolyhydrolase" groups:idRef="R_NTPTP1"/>
           <groups:member groups:name="Cytidylate kinase (dCMP)" groups:idRef="R_CYTK2"/>
-          <groups:member groups:name="Pyrimidine oxygenase" groups:idRef="R_PYROX"/>
-          <groups:member groups:name="Uridine kinase  ATPUridine" groups:idRef="R_URIK1"/>
-          <groups:member groups:name="Nucleoside-diphosphate kinase (ATP:dUDP)" groups:idRef="R_NDPK6"/>
-          <groups:member groups:name="Purine-nucleoside phosphorylase (Guanosine)" groups:idRef="R_PUNP3"/>
-          <groups:member groups:name="Uridine kinase (GTP:Uridine)" groups:idRef="R_URIK2"/>
+          <groups:member groups:name="5&apos;-nucleotidase (XMP)" groups:idRef="R_NTD10"/>
+          <groups:member groups:name="Nucleoside-triphosphatase (GTP)" groups:idRef="R_NTP3"/>
+          <groups:member groups:name="5&apos;-nucleotidase (dIMP) (periplasm)" groups:idRef="R_NTD12pp"/>
+          <groups:member groups:name="Nucleoside-diphosphate kinase (ATP:GDP)" groups:idRef="R_NDPK1"/>
+          <groups:member groups:name="2&apos;,3&apos;-cyclic-nucleotide phosphodiesterase (GMP) (periplasm)" groups:idRef="R_23PDE9pp"/>
+          <groups:member groups:name="5&apos;-nucleotidase (IMP)" groups:idRef="R_NTD11pp"/>
           <groups:member groups:name="Deoxyuridine phosphorylase" groups:idRef="R_DURIPP"/>
-          <groups:member groups:name="ATP:cytidine 5&apos;-phosphotransferase" groups:idRef="R_CYTDK1"/>
+          <groups:member groups:name="5&apos;-nucleotidase (dUMP)" groups:idRef="R_NTD1"/>
+          <groups:member groups:name="2&apos;,3&apos;-cyclic-nucleotide phosphodiesterase (CMP) (periplasm)" groups:idRef="R_23PDE4pp"/>
+          <groups:member groups:name="Adentylate kinase (GTP)" groups:idRef="R_ADK3"/>
+          <groups:member groups:name="Adenylate cyclase" groups:idRef="R_ADNCYC"/>
+          <groups:member groups:name="Deoxycytidine deaminase" groups:idRef="R_DCYTD"/>
+          <groups:member groups:name="Cytosine deaminase" groups:idRef="R_CSND"/>
+          <groups:member groups:name="Cytidine kinase (GTP)" groups:idRef="R_CYTDK2"/>
+          <groups:member groups:name="ADPribose diphosphatase" groups:idRef="R_ADPRDP"/>
           <groups:member groups:name="Deoxyadenosine deaminase" groups:idRef="R_DADA"/>
-          <groups:member groups:name="Deoxyuridine kinase (ATP:Deoxyuridine)" groups:idRef="R_DURIK1"/>
-          <groups:member groups:name="5&apos;-nucleotidase (dIMP)" groups:idRef="R_NTD12"/>
-          <groups:member groups:name="3&apos;-nucleotidase (CMP) (periplasm)" groups:idRef="R_3NTD4pp"/>
-          <groups:member groups:name="Guanine phosphoribosyltransferase" groups:idRef="R_GUAPRT"/>
-          <groups:member groups:name="Linear diguanylate phosphodiesterase" groups:idRef="R_LDGUNPD"/>
-          <groups:member groups:name="Ribonucleoside-diphosphate reductase (CDP)" groups:idRef="R_RNDR3"/>
-          <groups:member groups:name="Ribonucleoside-triphosphate reductase (ATP) (flavodoxin)" groups:idRef="R_RNTR1c2"/>
-          <groups:member groups:name="Nucleoside triphosphate pyrophosphorylase (itp)" groups:idRef="R_NTPP9"/>
-          <groups:member groups:name="Guanylate cyclase" groups:idRef="R_GUACYC"/>
-          <groups:member groups:name="5&apos;-nucleotidase (dUMP)" groups:idRef="R_NTD1pp"/>
-          <groups:member groups:name="5&apos;-nucleotidase (dTMP)" groups:idRef="R_NTD5"/>
-          <groups:member groups:name="Purine-nucleoside phosphorylase (Xanthosine)" groups:idRef="R_PUNP7"/>
-          <groups:member groups:name="Pyrimidine-nucleoside phosphorylase (uracil)" groups:idRef="R_PYNP2r"/>
-          <groups:member groups:name="DUTP diphosphatase" groups:idRef="R_DUTPDP"/>
-          <groups:member groups:name="UMP kinase" groups:idRef="R_UMPK"/>
-          <groups:member groups:name="Nucleoside-triphosphatase (dITP)" groups:idRef="R_NTP11"/>
-          <groups:member groups:name="Diguanylate cyclase" groups:idRef="R_DGUNC"/>
-          <groups:member groups:name="3-aminoacrylate hydrolase" groups:idRef="R_3AMACHYD"/>
+          <groups:member groups:name="DCTP deaminase" groups:idRef="R_DCTPD"/>
+          <groups:member groups:name="Nucleoside diphosphatase  GDP" groups:idRef="R_NDP3"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group29" sboTerm="SBO:0000633" groups:id="G_group29" groups:name="Oxidative Phosphorylation" groups:kind="partonomy">
         <groups:listOfMembers>
+          <groups:member groups:name="Trimethylamine N-oxide reductase (menaquinol 8)" groups:idRef="R_TMAOR1"/>
+          <groups:member groups:name="NADPH Quinone Reductase (Ubiquinone-8)" groups:idRef="R_NADPHQR2"/>
+          <groups:member groups:name="Nitrite Reductase (NADH)" groups:idRef="R_NTRIR2x"/>
+          <groups:member groups:name="D-lactate dehydrogenase" groups:idRef="R_LDH_D2"/>
+          <groups:member groups:name="Quinol monooxygenase (menaquinol 8)" groups:idRef="R_QMO3"/>
+          <groups:member groups:name="Glycerol-3-phosphate dehydrogenase (menaquinone-8)" groups:idRef="R_G3PD6"/>
+          <groups:member groups:name="Cytochrome oxidase bo3 (ubiquinol-8: 4 protons) (periplasm)" groups:idRef="R_CYTBO3_4pp"/>
+          <groups:member groups:name="Succinate dehydrogenase (irreversible)" groups:idRef="R_SUCDi"/>
           <groups:member groups:name="Thioredoxin reductase (NADPH)" groups:idRef="R_TRDR"/>
+          <groups:member groups:name="Glucose dehydrogenase (ubiquinone-8 as acceptor) (periplasm)" groups:idRef="R_GLCDpp"/>
+          <groups:member groups:name="D-Carnitine-CoA Ligase" groups:idRef="R_CRNDCAL2"/>
+          <groups:member groups:name="Hydrogenase (ubiquinone-8: 2 protons) (periplasm)" groups:idRef="R_HYD1pp"/>
+          <groups:member groups:name="ATP synthase (four protons for one ATP) (periplasm)" groups:idRef="R_ATPS4rpp"/>
+          <groups:member groups:name="L-Lactate dehydrogenase (menaquinone)" groups:idRef="R_L_LACD3"/>
+          <groups:member groups:name="NADH dehydrogenase (ubiquinone-8 &amp; 3 protons) (periplasm)" groups:idRef="R_NADH16pp"/>
           <groups:member groups:name="Pyruvate oxidase" groups:idRef="R_POX"/>
-          <groups:member groups:name="Formate dehydrogenase (quinone-8) (periplasm)" groups:idRef="R_FDH4pp"/>
           <groups:member groups:name="Crotonobetaine-CoA Ligase" groups:idRef="R_CTBTCAL2"/>
-          <groups:member groups:name="Glucose dehydrogenase (ubiquinone-8 as acceptor) (periplasm)" groups:idRef="R_GLCDpp"/>
-          <groups:member groups:name="D-lactate dehydrogenase" groups:idRef="R_LDH_D2"/>
-          <groups:member groups:name="NAD(P) transhydrogenase (periplasm)" groups:idRef="R_THD2pp"/>
+          <groups:member groups:name="NADH dehydrogenase (demethylmenaquinone-8 &amp; 3 protons) (periplasm)" groups:idRef="R_NADH18pp"/>
+          <groups:member groups:name="Hydrogenase (menaquinone8: 2 protons) (periplasm)" groups:idRef="R_HYD2pp"/>
           <groups:member groups:name="Gamma-butyrobetainyl-CoA: carnitine CoA transferase" groups:idRef="R_CRNBTCT"/>
-          <groups:member groups:name="L-Lactate dehydrogenase (menaquinone)" groups:idRef="R_L_LACD3"/>
-          <groups:member groups:name="L-Lactate dehydrogenase (ubiquinone)" groups:idRef="R_L_LACD2"/>
-          <groups:member groups:name="Carnitine-CoA Ligase" groups:idRef="R_CRNCAL2"/>
+          <groups:member groups:name="Carnitine-CoA racemase" groups:idRef="R_CRNCAR"/>
+          <groups:member groups:name="Polyphosphate kinase" groups:idRef="R_PPK2"/>
           <groups:member groups:name="Glycerol-3-phosphate dehydrogenase (ubiquinone-8)" groups:idRef="R_G3PD5"/>
-          <groups:member groups:name="Quinol monooxygenase (Ubiquinol-8)" groups:idRef="R_QMO2"/>
-          <groups:member groups:name="NAD transhydrogenase" groups:idRef="R_NADTRHD"/>
-          <groups:member groups:name="NADH dehydrogenase (demethylmenaquinone-8 &amp; 3 protons) (periplasm)" groups:idRef="R_NADH18pp"/>
-          <groups:member groups:name="NADH dehydrogenase (demethylmenaquinone-8 &amp; 0 protons)" groups:idRef="R_NADH9"/>
-          <groups:member groups:name="Hydrogenase (Demethylmenaquinone-8: 2 protons) (periplasm)" groups:idRef="R_HYD3pp"/>
-          <groups:member groups:name="NADH dehydrogenase (ubiquinone-8 )" groups:idRef="R_NADH5"/>
+          <groups:member groups:name="Carnitine-CoA Ligase" groups:idRef="R_CRNCAL2"/>
           <groups:member groups:name="Formate Dehydrogenase (menaquinone-8) (periplasm)" groups:idRef="R_FDH5pp"/>
-          <groups:member groups:name="Polyphosphate kinase" groups:idRef="R_PPK2"/>
-          <groups:member groups:name="Carnitine-CoA racemase" groups:idRef="R_CRNCAR"/>
-          <groups:member groups:name="Dimethyl sulfoxide reductase (Demethylmenaquinol 8) (periplasm)" groups:idRef="R_DMSOR2pp"/>
-          <groups:member groups:name="NADH dehydrogenase (menaquinone-8 &amp; 3 protons) (periplasm)" groups:idRef="R_NADH17pp"/>
-          <groups:member groups:name="Polyphosphate kinase" groups:idRef="R_PPK"/>
-          <groups:member groups:name="Cytochrome oxidase bd (menaquinol-8: 2 protons) (periplasm)" groups:idRef="R_CYTBD2pp"/>
-          <groups:member groups:name="Quinol monooxygenase (menaquinol 8)" groups:idRef="R_QMO3"/>
+          <groups:member groups:name="Nitrate reductase (Ubiquinol-8) (periplasm)" groups:idRef="R_NO3R1pp"/>
+          <groups:member groups:name="NAD(P) transhydrogenase (periplasm)" groups:idRef="R_THD2pp"/>
           <groups:member groups:name="Trimethylamine N-oxide reductase (menaquinol 8) (periplasm)" groups:idRef="R_TMAOR1pp"/>
-          <groups:member groups:name="Hydrogenase (ubiquinone-8: 2 protons) (periplasm)" groups:idRef="R_HYD1pp"/>
-          <groups:member groups:name="ATP synthase (four protons for one ATP) (periplasm)" groups:idRef="R_ATPS4rpp"/>
-          <groups:member groups:name="Dimethyl sulfoxide reductase (Demethylmenaquinol 8)" groups:idRef="R_DMSOR2"/>
-          <groups:member groups:name="Crotonobetainyl-CoA: carnitine CoA transferase" groups:idRef="R_CRNCBCT"/>
-          <groups:member groups:name="Carnityl-CoA dehydratse" groups:idRef="R_CRNCDH"/>
+          <groups:member groups:name="NADH dehydrogenase (menaquinone-8 &amp; 3 protons) (periplasm)" groups:idRef="R_NADH17pp"/>
+          <groups:member groups:name="NADH dehydrogenase (demethylmenaquinone-8 &amp; 0 protons)" groups:idRef="R_NADH9"/>
           <groups:member groups:name="Cytochrome oxidase bd (ubiquinol-8: 2 protons) (periplasm)" groups:idRef="R_CYTBDpp"/>
+          <groups:member groups:name="NADH dehydrogenase (ubiquinone-8 )" groups:idRef="R_NADH5"/>
+          <groups:member groups:name="Quinol monooxygenase (Ubiquinol-8)" groups:idRef="R_QMO2"/>
+          <groups:member groups:name="NAD transhydrogenase" groups:idRef="R_NADTRHD"/>
           <groups:member groups:name="Glycerol-3-phosphate dehydrogenase (demethylmenaquinone-8)" groups:idRef="R_G3PD7"/>
-          <groups:member groups:name="Nitrate reductase (Ubiquinol-8) (periplasm)" groups:idRef="R_NO3R1pp"/>
-          <groups:member groups:name="Trimethylamine N-oxide reductase (menaquinol 8)" groups:idRef="R_TMAOR1"/>
-          <groups:member groups:name="NADH dehydrogenase (ubiquinone-8 &amp; 3 protons) (periplasm)" groups:idRef="R_NADH16pp"/>
-          <groups:member groups:name="Cytochrome oxidase bo3 (ubiquinol-8: 4 protons) (periplasm)" groups:idRef="R_CYTBO3_4pp"/>
-          <groups:member groups:name="Nitrate reductase (Menaquinol-8) (periplasm)" groups:idRef="R_NO3R2pp"/>
-          <groups:member groups:name="NADPH Quinone Reductase (Menaquinone-8)" groups:idRef="R_NADPHQR3"/>
-          <groups:member groups:name="NADPH Quinone Reductase (2-Demethylmenaquinone-8)" groups:idRef="R_NADPHQR4"/>
-          <groups:member groups:name="Nitrite Reductase (NADH)" groups:idRef="R_NTRIR2x"/>
-          <groups:member groups:name="Succinate dehydrogenase (irreversible)" groups:idRef="R_SUCDi"/>
-          <groups:member groups:name="D-Carnitine-CoA Ligase" groups:idRef="R_CRNDCAL2"/>
-          <groups:member groups:name="Trimethylamine N-oxide reductase (demethylmenaquinol 8)" groups:idRef="R_TMAOR2"/>
-          <groups:member groups:name="Dimethyl sulfoxide reductase (Menaquinol 8)" groups:idRef="R_DMSOR1"/>
-          <groups:member groups:name="Glycerol-3-phosphate dehydrogenase (menaquinone-8)" groups:idRef="R_G3PD6"/>
-          <groups:member groups:name="Hydrogenase (menaquinone8: 2 protons) (periplasm)" groups:idRef="R_HYD2pp"/>
           <groups:member groups:name="NADH dehydrogenase (menaquinone-8 &amp; 0 protons)" groups:idRef="R_NADH10"/>
+          <groups:member groups:name="Cytochrome oxidase bd (menaquinol-8: 2 protons) (periplasm)" groups:idRef="R_CYTBD2pp"/>
+          <groups:member groups:name="Formate dehydrogenase (quinone-8) (periplasm)" groups:idRef="R_FDH4pp"/>
+          <groups:member groups:name="Hydrogenase (Demethylmenaquinone-8: 2 protons) (periplasm)" groups:idRef="R_HYD3pp"/>
+          <groups:member groups:name="NADPH Quinone Reductase (2-Demethylmenaquinone-8)" groups:idRef="R_NADPHQR4"/>
+          <groups:member groups:name="Dimethyl sulfoxide reductase (Demethylmenaquinol 8)" groups:idRef="R_DMSOR2"/>
+          <groups:member groups:name="Nitrate reductase (Menaquinol-8) (periplasm)" groups:idRef="R_NO3R2pp"/>
           <groups:member groups:name="Dimethyl sulfoxide reductase (Menaquinol 8) (periplasm)" groups:idRef="R_DMSOR1pp"/>
-          <groups:member groups:name="NADPH Quinone Reductase (Ubiquinone-8)" groups:idRef="R_NADPHQR2"/>
+          <groups:member groups:name="Dimethyl sulfoxide reductase (Demethylmenaquinol 8) (periplasm)" groups:idRef="R_DMSOR2pp"/>
+          <groups:member groups:name="Trimethylamine N-oxide reductase (demethylmenaquinol 8)" groups:idRef="R_TMAOR2"/>
+          <groups:member groups:name="Crotonobetainyl-CoA: carnitine CoA transferase" groups:idRef="R_CRNCBCT"/>
+          <groups:member groups:name="Carnityl-CoA dehydratse" groups:idRef="R_CRNCDH"/>
+          <groups:member groups:name="L-Lactate dehydrogenase (ubiquinone)" groups:idRef="R_L_LACD2"/>
           <groups:member groups:name="Trimethylamine N-oxide reductase (demethylmenaquinol 8) (periplasm)" groups:idRef="R_TMAOR2pp"/>
+          <groups:member groups:name="Polyphosphate kinase" groups:idRef="R_PPK"/>
+          <groups:member groups:name="Dimethyl sulfoxide reductase (Menaquinol 8)" groups:idRef="R_DMSOR1"/>
+          <groups:member groups:name="NADPH Quinone Reductase (Menaquinone-8)" groups:idRef="R_NADPHQR3"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group30" sboTerm="SBO:0000633" groups:id="G_group30" groups:name="Pentose Phosphate Pathway" groups:kind="partonomy">
         <groups:listOfMembers>
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-          <groups:member groups:name="Transaldolase" groups:idRef="R_TALA"/>
-          <groups:member groups:name="Ribulose 5-phosphate 3-epimerase" groups:idRef="R_RPE"/>
+          <groups:member groups:name="Sedoheptulose 1,7-bisphosphate D-glyceraldehyde-3-phosphate-lyase" groups:idRef="R_FBA3"/>
+          <groups:member groups:name="Glucose 6-phosphate dehydrogenase" groups:idRef="R_G6PDH2r"/>
           <groups:member groups:name="6-phosphogluconate dehydratase" groups:idRef="R_EDD"/>
-          <groups:member groups:name="Transketolase" groups:idRef="R_TKT2"/>
           <groups:member groups:name="Transketolase" groups:idRef="R_TKT1"/>
-          <groups:member groups:name="Glucose 6-phosphate dehydrogenase" groups:idRef="R_G6PDH2r"/>
-          <groups:member groups:name="2-dehydro-3-deoxy-phosphogluconate aldolase" groups:idRef="R_EDA"/>
+          <groups:member groups:name="Transaldolase" groups:idRef="R_TALA"/>
+          <groups:member groups:name="6-phosphogluconolactonase" groups:idRef="R_PGL"/>
+          <groups:member groups:name="Transketolase" groups:idRef="R_TKT2"/>
           <groups:member groups:name="Ribose-5-phosphate isomerase" groups:idRef="R_RPI"/>
+          <groups:member groups:name="Phosphofructokinase (s7p)" groups:idRef="R_PFK_3"/>
+          <groups:member groups:name="Ribulose 5-phosphate 3-epimerase" groups:idRef="R_RPE"/>
           <groups:member groups:name="Phosphogluconate dehydrogenase" groups:idRef="R_GND"/>
-          <groups:member groups:name="Sedoheptulose 1,7-bisphosphate D-glyceraldehyde-3-phosphate-lyase" groups:idRef="R_FBA3"/>
-          <groups:member groups:name="6-phosphogluconolactonase" groups:idRef="R_PGL"/>
+          <groups:member groups:name="2-dehydro-3-deoxy-phosphogluconate aldolase" groups:idRef="R_EDA"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group31" sboTerm="SBO:0000633" groups:id="G_group31" groups:name="Purine and Pyrimidine Biosynthesis" groups:kind="partonomy">
         <groups:listOfMembers>
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-          <groups:member groups:name="Phosphoribosylaminoimidazole synthase" groups:idRef="R_PRAIS"/>
-          <groups:member groups:name="Dihydroorotase" groups:idRef="R_DHORTS"/>
           <groups:member groups:name="Phosphoribosylformylglycinamidine synthase" groups:idRef="R_PRFGS"/>
-          <groups:member groups:name="Dihydoorotic acid dehydrogenase (quinone8)" groups:idRef="R_DHORD2"/>
-          <groups:member groups:name="GMP synthase" groups:idRef="R_GMPS2"/>
           <groups:member groups:name="Adenylosuccinate synthase" groups:idRef="R_ADSS"/>
-          <groups:member groups:name="GAR transformylase-T" groups:idRef="R_GART"/>
-          <groups:member groups:name="GMP synthase" groups:idRef="R_GMPS"/>
+          <groups:member groups:name="Phosphoribosylaminoimidazole carboxylase" groups:idRef="R_AIRC2"/>
+          <groups:member groups:name="Phosphoribosylaminoimidazole carboxylase (mutase rxn)" groups:idRef="R_AIRC3"/>
           <groups:member groups:name="Phosphoribosylaminoimidazolecarboxamide formyltransferase" groups:idRef="R_AICART"/>
-          <groups:member groups:name="Phosphoribosylaminoimidazolesuccinocarboxamide synthase" groups:idRef="R_PRASCSi"/>
-          <groups:member groups:name="Adenylsuccinate lyase" groups:idRef="R_ADSL1r"/>
           <groups:member groups:name="IMP cyclohydrolase" groups:idRef="R_IMPC"/>
-          <groups:member groups:name="Aspartate carbamoyltransferase" groups:idRef="R_ASPCT"/>
-          <groups:member groups:name="CTP synthase (glutamine)" groups:idRef="R_CTPS2"/>
-          <groups:member groups:name="Phosphoribosylaminoimidazole carboxylase (mutase rxn)" groups:idRef="R_AIRC3"/>
-          <groups:member groups:name="Phosphoribosylaminoimidazole carboxylase" groups:idRef="R_AIRC2"/>
-          <groups:member groups:name="YUMP synthetase" groups:idRef="R_YUMPS"/>
-          <groups:member groups:name="Pseudouridine kinase" groups:idRef="R_PSURIK"/>
-          <groups:member groups:name="Orotidine-5&apos;-phosphate decarboxylase" groups:idRef="R_OMPDC"/>
           <groups:member groups:name="Glutamine phosphoribosyldiphosphate amidotransferase" groups:idRef="R_GLUPRT"/>
+          <groups:member groups:name="Phosphoribosylglycinamide synthase" groups:idRef="R_PRAGSr"/>
+          <groups:member groups:name="GMP reductase" groups:idRef="R_GMPR"/>
+          <groups:member groups:name="Purine Nucleoside Phorphoramidase" groups:idRef="R_PNSPA"/>
+          <groups:member groups:name="GMP synthase" groups:idRef="R_GMPS"/>
+          <groups:member groups:name="Adenylsuccinate lyase" groups:idRef="R_ADSL1r"/>
+          <groups:member groups:name="GAR transformylase-T" groups:idRef="R_GART"/>
           <groups:member groups:name="Orotate phosphoribosyltransferase" groups:idRef="R_ORPT"/>
+          <groups:member groups:name="Dihydoorotic acid dehydrogenase (quinone8)" groups:idRef="R_DHORD2"/>
+          <groups:member groups:name="Phosphoribosylglycinamide formyltransferase" groups:idRef="R_GARFT"/>
           <groups:member groups:name="Fumarate dependent DHORD" groups:idRef="R_DHORDfum"/>
-          <groups:member groups:name="GMP reductase" groups:idRef="R_GMPR"/>
-          <groups:member groups:name="Phosphoribosylglycinamide synthase" groups:idRef="R_PRAGSr"/>
+          <groups:member groups:name="Orotidine-5&apos;-phosphate decarboxylase" groups:idRef="R_OMPDC"/>
+          <groups:member groups:name="Aspartate carbamoyltransferase" groups:idRef="R_ASPCT"/>
+          <groups:member groups:name="Dihydroorotic acid (menaquinone-8)" groups:idRef="R_DHORD5"/>
+          <groups:member groups:name="GMP synthase" groups:idRef="R_GMPS2"/>
+          <groups:member groups:name="Phosphoribosylaminoimidazolesuccinocarboxamide synthase" groups:idRef="R_PRASCSi"/>
           <groups:member groups:name="Adenylosuccinate lyase" groups:idRef="R_ADSL2r"/>
-          <groups:member groups:name="Phosphoribosylglycinamide formyltransferase" groups:idRef="R_GARFT"/>
+          <groups:member groups:name="Dihydroorotase" groups:idRef="R_DHORTS"/>
+          <groups:member groups:name="CTP synthase (glutamine)" groups:idRef="R_CTPS2"/>
+          <groups:member groups:name="Phosphoribosylaminoimidazole synthase" groups:idRef="R_PRAIS"/>
           <groups:member groups:name="IMP dehydrogenase" groups:idRef="R_IMPD"/>
-          <groups:member groups:name="Dihydroorotic acid (menaquinone-8)" groups:idRef="R_DHORD5"/>
+          <groups:member groups:name="Pseudouridine kinase" groups:idRef="R_PSURIK"/>
+          <groups:member groups:name="YUMP synthetase" groups:idRef="R_YUMPS"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group32" sboTerm="SBO:0000633" groups:id="G_group32" groups:name="Pyruvate Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="Pyruvate synthase" groups:idRef="R_POR5"/>
+          <groups:member groups:name="Formate-hydrogen lyase" groups:idRef="R_FHL"/>
           <groups:member groups:name="Phosphotransacetylase" groups:idRef="R_PTAr"/>
-          <groups:member groups:name="Oxaloacetate decarboxylase" groups:idRef="R_OAADC"/>
+          <groups:member groups:name="Acetate kinase" groups:idRef="R_ACKr"/>
           <groups:member groups:name="Alcohol dehydrogenase (ethanol)" groups:idRef="R_ALCD2x"/>
-          <groups:member groups:name="Acetyl-CoA synthetase" groups:idRef="R_ACS"/>
-          <groups:member groups:name="Formate-hydrogen lyase" groups:idRef="R_FHL"/>
-          <groups:member groups:name="D-lactate dehydrogenase" groups:idRef="R_LDH_D"/>
+          <groups:member groups:name="Oxaloacetate decarboxylase" groups:idRef="R_OAADC"/>
           <groups:member groups:name="Acetaldehyde dehydrogenase (acetylating)" groups:idRef="R_ACALD"/>
           <groups:member groups:name="Pyruvate formate lyase" groups:idRef="R_PFL"/>
-          <groups:member groups:name="Acetate kinase" groups:idRef="R_ACKr"/>
+          <groups:member groups:name="Acetyl-CoA synthetase" groups:idRef="R_ACS"/>
+          <groups:member groups:name="Pyruvate synthase" groups:idRef="R_POR5"/>
+          <groups:member groups:name="D-lactate dehydrogenase" groups:idRef="R_LDH_D"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group33" sboTerm="SBO:0000633" groups:id="G_group33" groups:name="Threonine and Lysine Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="L-2-amino-3-oxobutanoate decarboxylation (spontaneous)" groups:idRef="R_AOBUTDs"/>
+          <groups:member groups:name="Diaminopimelate decarboxylase" groups:idRef="R_DAPDC"/>
           <groups:member groups:name="Diaminopimelate epimerase" groups:idRef="R_DAPE"/>
           <groups:member groups:name="Threonine aldolase" groups:idRef="R_THRA"/>
-          <groups:member groups:name="Succinyldiaminopimelate transaminase" groups:idRef="R_SDPTA"/>
-          <groups:member groups:name="Tetrahydrodipicolinate succinylase" groups:idRef="R_THDPS"/>
-          <groups:member groups:name="Phospho-L-threonine phosphatase (periplasmic)" groups:idRef="R_PTHRpp"/>
+          <groups:member groups:name="Lysine 2,3-aminomutase" groups:idRef="R_LYSAM"/>
           <groups:member groups:name="L-allo-Threonine Aldolase" groups:idRef="R_THRA2"/>
-          <groups:member groups:name="Aminopropanol dehydrogenase reversible" groups:idRef="R_APPLDHr"/>
-          <groups:member groups:name="Homoserine dehydrogenase (NADPH)" groups:idRef="R_HSDy"/>
+          <groups:member groups:name="Phospho-L-threonine phosphatase (periplasmic)" groups:idRef="R_PTHRpp"/>
           <groups:member groups:name="Dihydrodipicolinate reductase (NADPH)" groups:idRef="R_DHDPRy"/>
-          <groups:member groups:name="Lysine decarboxylase" groups:idRef="R_LYSDC"/>
+          <groups:member groups:name="Threonine synthase" groups:idRef="R_THRS"/>
           <groups:member groups:name="L-allo-threonine dehydrogenase" groups:idRef="R_ATHRDHr"/>
+          <groups:member groups:name="Succinyldiaminopimelate transaminase" groups:idRef="R_SDPTA"/>
           <groups:member groups:name="Aspartate-semialdehyde dehydrogenase" groups:idRef="R_ASAD"/>
-          <groups:member groups:name="Diaminopimelate decarboxylase" groups:idRef="R_DAPDC"/>
+          <groups:member groups:name="Succinyl-diaminopimelate desuccinylase" groups:idRef="R_SDPDS"/>
+          <groups:member groups:name="Homoserine dehydrogenase (NADPH)" groups:idRef="R_HSDy"/>
           <groups:member groups:name="Homoserine kinase" groups:idRef="R_HSK"/>
+          <groups:member groups:name="Aminopropanol dehydrogenase reversible" groups:idRef="R_APPLDHr"/>
           <groups:member groups:name="Dihydrodipicolinate synthase" groups:idRef="R_DHDPS"/>
-          <groups:member groups:name="Succinyl-diaminopimelate desuccinylase" groups:idRef="R_SDPDS"/>
-          <groups:member groups:name="Threonine synthase" groups:idRef="R_THRS"/>
-          <groups:member groups:name="Lysine 2,3-aminomutase" groups:idRef="R_LYSAM"/>
           <groups:member groups:name="Aspartate kinase" groups:idRef="R_ASPK"/>
+          <groups:member groups:name="L-2-amino-3-oxobutanoate decarboxylation (spontaneous)" groups:idRef="R_AOBUTDs"/>
+          <groups:member groups:name="Tetrahydrodipicolinate succinylase" groups:idRef="R_THDPS"/>
+          <groups:member groups:name="Lysine decarboxylase" groups:idRef="R_LYSDC"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group34" sboTerm="SBO:0000633" groups:id="G_group34" groups:name="Transport, Inner Membrane" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="1,4-alpha-D-glucan transport via ABC system (periplasm)" groups:idRef="R_14GLUCANabcpp"/>
-          <groups:member groups:name="Phosphatidylglycerol transport via ABC system (n-C12:0, periplasm)" groups:idRef="R_PG120abcpp"/>
-          <groups:member groups:name="L-valine reversible transport via proton symport (periplasm)" groups:idRef="R_VALt2rpp"/>
-          <groups:member groups:name="D-fructose transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_FRUptspp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPG181tipp"/>
-          <groups:member groups:name="D-galactose transport in via proton symport (periplasm)" groups:idRef="R_GALt2pp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE160tipp"/>
-          <groups:member groups:name="Xanthosine transport via proton symport (periplasm)" groups:idRef="R_XTSNt2rpp"/>
-          <groups:member groups:name="3-hydroxypropionate transport via proton symport (periplasm)" groups:idRef="R_3HPPtpp"/>
-          <groups:member groups:name="Sulfoacetate transport via ABC system (periplasm)" groups:idRef="R_SULFACabcpp"/>
-          <groups:member groups:name="Pyruvate reversible transport via proton symport (periplasm)" groups:idRef="R_PYRt2rpp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE161tipp"/>
-          <groups:member groups:name="L-carnitine outward transport (H+ antiport)" groups:idRef="R_CRNt2rpp"/>
-          <groups:member groups:name="Formaldehyde transport via diffusion (periplasm)" groups:idRef="R_FALDtpp"/>
-          <groups:member groups:name="Methanesulfonate transport via ABC system (periplasm)" groups:idRef="R_MSO3abcpp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE180tipp"/>
-          <groups:member groups:name="Fructoselysine transport via proton symport (periplasm)" groups:idRef="R_FRULYSt2pp"/>
-          <groups:member groups:name="4-aminobutyrate/glutamate antiport (periplasm)" groups:idRef="R_GLUABUTt7pp"/>
-          <groups:member groups:name="Lysine/Cadaverine antiporter (periplasm)" groups:idRef="R_CADVtpp"/>
-          <groups:member groups:name="Cytosine transport in via proton symport (periplasm)" groups:idRef="R_CSNt2pp"/>
-          <groups:member groups:name="Na+/glutamate symport (periplasm)" groups:idRef="R_GLUt4pp"/>
-          <groups:member groups:name="Taurine transport via ABC system (periplasm)" groups:idRef="R_TAURabcpp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C12:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPG120tipp"/>
-          <groups:member groups:name="L-ascorbate transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_ASCBptspp"/>
-          <groups:member groups:name="Citrate transport out via proton antiport (periplasm)" groups:idRef="R_CITt3pp"/>
-          <groups:member groups:name="L-alanyl-D-glutamate transport in via proton symport (periplasm)" groups:idRef="R_LALADGLUtpp"/>
-          <groups:member groups:name="D-methionine transport via ABC system (periplasm)" groups:idRef="R_METDabcpp"/>
-          <groups:member groups:name="L-valine transport via ABC system (periplasm)" groups:idRef="R_VALabcpp"/>
-          <groups:member groups:name="Maltotriose transport via ABC system (periplasm)" groups:idRef="R_MALTTRabcpp"/>
-          <groups:member groups:name="Arbutin transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_ARBTptspp"/>
-          <groups:member groups:name="L-aspartate uptake via facillitated diffusion" groups:idRef="R_ASPtpp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE181tipp"/>
-          <groups:member groups:name="L-aspartate transport in via proton symport (periplasm)" groups:idRef="R_ASPt2pp"/>
-          <groups:member groups:name="Enterochelin transport (secretion)" groups:idRef="R_FEENTERtpp"/>
-          <groups:member groups:name="D-glucose transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_GLCptspp"/>
-          <groups:member groups:name="D-fructuronate transport via proton symport, reversible (periplasm)" groups:idRef="R_FRUURt2rpp"/>
-          <groups:member groups:name="L-isoleucine transport out via proton antiport (periplasm)" groups:idRef="R_ILEt3pp"/>
-          <groups:member groups:name="Deoxycytidine transport in via proton symport (periplasm)" groups:idRef="R_DCYTt2pp"/>
-          <groups:member groups:name="Phosphatidylethanolamine transport via ABC system (n-C16:0, periplasm)" groups:idRef="R_PE160abcpp"/>
-          <groups:member groups:name="Succintate transport via proton symport (3 H) (periplasm)" groups:idRef="R_SUCCt2_3pp"/>
-          <groups:member groups:name="Thymidine transport in via proton symport (periplasm)" groups:idRef="R_THMDt2pp_copy2"/>
-          <groups:member groups:name="L-alanine export via facilited diffusion" groups:idRef="R_ALAtpp"/>
-          <groups:member groups:name="Ornithine transport via ABC system (periplasm)" groups:idRef="R_ORNabcpp"/>
-          <groups:member groups:name="Phosphatidate transport via ABC system (n-C18:0, periplasm)" groups:idRef="R_PA180abcpp"/>
-          <groups:member groups:name="L-arginine transport via ABC system (periplasm)" groups:idRef="R_ARGabcpp"/>
-          <groups:member groups:name="Cyanate transport via proton symport (periplasm)" groups:idRef="R_CYNTt2pp"/>
-          <groups:member groups:name="Acetaldehyde reversible transport (periplasm)" groups:idRef="R_ACALDtpp"/>
-          <groups:member groups:name="Phosphatidate transport via ABC system (n-C12:0, periplasm)" groups:idRef="R_PA120abcpp"/>
-          <groups:member groups:name="L-Prolinylglycine (Pro-Gly) transport via ABC system (periplasm)" groups:idRef="R_PROGLYabcpp"/>
-          <groups:member groups:name="Uracil export via facillitated diffusion (periplasm)" groups:idRef="R_URAtpp"/>
-          <groups:member groups:name="L-fucose transport via proton symport (periplasm)" groups:idRef="R_FUCtpp"/>
-          <groups:member groups:name="L-lysine transport out via proton antiport (cytoplasm to periplasm)" groups:idRef="R_LYSt3pp"/>
-          <groups:member groups:name="Orotate transport via proton symport (2 H) (periplasm)" groups:idRef="R_OROTt2_2pp"/>
+          <groups:member groups:name="D-xylose transport in via proton symport (periplasm)" groups:idRef="R_XYLt2pp"/>
+          <groups:member groups:name="5-Methylthio-D-ribose transport via proton symport (periplasm)" groups:idRef="R_5MTRtpp"/>
+          <groups:member groups:name="2-oxoglutarate reversible transport via symport (periplasm)" groups:idRef="R_AKGt2rpp"/>
+          <groups:member groups:name="Glycine transport via facillitated diffusion" groups:idRef="R_GLYtpp"/>
+          <groups:member groups:name="Coprogen transport via ABC system (periplasm)" groups:idRef="R_CPGNabcpp"/>
           <groups:member groups:name="Acetate reversible transport via proton symport (periplasm)" groups:idRef="R_ACt2rpp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE141tipp"/>
-          <groups:member groups:name="Na+/ 2,3-Dioxo-L-gulonate symport (periplasm)" groups:idRef="R_23DOGULNt4pp"/>
-          <groups:member groups:name="Maltopentaose transport via ABC system (periplasm)" groups:idRef="R_MALTPTabcpp"/>
-          <groups:member groups:name="Aspartate transport via proton symport (2 H) (periplasm)" groups:idRef="R_ASPt2_2pp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphatidate (n-C14:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPA141tipp"/>
-          <groups:member groups:name="Glycerol-3-phosphate : phosphate antiporter (periplasm)" groups:idRef="R_GLYC3Pt6pp"/>
-          <groups:member groups:name="Na+/Acetate symport (periplasm)" groups:idRef="R_ACt4pp"/>
-          <groups:member groups:name="Arsenite efflux via ATP hydrolysis (periplasm)" groups:idRef="R_ASO3t8pp"/>
-          <groups:member groups:name="L-idonate transport via proton symport, reversible (periplasm)" groups:idRef="R_IDONt2rpp"/>
-          <groups:member groups:name="D-galactarte transport via proton symport, reversible (periplasm)" groups:idRef="R_GALCTt2rpp"/>
+          <groups:member groups:name="Arginine/agmatine antiport (periplasm)" groups:idRef="R_ARGAGMt7pp"/>
           <groups:member groups:name="Inosine transport out via proton antiport (perisplasm)" groups:idRef="R_INSt3pp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphatidate (n-C18:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPA180tipp"/>
-          <groups:member groups:name="Xanthine reversible transport (periplasm)" groups:idRef="R_XANtpp"/>
-          <groups:member groups:name="D-Glucosamine 6-phosphate transport via phosphate antiport (periplasm)" groups:idRef="R_GAM6Pt6_2pp"/>
-          <groups:member groups:name="Isethionate transport via ABC system (periplasm)" groups:idRef="R_ISETACabcpp"/>
+          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C14:1, periplasm)" groups:idRef="R_PGP141abcpp"/>
+          <groups:member groups:name="D-ribose transport via ABC system (periplasm)" groups:idRef="R_RIBabcpp"/>
+          <groups:member groups:name="Propanal transport via channel (periplasm)" groups:idRef="R_PPALtpp"/>
+          <groups:member groups:name="Na+/ 2,3-Dioxo-L-gulonate symport (periplasm)" groups:idRef="R_23DOGULNt4pp"/>
+          <groups:member groups:name="Glycerol transport via channel (periplasm)" groups:idRef="R_GLYCtpp"/>
+          <groups:member groups:name="NMN permease (periplasm)" groups:idRef="R_NMNPtpp"/>
+          <groups:member groups:name="Sn-Glycerol 3-phosphate transport via ABC system (periplasm)" groups:idRef="R_GLYC3Pabcpp"/>
+          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C16:0, periplasm)" groups:idRef="R_PGP160abcpp"/>
+          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C14:0, periplasm)" groups:idRef="R_PGP140abcpp"/>
+          <groups:member groups:name="Phosphatidate transport via ABC system (n-C18:1, periplasm)" groups:idRef="R_PA181abcpp"/>
+          <groups:member groups:name="Glycine transport in via sodium symport (periplasm)" groups:idRef="R_GLYt4pp"/>
+          <groups:member groups:name="Phosphatidate transport via ABC system (n-C18:0, periplasm)" groups:idRef="R_PA180abcpp"/>
+          <groups:member groups:name="Deoxyguanosine transport in via proton symport (periplasm)" groups:idRef="R_DGSNt2pp"/>
           <groups:member groups:name="D-glucosamine transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_GAMptspp"/>
-          <groups:member groups:name="D-galacturonate transport via proton symport, reversible (periplasm)" groups:idRef="R_GALURt2rpp"/>
-          <groups:member groups:name="Mannose-6-phosphate transport via phosphate antiport (periplasm)" groups:idRef="R_MAN6Pt6_2pp"/>
-          <groups:member groups:name="Glycine transport via facillitated diffusion" groups:idRef="R_GLYtpp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphatidate (n-C18:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPA181tipp"/>
-          <groups:member groups:name="Reduced glutathione via ABC system (periplasm)" groups:idRef="R_GTHRDabcpp"/>
-          <groups:member groups:name="Spermidine transport via ABC system (periplasm)" groups:idRef="R_SPMDabcpp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphatidate (n-C14:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPA140tipp"/>
-          <groups:member groups:name="L-lysine transport in via proton symport (periplasm)" groups:idRef="R_LYSt2pp"/>
-          <groups:member groups:name="Cholate transport via proton antiport" groups:idRef="R_CHOLATEtpp"/>
+          <groups:member groups:name="L-valine reversible transport via proton symport (periplasm)" groups:idRef="R_VALt2rpp"/>
+          <groups:member groups:name="4-aminobutyrate transport in via proton symport (periplasm)" groups:idRef="R_ABUTt2pp"/>
+          <groups:member groups:name="Maltose transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_MALTptspp"/>
           <groups:member groups:name="D-lactate transport via proton symport (periplasm)" groups:idRef="R_D_LACt2pp"/>
-          <groups:member groups:name="L-threonine transport via ABC system (periplasm)" groups:idRef="R_THRabcpp"/>
-          <groups:member groups:name="Uridine transport in via proton symport (periplasm)" groups:idRef="R_URIt2pp_copy1"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C12:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE120tipp"/>
-          <groups:member groups:name="Dihydroxyacetone transport via facilitated diffusion (periplasm)" groups:idRef="R_DHAtpp"/>
-          <groups:member groups:name="Hypoxanthine transport (periplasm)" groups:idRef="R_HYXNtpp"/>
-          <groups:member groups:name="L-alanyl-L-glutamate transport in via proton symport (periplasm)" groups:idRef="R_LALALGLUtpp"/>
-          <groups:member groups:name="Lipoate transport via proton symport (periplasm)" groups:idRef="R_LIPOt2pp"/>
-          <groups:member groups:name="L-threonine efflux transport via proton antiport (periplasm)" groups:idRef="R_THRt2pp"/>
-          <groups:member groups:name="Manganese transport in via permease (no H+)" groups:idRef="R_MN2tipp"/>
-          <groups:member groups:name="L-Lyxose transport via proton symport (periplasm)" groups:idRef="R_LYXt2pp"/>
-          <groups:member groups:name="Uridine transport in via proton symport (periplasm)" groups:idRef="R_URIt2pp_copy2"/>
-          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C18:0, periplasm)" groups:idRef="R_PGP180abcpp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE140tipp"/>
-          <groups:member groups:name="Copper transport out via permease (no H+)" groups:idRef="R_CUt2pp"/>
-          <groups:member groups:name="L-cysteine export via facilitated transport" groups:idRef="R_CYStpp"/>
+          <groups:member groups:name="Arbutin transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_ARBTptspp"/>
+          <groups:member groups:name="Na+/Acetate symport (periplasm)" groups:idRef="R_ACt4pp"/>
+          <groups:member groups:name="D-glycerate transport via proton symport, reversible (periplasm)" groups:idRef="R_GLYCAt2rpp"/>
+          <groups:member groups:name="D-sorbitol transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_SBTptspp"/>
+          <groups:member groups:name="Thymidine transport in via proton symport (periplasm)" groups:idRef="R_THMDt2pp_copy2"/>
           <groups:member groups:name="L-alanine transport in via sodium symport (periplasm)" groups:idRef="R_ALAt4pp"/>
-          <groups:member groups:name="Fructose transport via PEP:Pyr PTS (f6p generating) (periplasm)" groups:idRef="R_FRUpts2pp"/>
-          <groups:member groups:name="Phosphatidate transport via ABC system (n-C18:1, periplasm)" groups:idRef="R_PA181abcpp"/>
-          <groups:member groups:name="Phosphatidylethanolamine transport via ABC system (n-C16:1, periplasm)" groups:idRef="R_PE161abcpp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphatidate (n-C16:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPA160tipp"/>
-          <groups:member groups:name="Deoxyadenosine transport in via proton symport (periplasm)" groups:idRef="R_DADNt2pp"/>
-          <groups:member groups:name="Glycine transport in via sodium symport (periplasm)" groups:idRef="R_GLYt4pp"/>
+          <groups:member groups:name="Lactose transport via proton aniport (periplasm)" groups:idRef="R_LCTSt3ipp"/>
+          <groups:member groups:name="Lysine/Cadaverine antiporter (periplasm)" groups:idRef="R_CADVtpp"/>
+          <groups:member groups:name="Cronobetaine outward transport (H+ antiport)" groups:idRef="R_CTBTt2rpp"/>
+          <groups:member groups:name="2-O-alpha-mannosyl-D-glycerate transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_MANGLYCptspp"/>
+          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C18:1, periplasm)" groups:idRef="R_PGP181abcpp"/>
+          <groups:member groups:name="Spermidine transport out via proton antiport (periplasm)" groups:idRef="R_SPMDt3pp"/>
+          <groups:member groups:name="Arginine/ornithine antiporter (periplasm)" groups:idRef="R_ARGORNt7pp"/>
+          <groups:member groups:name="Crotonobetaine transport via ABC system (periplasm)" groups:idRef="R_CTBTabcpp"/>
+          <groups:member groups:name="Enterochelin transport (secretion)" groups:idRef="R_FEENTERtpp"/>
+          <groups:member groups:name="Xanthine transport in via proton symport (periplasm)" groups:idRef="R_XANt2pp"/>
+          <groups:member groups:name="Hexanoate transport via proton symport, reversible (periplasm)" groups:idRef="R_HEXt2rpp"/>
+          <groups:member groups:name="H2s transport (periplasm)" groups:idRef="R_H2St1pp"/>
+          <groups:member groups:name="Indole transport via proton symport, irreversible (periplasm)" groups:idRef="R_INDOLEt2pp"/>
+          <groups:member groups:name="Mannitol transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_MNLptspp"/>
+          <groups:member groups:name="Guanosine transport out via proton antiport (periplasm)" groups:idRef="R_GSNt3pp"/>
+          <groups:member groups:name="D-xylonate reversible tranposrt (periplasm)" groups:idRef="R_DXYLONtpp"/>
+          <groups:member groups:name="D-galactarte transport via proton symport, reversible (periplasm)" groups:idRef="R_GALCTt2rpp"/>
+          <groups:member groups:name="Cytidine transport in via proton symport (periplasm)" groups:idRef="R_CYTDt2pp_copy2"/>
+          <groups:member groups:name="Pseudouridine transport via permease" groups:idRef="R_PSURItpp"/>
+          <groups:member groups:name="Phosphatidylglycerol transport via ABC system (n-C14:1, periplasm)" groups:idRef="R_PG141abcpp"/>
+          <groups:member groups:name="Cobinamide transport via ABC system (uptake, periplasm)" groups:idRef="R_CBIuabcpp"/>
+          <groups:member groups:name="Cytosine transport in via proton symport (periplasm)" groups:idRef="R_CSNt2pp"/>
+          <groups:member groups:name="L-malate transport out via proton antiport (periplasm)" groups:idRef="R_MALt3pp"/>
           <groups:member groups:name="L-isoleucine reversible transport via proton symport (periplasm)" groups:idRef="R_ILEt2rpp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphatidate (n-C16:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPA161tipp"/>
-          <groups:member groups:name="4-aminobutyrate transport in via proton symport (periplasm)" groups:idRef="R_ABUTt2pp"/>
-          <groups:member groups:name="Phosphatidylglycerol transport via ABC system (n-C16:1, periplasm)" groups:idRef="R_PG161abcpp"/>
-          <groups:member groups:name="Formate transport via proton symport (uptake only, periplasm)" groups:idRef="R_FORt2pp"/>
-          <groups:member groups:name="D-carnitine transport via ABC system (periplasm)" groups:idRef="R_CRNDabcpp"/>
-          <groups:member groups:name="L-cysteine uptake via ABC system (periplasm)" groups:idRef="R_CYSabcpp"/>
-          <groups:member groups:name="Thymine transport out via proton antiport (periplasm)" groups:idRef="R_THYMt3pp"/>
-          <groups:member groups:name="P-aminobenzoyl glutamate:H+ symporter" groups:idRef="R_4ABZGLUtr"/>
-          <groups:member groups:name="Chitobiose transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_CHTBSptspp"/>
-          <groups:member groups:name="L-isoleucine transport via ABC system (periplasm)" groups:idRef="R_ILEabcpp"/>
-          <groups:member groups:name="D-galactonate transport via proton symport (periplasm)" groups:idRef="R_GALCTNt2pp"/>
-          <groups:member groups:name="D-tartrate transport via proton symport (3 H) (periplasm)" groups:idRef="R_TARTt2_3pp"/>
-          <groups:member groups:name="L-histidine reversible transport via proton symport (periplasm)" groups:idRef="R_HISt2rpp"/>
-          <groups:member groups:name="D-carnitine outward transport (H+ antiport)" groups:idRef="R_CRNDt2rpp"/>
-          <groups:member groups:name="Transport of poly-?-1,6-N-acetyl-D-glucosamine (poly-?-1,6-N-acetyl-D-glucosamine synthase)" groups:idRef="R_PUACGAMtr"/>
-          <groups:member groups:name="L-histidine transport via ABC system (periplasm)" groups:idRef="R_HISabcpp"/>
-          <groups:member groups:name="L-tryptophan transport out (periplasm)" groups:idRef="R_TRPtipp"/>
-          <groups:member groups:name="L-serine reversible transport via proton symport (periplasm)" groups:idRef="R_SERt2rpp"/>
-          <groups:member groups:name="L-alanine transport via ABC system (periplasm)" groups:idRef="R_ALAabcpp"/>
+          <groups:member groups:name="Guanosine transport in via proton symport (periplasm)" groups:idRef="R_GSNt2pp"/>
+          <groups:member groups:name="Thiamine transport via ABC system (periplasm)" groups:idRef="R_THMabcpp"/>
+          <groups:member groups:name="L-tryptophan reversible transport via proton symport (periplasm)" groups:idRef="R_TRPt2rpp"/>
+          <groups:member groups:name="Tartrate/succinate antiporter (periplasm)" groups:idRef="R_TARTRt7pp"/>
           <groups:member groups:name="Phosphatidylglycerol transport via ABC system (n-C18:1, periplasm)" groups:idRef="R_PG181abcpp"/>
-          <groups:member groups:name="Na+/Propionate symporter (periplasm)" groups:idRef="R_PPAt4pp"/>
-          <groups:member groups:name="L-methionine R-oxide transport via ABC system (periplasm)" groups:idRef="R_METSOX2abcpp"/>
-          <groups:member groups:name="KDO(2)-lipid IV A transport via ABC system (periplasm)" groups:idRef="R_K2L4Aabcpp"/>
-          <groups:member groups:name="Succinate:fumarate antiporter (periplasm)" groups:idRef="R_SUCFUMtpp"/>
-          <groups:member groups:name="Melibiose transport in via antiport (periplasm)" groups:idRef="R_MELIBt3ipp"/>
-          <groups:member groups:name="L-threonine  via sodium symport (periplasm)" groups:idRef="R_THRt4pp"/>
-          <groups:member groups:name="L-xylulose transport in via proton symport (periplasm)" groups:idRef="R_XYLUt2pp"/>
-          <groups:member groups:name="Sn-Glycerol 2-phosphate transport via ABC system (periplasm)" groups:idRef="R_GLYC2Pabcpp"/>
-          <groups:member groups:name="Putrescine transport in via proton symport" groups:idRef="R_PTRCt2pp"/>
-          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C12:0, periplasm)" groups:idRef="R_PGP120abcpp"/>
-          <groups:member groups:name="L-proline transport via ABC system (periplasm)" groups:idRef="R_PROabcpp"/>
-          <groups:member groups:name="Phosphatidylethanolamine transport via ABC system (n-C18:1, periplasm)" groups:idRef="R_PE181abcpp"/>
-          <groups:member groups:name="Methane Transport(periplasm)" groups:idRef="R_CH4t2pp"/>
-          <groups:member groups:name="Glycine betaine transport via proton antiport (periplasm)" groups:idRef="R_GLYBt3pp"/>
-          <groups:member groups:name="Succinate:aspartate antiporter (periplasm)" groups:idRef="R_SUCASPtpp"/>
-          <groups:member groups:name="L-serine export via facilitated transport" groups:idRef="R_SERtpp"/>
-          <groups:member groups:name="L-phenylalanine reversible transport via proton symport (periplasm)" groups:idRef="R_PHEt2rpp"/>
-          <groups:member groups:name="L-Cysteinylglycine (Cys-Gly) transport via ABC system (periplasm)" groups:idRef="R_CGLYabcpp"/>
-          <groups:member groups:name="FAD transporter, periplasm" groups:idRef="R_FADt"/>
-          <groups:member groups:name="F- efflux transport" groups:idRef="R_Ftpp"/>
-          <groups:member groups:name="N-acetylneuraminate proton symport (periplasm)" groups:idRef="R_ACNAMt2pp"/>
-          <groups:member groups:name="4-hydroxybenzoate transport out via antiporter" groups:idRef="R_4HBZt3pp"/>
-          <groups:member groups:name="Inosine transport in via proton symport (periplasm)" groups:idRef="R_INSt2pp"/>
-          <groups:member groups:name="D-Malate transport via proton symport (2 H) (periplasm)" groups:idRef="R_MALDt2_2pp"/>
-          <groups:member groups:name="Hexanoate transport via proton symport, reversible (periplasm)" groups:idRef="R_HEXt2rpp"/>
+          <groups:member groups:name="Hydrogen transport diffusion (periplasm)" groups:idRef="R_H2tpp"/>
+          <groups:member groups:name="Citrate transport out via proton antiport (periplasm)" groups:idRef="R_CITt3pp"/>
+          <groups:member groups:name="L-carnitine/D-carnitine antiporter (periplasm)" groups:idRef="R_CRNt8pp"/>
           <groups:member groups:name="L-methionine transport via ABC system (periplasm)" groups:idRef="R_METabcpp"/>
-          <groups:member groups:name="N-acetyl-D-mannosamine transport via PTS  (periplasm)" groups:idRef="R_ACMANAptspp"/>
-          <groups:member groups:name="L-glutamate transport via proton symport, reversible (periplasm)" groups:idRef="R_GLUt2rpp"/>
-          <groups:member groups:name="Succinate transport via diffusion in (periplasm)" groups:idRef="R_SUCCt1pp"/>
-          <groups:member groups:name="Autoinducer-2 ABC transporter" groups:idRef="R_AI2abcpp"/>
-          <groups:member groups:name="Psicoselysine transport via proton symport (periplasm)" groups:idRef="R_PSCLYSt2pp"/>
-          <groups:member groups:name="Spermidine transport out via proton antiport (periplasm)" groups:idRef="R_SPMDt3pp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPG141tipp"/>
-          <groups:member groups:name="L-methionine tranport out via proton antiport (periplasm)" groups:idRef="R_METt3pp"/>
-          <groups:member groups:name="Fructose-6-phosphate transport via phosphate antiport (periplasm)" groups:idRef="R_F6Pt6_2pp"/>
-          <groups:member groups:name="L-tryptophan reversible transport via proton symport (periplasm)" groups:idRef="R_TRPt2rpp"/>
-          <groups:member groups:name="Guanosine transport in via proton symport (periplasm)" groups:idRef="R_GSNt2pp"/>
-          <groups:member groups:name="Succinate:D-tartrate antiporter (periplasm)" groups:idRef="R_SUCTARTtpp"/>
+          <groups:member groups:name="D-xylose transport via ABC system (periplasm)" groups:idRef="R_XYLabcpp"/>
+          <groups:member groups:name="D-alanyl-D-alanine (DalaDala) transport via ABC system (periplasm)" groups:idRef="R_ALAALAabcpp"/>
+          <groups:member groups:name="L-carnitine outward transport (H+ antiport)" groups:idRef="R_CRNt2rpp"/>
+          <groups:member groups:name="L-tyrosine transport out (periplasm)" groups:idRef="R_TYRtipp"/>
+          <groups:member groups:name="Carnitine/butyrobetaine antiporter (periplasm)" groups:idRef="R_CRNt7pp"/>
+          <groups:member groups:name="FMN transporter, periplasm" groups:idRef="R_FMNt"/>
+          <groups:member groups:name="Pantothenate sodium symporter (periplasm)" groups:idRef="R_PNTOt4pp"/>
+          <groups:member groups:name="Dihydroxyacetone transport via facilitated diffusion (periplasm)" groups:idRef="R_DHAtpp"/>
+          <groups:member groups:name="Citrate transport via succinate antiport (periplasm)" groups:idRef="R_CITt7pp"/>
+          <groups:member groups:name="Arsenite efflux via ATP hydrolysis (periplasm)" groups:idRef="R_ASO3t8pp"/>
+          <groups:member groups:name="Succintate transport via proton symport (3 H) (periplasm)" groups:idRef="R_SUCCt2_3pp"/>
           <groups:member groups:name="L-cysteine export via ABC system (cytoplasm to periplasm)" groups:idRef="R_CYSabc2pp"/>
-          <groups:member groups:name="Deoxyuridine transport in via proton symport (periplasm)" groups:idRef="R_DURIt2pp"/>
-          <groups:member groups:name="Guanosine transport out via proton antiport (periplasm)" groups:idRef="R_GSNt3pp"/>
-          <groups:member groups:name="Phosphatidylethanolamine transport via ABC system (n-C12:0, periplasm)" groups:idRef="R_PE120abcpp"/>
-          <groups:member groups:name="L-lactate reversible transport via proton symport (periplasm)" groups:idRef="R_L_LACt2rpp"/>
-          <groups:member groups:name="Succinate transport via proton symport (2 H) (periplasm)" groups:idRef="R_SUCCt2_2pp"/>
-          <groups:member groups:name="Glucose-6-phosphate transport via phosphate antiport (periplasm)" groups:idRef="R_G6Pt6_2pp"/>
-          <groups:member groups:name="Sucrose transport via PEP:Pyr  (periplasm)" groups:idRef="R_SUCptspp"/>
-          <groups:member groups:name="Putrescine/ornithine antiporter (periplasm)" groups:idRef="R_PTRCORNt7pp"/>
-          <groups:member groups:name="D-xylose transport in via proton symport (periplasm)" groups:idRef="R_XYLt2pp"/>
+          <groups:member groups:name="2-Deoxy-D-glucose transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_2DGLCptspp"/>
+          <groups:member groups:name="L-isoleucine transport out via proton antiport (periplasm)" groups:idRef="R_ILEt3pp"/>
+          <groups:member groups:name="3-phenylpropionate transport via proton symport, reversible (periplasm)" groups:idRef="R_PPPNt2rpp"/>
           <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPG160tipp"/>
-          <groups:member groups:name="Lactose transport via proton aniport (periplasm)" groups:idRef="R_LCTSt3ipp"/>
-          <groups:member groups:name="NMN permease (periplasm)" groups:idRef="R_NMNPtpp"/>
-          <groups:member groups:name="Ethanesulfonate transport via ABC system (periplasm)" groups:idRef="R_ETHSO3abcpp"/>
-          <groups:member groups:name="L-phenylalanine transport out (periplasm)" groups:idRef="R_PHEtipp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphatidate (n-C12:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPA120tipp"/>
-          <groups:member groups:name="L-asparate transport via proton symport (3 H) (periplasm)" groups:idRef="R_ASPt2_3pp"/>
-          <groups:member groups:name="D-glucuronate transport via proton symport, reversible (periplasm)" groups:idRef="R_GLCURt2rpp"/>
-          <groups:member groups:name="Sn-glycerol-3-phosphoglycerol transport via ABC system (periplasm)" groups:idRef="R_G3PGabcpp"/>
-          <groups:member groups:name="3-(3-hydroxyphenyl)propionate transport via proton symport, reversible (periplasm)" groups:idRef="R_HPPPNt2rpp"/>
-          <groups:member groups:name="Coprogen transport via ABC system (periplasm)" groups:idRef="R_CPGNabcpp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPG180tipp"/>
-          <groups:member groups:name="CO2 transporter via diffusion (periplasm)" groups:idRef="R_CO2tpp"/>
-          <groups:member groups:name="Sn-glycerol-3-phosphoserine transport via ABC system (periplasm)" groups:idRef="R_G3PSabcpp"/>
-          <groups:member groups:name="Ethanolamine transport in via proton symport" groups:idRef="R_ETHAt2pp"/>
-          <groups:member groups:name="D-mannose transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_MANptspp"/>
-          <groups:member groups:name="Phosphatidate transport via ABC system (n-C14:1, periplasm)" groups:idRef="R_PA141abcpp"/>
-          <groups:member groups:name="Arginine/ornithine antiporter (periplasm)" groups:idRef="R_ARGORNt7pp"/>
-          <groups:member groups:name="Adenosylcobalamin transport via ABC system (periplasm)" groups:idRef="R_ADOCBLabcpp"/>
-          <groups:member groups:name="Beta-alanine transport in via proton symport (periplasm)" groups:idRef="R_BALAt2pp"/>
-          <groups:member groups:name="Glycerol transport via channel (periplasm)" groups:idRef="R_GLYCtpp"/>
-          <groups:member groups:name="D-sorbitol transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_SBTptspp"/>
-          <groups:member groups:name="L-leucine transport via ABC system (periplasm)" groups:idRef="R_LEUabcpp"/>
-          <groups:member groups:name="L-alanine transport in via proton symport (periplasm)" groups:idRef="R_ALAt2pp"/>
-          <groups:member groups:name="Phosphatidate transport via ABC system (n-C16:1, periplasm)" groups:idRef="R_PA161abcpp"/>
-          <groups:member groups:name="Acetoacetate transport via proton symport  (periplasm)" groups:idRef="R_ACACt2pp"/>
-          <groups:member groups:name="Pseudouridine transport via permease" groups:idRef="R_PSURItpp"/>
-          <groups:member groups:name="H2O transport via diffusion (periplasm)" groups:idRef="R_H2Otpp"/>
-          <groups:member groups:name="Na+/myo-inositol symporter (periplasm)" groups:idRef="R_INOSTt4pp"/>
-          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C18:1, periplasm)" groups:idRef="R_PGP181abcpp"/>
-          <groups:member groups:name="Phenylacetaldehyde reversible transport via proton symport (periplasm)" groups:idRef="R_PACALDt2rpp"/>
-          <groups:member groups:name="Glycolate transport via sodium symport (periplasm)" groups:idRef="R_GLYCLTt4pp"/>
-          <groups:member groups:name="Pyridoxine import" groups:idRef="R_PYDXNtpp"/>
-          <groups:member groups:name="Phosphatidylethanolamine transport via ABC system (n-C14:0, periplasm)" groups:idRef="R_PE140abcpp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPG161tipp"/>
-          <groups:member groups:name="L-methionine S-oxide transport via ABC system (periplasm)" groups:idRef="R_METSOX1abcpp"/>
-          <groups:member groups:name="D-xylose transport via ABC system (periplasm)" groups:idRef="R_XYLabcpp"/>
-          <groups:member groups:name="L-homoserineserine efflux via proton symport" groups:idRef="R_HOMt2pp"/>
-          <groups:member groups:name="2-dehydro-3-deoxy-D-gluconate transport via proton symport, reversible (periplasm)" groups:idRef="R_DDGLCNt2rpp"/>
-          <groups:member groups:name="Glyceraldehyde facilitated diffusion (periplasm)" groups:idRef="R_GLYALDtpp"/>
-          <groups:member groups:name="NMN transport via NMN glycohydrolase (periplasm)" groups:idRef="R_NMNt7pp"/>
+          <groups:member groups:name="Aerobactin transport via ABC system (periplasm)" groups:idRef="R_ARBTNabcpp"/>
+          <groups:member groups:name="Formaldehyde transport via diffusion (periplasm)" groups:idRef="R_FALDtpp"/>
+          <groups:member groups:name="Spermidine transport via ABC system (periplasm)" groups:idRef="R_SPMDabcpp"/>
+          <groups:member groups:name="Uridine transport in via proton symport (periplasm)" groups:idRef="R_URIt2pp_copy2"/>
+          <groups:member groups:name="Pyridoxamine import" groups:idRef="R_PYDAMtpp"/>
+          <groups:member groups:name="Cellobiose transport via PEPPyr PTS" groups:idRef="R_CELBpts"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPG141tipp"/>
+          <groups:member groups:name="Quorum signal AI-2 exporter" groups:idRef="R_AI2tpp"/>
+          <groups:member groups:name="Maltohexaose transport via ABC system (periplasm)" groups:idRef="R_MALTHXabcpp"/>
+          <groups:member groups:name="Manganese transport in via permease (no H+)" groups:idRef="R_MN2tipp"/>
+          <groups:member groups:name="L-alanyl-L-glutamate transport in via proton symport (periplasm)" groups:idRef="R_LALALGLUtpp"/>
+          <groups:member groups:name="F- efflux transport" groups:idRef="R_Ftpp"/>
+          <groups:member groups:name="Succinate:malate antiporter (periplasm)" groups:idRef="R_SUCMALtpp"/>
+          <groups:member groups:name="Lactose transport via proton symport (periplasm)" groups:idRef="R_LCTStpp"/>
+          <groups:member groups:name="Nicotinic acid uptake (periplasm)" groups:idRef="R_NACtpp"/>
           <groups:member groups:name="D-serine transport in via proton symport (periplasm)" groups:idRef="R_DSERt2pp"/>
-          <groups:member groups:name="D-gluconate transport via proton symport, reversible (periplasm)" groups:idRef="R_GLCNt2rpp"/>
-          <groups:member groups:name="Sn-glycerol-3-phosphoethanolamine transport via ABC system (periplasm)" groups:idRef="R_G3PEabcpp"/>
-          <groups:member groups:name="D-glucarate transport via proton symport, reversible (periplasm)" groups:idRef="R_GLCRt2rpp"/>
-          <groups:member groups:name="Fumarate transport via diffusion in (periplasm)" groups:idRef="R_FUMt1pp"/>
-          <groups:member groups:name="Shikimate transport in via proton symport (periplasm)" groups:idRef="R_SKMt2pp"/>
-          <groups:member groups:name="Phosphatidylethanolamine transport via ABC system (n-C18:0, periplasm)" groups:idRef="R_PE180abcpp"/>
-          <groups:member groups:name="2-oxoglutarate reversible transport via symport (periplasm)" groups:idRef="R_AKGt2rpp"/>
-          <groups:member groups:name="L-malate transport out via proton antiport (periplasm)" groups:idRef="R_MALt3pp"/>
-          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C14:0, periplasm)" groups:idRef="R_PGP140abcpp"/>
-          <groups:member groups:name="D-cysteine uptake via ABC system (periplasm)" groups:idRef="R_CYSDabcpp"/>
-          <groups:member groups:name="L-leucine transport out via proton antiport (periplasm)" groups:idRef="R_LEUt3pp"/>
-          <groups:member groups:name="Cobinamide transport via ABC system (uptake, periplasm)" groups:idRef="R_CBIuabcpp"/>
-          <groups:member groups:name="Quinate transport (periplasm)" groups:idRef="R_QUIN2tpp"/>
+          <groups:member groups:name="Thymidine transport in via proton symport (periplasm)" groups:idRef="R_THMDt2pp_copy1"/>
+          <groups:member groups:name="D-galactose transport via ABC system (periplasm)" groups:idRef="R_GALabcpp"/>
+          <groups:member groups:name="L-glutamate transport via proton symport, reversible (periplasm)" groups:idRef="R_GLUt2rpp"/>
           <groups:member groups:name="Thiol:disulfide reductase (DsbG)" groups:idRef="R_TDSR2"/>
-          <groups:member groups:name="Uric acid transporter" groups:idRef="R_URATEtpp"/>
-          <groups:member groups:name="Malate transport via proton symport (2 H) (periplasm)" groups:idRef="R_MALt2_2pp"/>
-          <groups:member groups:name="Thiamine transport via ABC system (periplasm)" groups:idRef="R_THMabcpp"/>
-          <groups:member groups:name="Choline transport via proton symport (periplasm)" groups:idRef="R_CHLt2pp"/>
-          <groups:member groups:name="Deoxyguanosine transport in via proton symport (periplasm)" groups:idRef="R_DGSNt2pp"/>
+          <groups:member groups:name="Glycine betaine transport via ABC system (periplasm)" groups:idRef="R_GLYBabcpp"/>
+          <groups:member groups:name="1-O-methyl-Beta-D-glucuronate transport via proton symport (periplasm)" groups:idRef="R_METGLCURt2pp"/>
           <groups:member groups:name="Dimethyl sulfoxide transport via diffusion (periplasm)" groups:idRef="R_DMSOtpp"/>
-          <groups:member groups:name="Aerobactin transport via ABC system (periplasm)" groups:idRef="R_ARBTNabcpp"/>
-          <groups:member groups:name="Choline transport via ABC system (periplasm)" groups:idRef="R_CHLabcpp"/>
-          <groups:member groups:name="Malate transport via proton symport (3 H) (periplasm)" groups:idRef="R_MALt2_3pp"/>
-          <groups:member groups:name="Sulfoquinovose transporter" groups:idRef="R_SQtr"/>
-          <groups:member groups:name="Tartrate/succinate antiporter (periplasm)" groups:idRef="R_TARTRt7pp"/>
-          <groups:member groups:name="D-ribose transport via ABC system (periplasm)" groups:idRef="R_RIBabcpp"/>
-          <groups:member groups:name="L-leucine reversible transport via proton symport (periplasm)" groups:idRef="R_LEUt2rpp"/>
-          <groups:member groups:name="Pantothenate sodium symporter (periplasm)" groups:idRef="R_PNTOt4pp"/>
-          <groups:member groups:name="Phosphatidylethanolamine transport via ABC system (n-C14:1, periplasm)" groups:idRef="R_PE141abcpp"/>
-          <groups:member groups:name="L-asparagine reversible transport via proton symport (periplasm)" groups:idRef="R_ASNt2rpp"/>
-          <groups:member groups:name="Putrescine transport via ABC system (periplasm)" groups:idRef="R_PTRCabcpp"/>
-          <groups:member groups:name="5-Dehydro-D-gluconate transport via proton symport, reversible (periplasm)" groups:idRef="R_5DGLCNt2rpp"/>
-          <groups:member groups:name="Citrate transport via succinate antiport (periplasm)" groups:idRef="R_CITt7pp"/>
-          <groups:member groups:name="2,3-dihydroxypropane 1-sulfonate transporter" groups:idRef="R_DHPStr"/>
-          <groups:member groups:name="Protoheme transport via ABC system (periplasm)" groups:idRef="R_PHEMEabcpp"/>
-          <groups:member groups:name="2-Deoxy-D-glucose transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_2DGLCptspp"/>
-          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPG140tipp"/>
-          <groups:member groups:name="Adenosine transport in via proton symport (periplasm)" groups:idRef="R_ADNt2pp_copy2"/>
-          <groups:member groups:name="L-galactonate transport via proton symport (periplasm)" groups:idRef="R_GALCTNLt2pp"/>
+          <groups:member groups:name="Fructoselysine transport via proton symport (periplasm)" groups:idRef="R_FRULYSt2pp"/>
+          <groups:member groups:name="Phosphatidate transport via ABC system (n-C14:0, periplasm)" groups:idRef="R_PA140abcpp"/>
+          <groups:member groups:name="Isethionate transport via ABC system (periplasm)" groups:idRef="R_ISETACabcpp"/>
+          <groups:member groups:name="Glycolate transport via sodium symport (periplasm)" groups:idRef="R_GLYCLTt4pp"/>
           <groups:member groups:name="O-Acetyl-L-serine export via facilitated transport" groups:idRef="R_ACSERtpp"/>
-          <groups:member groups:name="Ethanol reversible transport via diffusion (periplasm)" groups:idRef="R_ETOHtrpp"/>
-          <groups:member groups:name="Sn-glycerol-3-phosphoethanolamine transport via ABC system (periplasm)" groups:idRef="R_G3PIabcpp"/>
-          <groups:member groups:name="Sn-Glycerol 3-phosphate transport via ABC system (periplasm)" groups:idRef="R_GLYC3Pabcpp"/>
-          <groups:member groups:name="Phosphatidylglycerol transport via ABC system (n-C14:1, periplasm)" groups:idRef="R_PG141abcpp"/>
-          <groups:member groups:name="Choline transport via proton antiport (periplasm)" groups:idRef="R_CHLt3pp"/>
-          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C14:1, periplasm)" groups:idRef="R_PGP141abcpp"/>
-          <groups:member groups:name="Adenosine transport in via proton symport (periplasm)" groups:idRef="R_ADNt2pp_copy1"/>
+          <groups:member groups:name="Sn-glycerol-3-phosphoethanolamine transport via ABC system (periplasm)" groups:idRef="R_G3PEabcpp"/>
           <groups:member groups:name="Urea transport via facilitate diffusion (periplasm)" groups:idRef="R_UREAtpp"/>
-          <groups:member groups:name="Phosphatidylglycerol transport via ABC system (n-C14:0, periplasm)" groups:idRef="R_PG140abcpp"/>
-          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C16:0, periplasm)" groups:idRef="R_PGP160abcpp"/>
-          <groups:member groups:name="Propanal transport via channel (periplasm)" groups:idRef="R_PPALtpp"/>
-          <groups:member groups:name="D-alanine transport in via proton symport (periplasm)" groups:idRef="R_DALAt2pp"/>
-          <groups:member groups:name="D-glycerate transport via proton symport, reversible (periplasm)" groups:idRef="R_GLYCAt2rpp"/>
-          <groups:member groups:name="Maltohexaose transport via ABC system (periplasm)" groups:idRef="R_MALTHXabcpp"/>
+          <groups:member groups:name="L-alanine transport via ABC system (periplasm)" groups:idRef="R_ALAabcpp"/>
+          <groups:member groups:name="Manganese (Mn+2) transport in via proton symport (periplasm)" groups:idRef="R_MNt2pp"/>
+          <groups:member groups:name="Shikimate transport in via proton symport (periplasm)" groups:idRef="R_SKMt2pp"/>
+          <groups:member groups:name="Sn-glycerol-3-phosphocholine transport via ABC system (periplasm)" groups:idRef="R_G3PCabcpp"/>
+          <groups:member groups:name="Guanine transport in via proton symport (periplasm)" groups:idRef="R_GUAt2pp"/>
+          <groups:member groups:name="L-galactonate transport via proton symport (periplasm)" groups:idRef="R_GALCTNLt2pp"/>
+          <groups:member groups:name="D-fructuronate transport via proton symport, reversible (periplasm)" groups:idRef="R_FRUURt2rpp"/>
+          <groups:member groups:name="L-aspartate transport via ABC system (periplasm)" groups:idRef="R_ASPabcpp"/>
           <groups:member groups:name="L-rhamnose transport via proton symport (periplasm)" groups:idRef="R_RMNtpp"/>
-          <groups:member groups:name="L-tyrosine transport out (periplasm)" groups:idRef="R_TYRtipp"/>
-          <groups:member groups:name="Xanthine transport in via proton symport (periplasm)" groups:idRef="R_XANt2pp"/>
-          <groups:member groups:name="L-glutamine transport via ABC system (periplasm)" groups:idRef="R_GLNabcpp"/>
-          <groups:member groups:name="Succinate:malate antiporter (periplasm)" groups:idRef="R_SUCMALtpp"/>
+          <groups:member groups:name="Fumarate transport via diffusion in (periplasm)" groups:idRef="R_FUMt1pp"/>
+          <groups:member groups:name="Cob(1)alamin transport via ABC system (periplasm)" groups:idRef="R_CBL1abcpp"/>
+          <groups:member groups:name="3-(3-hydroxyphenyl)propionate transport via proton symport, reversible (periplasm)" groups:idRef="R_HPPPNt2rpp"/>
+          <groups:member groups:name="D-allose transport via ABC system (periplasm)" groups:idRef="R_ALLabcpp"/>
+          <groups:member groups:name="Cytidine transport in via proton symport (periplasm)" groups:idRef="R_CYTDt2pp_copy1"/>
+          <groups:member groups:name="Fumarate transport via proton symport (3 H) (periplasm)" groups:idRef="R_FUMt2_3pp"/>
+          <groups:member groups:name="Maltose transport via ABC system (periplasm)" groups:idRef="R_MALTabcpp"/>
+          <groups:member groups:name="L-histidine reversible transport via proton symport (periplasm)" groups:idRef="R_HISt2rpp"/>
+          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C12:0, periplasm)" groups:idRef="R_PGP120abcpp"/>
+          <groups:member groups:name="Thymine transport out via proton antiport (periplasm)" groups:idRef="R_THYMt3pp"/>
+          <groups:member groups:name="Fructose-6-phosphate transport via phosphate antiport (periplasm)" groups:idRef="R_F6Pt6_2pp"/>
+          <groups:member groups:name="D-carnitine transport via ABC system (periplasm)" groups:idRef="R_CRNDabcpp"/>
+          <groups:member groups:name="L-proline transport via ABC system (periplasm)" groups:idRef="R_PROabcpp"/>
+          <groups:member groups:name="Acetaldehyde reversible transport (periplasm)" groups:idRef="R_ACALDtpp"/>
+          <groups:member groups:name="L-serine via sodium symport (periplasm)" groups:idRef="R_SERt4pp"/>
+          <groups:member groups:name="Sulfoacetate transport via ABC system (periplasm)" groups:idRef="R_SULFACabcpp"/>
+          <groups:member groups:name="Na+/Proline-L symporter (periplasm)" groups:idRef="R_PROt4pp"/>
+          <groups:member groups:name="Sn-Glycerol 2-phosphate transport via ABC system (periplasm)" groups:idRef="R_GLYC2Pabcpp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphatidate (n-C14:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPA140tipp"/>
+          <groups:member groups:name="Adenosylcobalamin transport via ABC system (periplasm)" groups:idRef="R_ADOCBLabcpp"/>
+          <groups:member groups:name="Quinate transport (periplasm)" groups:idRef="R_QUIN2tpp"/>
+          <groups:member groups:name="Mannose-6-phosphate transport via phosphate antiport (periplasm)" groups:idRef="R_MAN6Pt6_2pp"/>
           <groups:member groups:name="Methanol reversible transport via diffusion (periplasm)" groups:idRef="R_MEOHtrpp"/>
-          <groups:member groups:name="2-O-alpha-mannosyl-D-glycerate transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_MANGLYCptspp"/>
-          <groups:member groups:name="Glycine betaine transport via ABC system (periplasm)" groups:idRef="R_GLYBabcpp"/>
-          <groups:member groups:name="D-alanyl-D-alanine (DalaDala) transport via ABC system (periplasm)" groups:idRef="R_ALAALAabcpp"/>
-          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C12:0)" groups:idRef="R_12DGR120tipp"/>
-          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:0)" groups:idRef="R_12DGR140tipp"/>
-          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C18:0)" groups:idRef="R_12DGR180tipp"/>
-          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C18:1)" groups:idRef="R_12DGR181tipp"/>
-          <groups:member groups:name="Mannitol transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_MNLptspp"/>
-          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:1)" groups:idRef="R_12DGR141tipp"/>
-          <groups:member groups:name="D-xylonate reversible tranposrt (periplasm)" groups:idRef="R_DXYLONtpp"/>
-          <groups:member groups:name="Melibiose transport in via symport (periplasm)" groups:idRef="R_MELIBt2pp"/>
-          <groups:member groups:name="Thymidine transport in via proton symport (periplasm)" groups:idRef="R_THMDt2pp_copy1"/>
+          <groups:member groups:name="Adenosine transport in via proton symport (periplasm)" groups:idRef="R_ADNt2pp_copy2"/>
+          <groups:member groups:name="Sulfoquinovose transporter" groups:idRef="R_SQtr"/>
+          <groups:member groups:name="D-fructose transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_FRUptspp"/>
+          <groups:member groups:name="Phosphatidate transport via ABC system (n-C16:1, periplasm)" groups:idRef="R_PA161abcpp"/>
           <groups:member groups:name="Methylpshophonic acid abc transporter" groups:idRef="R_MEPNabcpp"/>
-          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C16:0)" groups:idRef="R_12DGR160tipp"/>
-          <groups:member groups:name="M-diaminopimelic acid ABC transport (periplasm)" groups:idRef="R_DAPabcpp"/>
-          <groups:member groups:name="L-lysine transport via ABC system (periplasm)" groups:idRef="R_LYSabcpp"/>
-          <groups:member groups:name="Cronobetaine outward transport (H+ antiport)" groups:idRef="R_CTBTt2rpp"/>
-          <groups:member groups:name="D-galactose transport via ABC system (periplasm)" groups:idRef="R_GALabcpp"/>
-          <groups:member groups:name="Quorum signal AI-2 exporter" groups:idRef="R_AI2tpp"/>
-          <groups:member groups:name="L-valine transport out via proton antiport (periplasm)" groups:idRef="R_VALt3pp"/>
-          <groups:member groups:name="S-methylmethionine permease (periplasm)" groups:idRef="R_MMETt2pp"/>
-          <groups:member groups:name="Uracil transport in via proton symport (periplasm)" groups:idRef="R_URAt2pp"/>
-          <groups:member groups:name="Biotin transport via proton symport (periplasm)" groups:idRef="R_BTNt2ipp"/>
-          <groups:member groups:name="N-Acetyl-D-glucosamine transport via PEP:Pyr PTS  (periplasm)" groups:idRef="R_ACGAptspp"/>
-          <groups:member groups:name="FMN transporter, periplasm" groups:idRef="R_FMNt"/>
-          <groups:member groups:name="H2s transport (periplasm)" groups:idRef="R_H2St1pp"/>
-          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C16:1)" groups:idRef="R_12DGR161tipp"/>
-          <groups:member groups:name="D-glucose transport in via proton symport (periplasm)" groups:idRef="R_GLCt2pp"/>
-          <groups:member groups:name="Butanesulfonate transport via ABC system (periplasm)" groups:idRef="R_BUTSO3abcpp"/>
-          <groups:member groups:name="Phosphatidylglycerol transport via ABC system (n-C16:0, periplasm)" groups:idRef="R_PG160abcpp"/>
-          <groups:member groups:name="3-phenylpropionate transport via proton symport, reversible (periplasm)" groups:idRef="R_PPPNt2rpp"/>
-          <groups:member groups:name="Allantoin transport in via proton symport (periplasm)" groups:idRef="R_ALLTNt2rpp"/>
+          <groups:member groups:name="Fumarate transport via proton symport (2 H) (periplasm)" groups:idRef="R_FUMt2_2pp"/>
+          <groups:member groups:name="Glycine betaine transport via proton antiport (periplasm)" groups:idRef="R_GLYBt3pp"/>
+          <groups:member groups:name="Sn-glycerol-3-phosphoethanolamine transport via ABC system (periplasm)" groups:idRef="R_G3PIabcpp"/>
+          <groups:member groups:name="4-hydroxybenzoate transport out via antiporter" groups:idRef="R_4HBZt3pp"/>
+          <groups:member groups:name="Inosine transport in via proton symport (periplasm)" groups:idRef="R_INSt2pp"/>
+          <groups:member groups:name="Acetoacetate transport via proton symport  (periplasm)" groups:idRef="R_ACACt2pp"/>
+          <groups:member groups:name="2,3-diaminopropionate transport in via proton symport" groups:idRef="R_23DAPPAt2pp"/>
+          <groups:member groups:name="D-gluconate transport via proton symport, reversible (periplasm)" groups:idRef="R_GLCNt2rpp"/>
           <groups:member groups:name="Glycine betaine transport via proton symport (periplasm)" groups:idRef="R_GLYBt2pp"/>
-          <groups:member groups:name="N-acetylmuramate transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_ACMUMptspp"/>
-          <groups:member groups:name="Cob(1)alamin transport via ABC system (periplasm)" groups:idRef="R_CBL1abcpp"/>
-          <groups:member groups:name="Indole transport via proton symport, irreversible (periplasm)" groups:idRef="R_INDOLEt2pp"/>
-          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C16:1, periplasm)" groups:idRef="R_PGP161abcpp"/>
+          <groups:member groups:name="Uric acid transporter" groups:idRef="R_URATEtpp"/>
+          <groups:member groups:name="L-alanine transport in via proton symport (periplasm)" groups:idRef="R_ALAt2pp"/>
+          <groups:member groups:name="KDO(2)-lipid IV A transport via ABC system (periplasm)" groups:idRef="R_K2L4Aabcpp"/>
+          <groups:member groups:name="L-Lyxose transport via proton symport (periplasm)" groups:idRef="R_LYXt2pp"/>
+          <groups:member groups:name="L-proline reversible transport via proton symport (periplasm)" groups:idRef="R_PROt2rpp"/>
           <groups:member groups:name="Phosphatidylglycerol transport via ABC system (n-C18:0, periplasm)" groups:idRef="R_PG180abcpp"/>
-          <groups:member groups:name="L-threonine reversible transport via proton symport (periplasm)" groups:idRef="R_THRt2rpp"/>
-          <groups:member groups:name="Phosphatidate transport via ABC system (n-C14:0, periplasm)" groups:idRef="R_PA140abcpp"/>
-          <groups:member groups:name="Galactitol transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_GALTptspp"/>
-          <groups:member groups:name="Phosphatidate transport via ABC system (n-C16:0, periplasm)" groups:idRef="R_PA160abcpp"/>
+          <groups:member groups:name="Copper transport out via permease (no H+)" groups:idRef="R_CUt2pp"/>
           <groups:member groups:name="Glycine transport in via proton symport (periplasm)" groups:idRef="R_GLYt2pp"/>
-          <groups:member groups:name="Trehalose transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_TREptspp"/>
-          <groups:member groups:name="Crotonobetaine transport via ABC system (periplasm)" groups:idRef="R_CTBTabcpp"/>
-          <groups:member groups:name="D-glucose transport via ABC system (periplasm)" groups:idRef="R_GLCabcpp"/>
+          <groups:member groups:name="Maltotriose transport via ABC system (periplasm)" groups:idRef="R_MALTTRabcpp"/>
+          <groups:member groups:name="D-carnitine outward transport (H+ antiport)" groups:idRef="R_CRNDt2rpp"/>
+          <groups:member groups:name="Succinate:aspartate antiporter (periplasm)" groups:idRef="R_SUCASPtpp"/>
+          <groups:member groups:name="(S)-Propane-1,2-diol facilitated transport (periplasm)" groups:idRef="R_12PPDStpp"/>
+          <groups:member groups:name="Xanthosine transport via proton symport (periplasm)" groups:idRef="R_XTSNt2rpp"/>
+          <groups:member groups:name="Taurine transport via ABC system (periplasm)" groups:idRef="R_TAURabcpp"/>
+          <groups:member groups:name="Ethanesulfonate transport via ABC system (periplasm)" groups:idRef="R_ETHSO3abcpp"/>
+          <groups:member groups:name="Melibiose transport in via symport (periplasm)" groups:idRef="R_MELIBt2pp"/>
           <groups:member groups:name="L-tyrosine reversible transport via proton symport (periplasm)" groups:idRef="R_TYRt2rpp"/>
-          <groups:member groups:name="Butyrate transport via proton symport, reversible (periplasm)" groups:idRef="R_BUTt2rpp"/>
+          <groups:member groups:name="S-methylmethionine permease (periplasm)" groups:idRef="R_MMETt2pp"/>
+          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C18:0)" groups:idRef="R_12DGR180tipp"/>
+          <groups:member groups:name="CO2 transporter via diffusion (periplasm)" groups:idRef="R_CO2tpp"/>
           <groups:member groups:name="Maltotetraose transport via ABC system (periplasm)" groups:idRef="R_MALTTTRabcpp"/>
-          <groups:member groups:name="Deoxyinosine transport in via proton symport (periplasm)" groups:idRef="R_DINSt2pp"/>
-          <groups:member groups:name="Cytidine transport in via proton symport (periplasm)" groups:idRef="R_CYTDt2pp_copy2"/>
           <groups:member groups:name="Pyridoxal import" groups:idRef="R_PYDXtpp"/>
-          <groups:member groups:name="L-serine via sodium symport (periplasm)" groups:idRef="R_SERt4pp"/>
-          <groups:member groups:name="2,3-diaminopropionate transport in via proton symport" groups:idRef="R_23DAPPAt2pp"/>
-          <groups:member groups:name="Maltose transport via ABC system (periplasm)" groups:idRef="R_MALTabcpp"/>
-          <groups:member groups:name="Guanine transport in via proton symport (periplasm)" groups:idRef="R_GUAt2pp"/>
-          <groups:member groups:name="(S)-Propane-1,2-diol facilitated transport (periplasm)" groups:idRef="R_12PPDStpp"/>
-          <groups:member groups:name="3-hydroxycinnamic acid transport via proton symport, reversible (periplasm)" groups:idRef="R_HCINNMt2rpp"/>
-          <groups:member groups:name="Hydrogen transport diffusion (periplasm)" groups:idRef="R_H2tpp"/>
-          <groups:member groups:name="L-arabinose transport via proton symport (periplasm)" groups:idRef="R_ARBt2rpp"/>
-          <groups:member groups:name="L-arabinose transport via ABC system (periplasm)" groups:idRef="R_ARBabcpp"/>
-          <groups:member groups:name="Fumarate transport via proton symport (3 H) (periplasm)" groups:idRef="R_FUMt2_3pp"/>
-          <groups:member groups:name="Arginine/agmatine antiport (periplasm)" groups:idRef="R_ARGAGMt7pp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE181tipp"/>
+          <groups:member groups:name="Ethanolamine transport in via proton symport" groups:idRef="R_ETHAt2pp"/>
+          <groups:member groups:name="L-alanine export via facilited diffusion" groups:idRef="R_ALAtpp"/>
+          <groups:member groups:name="L-valine transport via ABC system (periplasm)" groups:idRef="R_VALabcpp"/>
+          <groups:member groups:name="D-Glucosamine 6-phosphate transport via phosphate antiport (periplasm)" groups:idRef="R_GAM6Pt6_2pp"/>
+          <groups:member groups:name="L-carnitine transport via ABC system (periplasm)" groups:idRef="R_CRNabcpp"/>
+          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C18:1)" groups:idRef="R_12DGR181tipp"/>
+          <groups:member groups:name="1,4-alpha-D-glucan transport via ABC system (periplasm)" groups:idRef="R_14GLUCANabcpp"/>
+          <groups:member groups:name="L-alanyl-D-glutamate transport in via proton symport (periplasm)" groups:idRef="R_LALADGLUtpp"/>
+          <groups:member groups:name="L-lactate reversible transport via proton symport (periplasm)" groups:idRef="R_L_LACt2rpp"/>
+          <groups:member groups:name="L-phenylalanine transport out (periplasm)" groups:idRef="R_PHEtipp"/>
+          <groups:member groups:name="L-ascorbate transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_ASCBptspp"/>
+          <groups:member groups:name="Thiol:disulfide reductase (DsbC)" groups:idRef="R_TDSR1"/>
+          <groups:member groups:name="Adenosine transport in via proton symport (periplasm)" groups:idRef="R_ADNt2pp_copy1"/>
+          <groups:member groups:name="L-threonine transport via ABC system (periplasm)" groups:idRef="R_THRabcpp"/>
+          <groups:member groups:name="D-glucarate transport via proton symport, reversible (periplasm)" groups:idRef="R_GLCRt2rpp"/>
+          <groups:member groups:name="Phosphatidylethanolamine transport via ABC system (n-C16:1, periplasm)" groups:idRef="R_PE161abcpp"/>
+          <groups:member groups:name="Butyrate transport via proton symport, reversible (periplasm)" groups:idRef="R_BUTt2rpp"/>
+          <groups:member groups:name="D-cysteine uptake via ABC system (periplasm)" groups:idRef="R_CYSDabcpp"/>
+          <groups:member groups:name="Hypoxanthine transport (periplasm)" groups:idRef="R_HYXNtpp"/>
+          <groups:member groups:name="L-methionine R-oxide transport via ABC system (periplasm)" groups:idRef="R_METSOX2abcpp"/>
+          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C18:0, periplasm)" groups:idRef="R_PGP180abcpp"/>
           <groups:member groups:name="Glycolate transport via proton symport, reversible (periplasm)" groups:idRef="R_GLYCLTt2rpp"/>
-          <groups:member groups:name="Pyridoxamine import" groups:idRef="R_PYDAMtpp"/>
+          <groups:member groups:name="Pyruvate reversible transport via proton symport (periplasm)" groups:idRef="R_PYRt2rpp"/>
+          <groups:member groups:name="D-glucose transport in via proton symport (periplasm)" groups:idRef="R_GLCt2pp"/>
+          <groups:member groups:name="Ornithine transport via ABC system (periplasm)" groups:idRef="R_ORNabcpp"/>
+          <groups:member groups:name="Phosphatidylglycerophosphate transport via ABC system (n-C16:1, periplasm)" groups:idRef="R_PGP161abcpp"/>
+          <groups:member groups:name="L-Prolinylglycine (Pro-Gly) transport via ABC system (periplasm)" groups:idRef="R_PROGLYabcpp"/>
           <groups:member groups:name="(R)-Propane-1,2-diol facilitated transport (periplasm)" groups:idRef="R_12PPDRtpp"/>
-          <groups:member groups:name="L-aspartate transport via ABC system (periplasm)" groups:idRef="R_ASPabcpp"/>
-          <groups:member groups:name="Cellobiose transport via PEPPyr PTS" groups:idRef="R_CELBpts"/>
-          <groups:member groups:name="L-carnitine/D-carnitine antiporter (periplasm)" groups:idRef="R_CRNt8pp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C18:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE180tipp"/>
+          <groups:member groups:name="Orotate transport via proton symport (2 H) (periplasm)" groups:idRef="R_OROTt2_2pp"/>
+          <groups:member groups:name="L-arabinose transport via proton symport (periplasm)" groups:idRef="R_ARBt2rpp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C12:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE120tipp"/>
+          <groups:member groups:name="Deoxycytidine transport in via proton symport (periplasm)" groups:idRef="R_DCYTt2pp"/>
+          <groups:member groups:name="Deoxyinosine transport in via proton symport (periplasm)" groups:idRef="R_DINSt2pp"/>
+          <groups:member groups:name="Sn-glycerol-3-phosphoserine transport via ABC system (periplasm)" groups:idRef="R_G3PSabcpp"/>
+          <groups:member groups:name="D-galactose transport in via proton symport (periplasm)" groups:idRef="R_GALt2pp"/>
+          <groups:member groups:name="L-phenylalanine reversible transport via proton symport (periplasm)" groups:idRef="R_PHEt2rpp"/>
+          <groups:member groups:name="Uracil export via facillitated diffusion (periplasm)" groups:idRef="R_URAtpp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C16:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPG161tipp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE140tipp"/>
           <groups:member groups:name="L-arabinose transport via proton antiport (periplasm)" groups:idRef="R_ARBt3ipp"/>
-          <groups:member groups:name="Carnitine/butyrobetaine antiporter (periplasm)" groups:idRef="R_CRNt7pp"/>
-          <groups:member groups:name="Maltose transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_MALTptspp"/>
-          <groups:member groups:name="Fumarate transport via proton symport (2 H) (periplasm)" groups:idRef="R_FUMt2_2pp"/>
-          <groups:member groups:name="Nicotinic acid uptake (periplasm)" groups:idRef="R_NACtpp"/>
-          <groups:member groups:name="Na+/Proline-L symporter (periplasm)" groups:idRef="R_PROt4pp"/>
-          <groups:member groups:name="D-allose transport via ABC system (periplasm)" groups:idRef="R_ALLabcpp"/>
-          <groups:member groups:name="Sn-glycerol-3-phosphocholine transport via ABC system (periplasm)" groups:idRef="R_G3PCabcpp"/>
-          <groups:member groups:name="Lactose transport via proton symport (periplasm)" groups:idRef="R_LCTStpp"/>
-          <groups:member groups:name="Manganese (Mn+2) transport in via proton symport (periplasm)" groups:idRef="R_MNt2pp"/>
-          <groups:member groups:name="L-proline reversible transport via proton symport (periplasm)" groups:idRef="R_PROt2rpp"/>
-          <groups:member groups:name="Cystine efflux transport" groups:idRef="R_CYSItpp"/>
+          <groups:member groups:name="L-aspartate transport in via proton symport (periplasm)" groups:idRef="R_ASPt2pp"/>
+          <groups:member groups:name="NMN transport via NMN glycohydrolase (periplasm)" groups:idRef="R_NMNt7pp"/>
+          <groups:member groups:name="P-aminobenzoyl glutamate:H+ symporter" groups:idRef="R_4ABZGLUtr"/>
+          <groups:member groups:name="D-mannose transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_MANptspp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C12:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPG120tipp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPG180tipp"/>
+          <groups:member groups:name="Putrescine transport via ABC system (periplasm)" groups:idRef="R_PTRCabcpp"/>
+          <groups:member groups:name="Succinate:fumarate antiporter (periplasm)" groups:idRef="R_SUCFUMtpp"/>
+          <groups:member groups:name="Choline transport via proton symport (periplasm)" groups:idRef="R_CHLt2pp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C14:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE141tipp"/>
+          <groups:member groups:name="Biotin transport via proton symport (periplasm)" groups:idRef="R_BTNt2ipp"/>
+          <groups:member groups:name="Choline transport via ABC system (periplasm)" groups:idRef="R_CHLabcpp"/>
+          <groups:member groups:name="D-galacturonate transport via proton symport, reversible (periplasm)" groups:idRef="R_GALURt2rpp"/>
+          <groups:member groups:name="N-Acetyl-D-glucosamine transport via PEP:Pyr PTS  (periplasm)" groups:idRef="R_ACGAptspp"/>
+          <groups:member groups:name="Methanesulfonate transport via ABC system (periplasm)" groups:idRef="R_MSO3abcpp"/>
+          <groups:member groups:name="Aspartate transport via proton symport (2 H) (periplasm)" groups:idRef="R_ASPt2_2pp"/>
+          <groups:member groups:name="Phosphatidylglycerol transport via ABC system (n-C12:0, periplasm)" groups:idRef="R_PG120abcpp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE160tipp"/>
+          <groups:member groups:name="Choline transport via proton antiport (periplasm)" groups:idRef="R_CHLt3pp"/>
+          <groups:member groups:name="D-methionine transport via ABC system (periplasm)" groups:idRef="R_METDabcpp"/>
+          <groups:member groups:name="Deoxyadenosine transport in via proton symport (periplasm)" groups:idRef="R_DADNt2pp"/>
+          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C12:0)" groups:idRef="R_12DGR120tipp"/>
+          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:0)" groups:idRef="R_12DGR140tipp"/>
+          <groups:member groups:name="D-alanine transport in via proton symport (periplasm)" groups:idRef="R_DALAt2pp"/>
+          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C16:0)" groups:idRef="R_12DGR160tipp"/>
+          <groups:member groups:name="Butanesulfonate transport via ABC system (periplasm)" groups:idRef="R_BUTSO3abcpp"/>
+          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C16:1)" groups:idRef="R_12DGR161tipp"/>
+          <groups:member groups:name="Glyceraldehyde facilitated diffusion (periplasm)" groups:idRef="R_GLYALDtpp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C18:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPG181tipp"/>
+          <groups:member groups:name="Lipoate transport via proton symport (periplasm)" groups:idRef="R_LIPOt2pp"/>
+          <groups:member groups:name="Uracil transport in via proton symport (periplasm)" groups:idRef="R_URAt2pp"/>
           <groups:member groups:name="Formate transport via diffusion (cytoplasm to periplasm)" groups:idRef="R_FORtppi"/>
-          <groups:member groups:name="1-O-methyl-Beta-D-glucuronate transport via proton symport (periplasm)" groups:idRef="R_METGLCURt2pp"/>
-          <groups:member groups:name="5-Methylthio-D-ribose transport via proton symport (periplasm)" groups:idRef="R_5MTRtpp"/>
+          <groups:member groups:name="L-homoserineserine efflux via proton symport" groups:idRef="R_HOMt2pp"/>
+          <groups:member groups:name="1,2 diacylglycerol transport via flipping (periplasm to cytoplasm, n-C14:1)" groups:idRef="R_12DGR141tipp"/>
+          <groups:member groups:name="L-methionine tranport out via proton antiport (periplasm)" groups:idRef="R_METt3pp"/>
+          <groups:member groups:name="H2O transport via diffusion (periplasm)" groups:idRef="R_H2Otpp"/>
+          <groups:member groups:name="L-asparate transport via proton symport (3 H) (periplasm)" groups:idRef="R_ASPt2_3pp"/>
+          <groups:member groups:name="L-Cysteinylglycine (Cys-Gly) transport via ABC system (periplasm)" groups:idRef="R_CGLYabcpp"/>
+          <groups:member groups:name="D-Malate transport via proton symport (2 H) (periplasm)" groups:idRef="R_MALDt2_2pp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoethanolamine (n-C16:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPE161tipp"/>
+          <groups:member groups:name="Putrescine transport in via proton symport" groups:idRef="R_PTRCt2pp"/>
+          <groups:member groups:name="Phosphatidylethanolamine transport via ABC system (n-C16:0, periplasm)" groups:idRef="R_PE160abcpp"/>
+          <groups:member groups:name="Galactitol transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_GALTptspp"/>
+          <groups:member groups:name="Phosphatidylethanolamine transport via ABC system (n-C18:0, periplasm)" groups:idRef="R_PE180abcpp"/>
+          <groups:member groups:name="L-aspartate uptake via facillitated diffusion" groups:idRef="R_ASPtpp"/>
+          <groups:member groups:name="Cystine efflux transport" groups:idRef="R_CYSItpp"/>
+          <groups:member groups:name="Methane Transport(periplasm)" groups:idRef="R_CH4t2pp"/>
+          <groups:member groups:name="3-hydroxypropionate transport via proton symport (periplasm)" groups:idRef="R_3HPPtpp"/>
+          <groups:member groups:name="L-asparagine reversible transport via proton symport (periplasm)" groups:idRef="R_ASNt2rpp"/>
+          <groups:member groups:name="L-xylulose transport in via proton symport (periplasm)" groups:idRef="R_XYLUt2pp"/>
+          <groups:member groups:name="L-serine export via facilitated transport" groups:idRef="R_SERtpp"/>
+          <groups:member groups:name="Ethanol reversible transport via diffusion (periplasm)" groups:idRef="R_ETOHtrpp"/>
+          <groups:member groups:name="Phosphatidylethanolamine transport via ABC system (n-C12:0, periplasm)" groups:idRef="R_PE120abcpp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphatidate (n-C18:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPA180tipp"/>
           <groups:member groups:name="Indole transport via proton symport, reversible (periplasm)" groups:idRef="R_INDOLEt2rpp"/>
-          <groups:member groups:name="Thiol:disulfide reductase (DsbC)" groups:idRef="R_TDSR1"/>
+          <groups:member groups:name="Phosphatidate transport via ABC system (n-C12:0, periplasm)" groups:idRef="R_PA120abcpp"/>
+          <groups:member groups:name="L-valine transport out via proton antiport (periplasm)" groups:idRef="R_VALt3pp"/>
+          <groups:member groups:name="Xanthine reversible transport (periplasm)" groups:idRef="R_XANtpp"/>
+          <groups:member groups:name="L-arabinose transport via ABC system (periplasm)" groups:idRef="R_ARBabcpp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphatidate (n-C14:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPA141tipp"/>
+          <groups:member groups:name="Maltopentaose transport via ABC system (periplasm)" groups:idRef="R_MALTPTabcpp"/>
+          <groups:member groups:name="L-glutamine transport via ABC system (periplasm)" groups:idRef="R_GLNabcpp"/>
+          <groups:member groups:name="D-glucuronate transport via proton symport, reversible (periplasm)" groups:idRef="R_GLCURt2rpp"/>
+          <groups:member groups:name="N-acetylneuraminate proton symport (periplasm)" groups:idRef="R_ACNAMt2pp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphatidate (n-C16:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPA160tipp"/>
+          <groups:member groups:name="D-galactonate transport via proton symport (periplasm)" groups:idRef="R_GALCTNt2pp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphatidate (n-C18:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPA181tipp"/>
+          <groups:member groups:name="5-Dehydro-D-gluconate transport via proton symport, reversible (periplasm)" groups:idRef="R_5DGLCNt2rpp"/>
+          <groups:member groups:name="Fructose transport via PEP:Pyr PTS (f6p generating) (periplasm)" groups:idRef="R_FRUpts2pp"/>
+          <groups:member groups:name="Allantoin transport in via proton symport (periplasm)" groups:idRef="R_ALLTNt2rpp"/>
+          <groups:member groups:name="L-isoleucine transport via ABC system (periplasm)" groups:idRef="R_ILEabcpp"/>
+          <groups:member groups:name="L-threonine efflux transport via proton antiport (periplasm)" groups:idRef="R_THRt2pp"/>
+          <groups:member groups:name="Protoheme transport via ABC system (periplasm)" groups:idRef="R_PHEMEabcpp"/>
+          <groups:member groups:name="L-arginine transport via ABC system (periplasm)" groups:idRef="R_ARGabcpp"/>
+          <groups:member groups:name="2,3-dihydroxypropane 1-sulfonate transporter" groups:idRef="R_DHPStr"/>
+          <groups:member groups:name="FAD transporter, periplasm" groups:idRef="R_FADt"/>
+          <groups:member groups:name="L-lysine transport out via proton antiport (cytoplasm to periplasm)" groups:idRef="R_LYSt3pp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphatidate (n-C16:1) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPA161tipp"/>
+          <groups:member groups:name="Glucose-6-phosphate transport via phosphate antiport (periplasm)" groups:idRef="R_G6Pt6_2pp"/>
+          <groups:member groups:name="Psicoselysine transport via proton symport (periplasm)" groups:idRef="R_PSCLYSt2pp"/>
+          <groups:member groups:name="L-threonine  via sodium symport (periplasm)" groups:idRef="R_THRt4pp"/>
+          <groups:member groups:name="Transport of poly-?-1,6-N-acetyl-D-glucosamine (poly-?-1,6-N-acetyl-D-glucosamine synthase)" groups:idRef="R_PUACGAMtr"/>
+          <groups:member groups:name="L-threonine reversible transport via proton symport (periplasm)" groups:idRef="R_THRt2rpp"/>
+          <groups:member groups:name="L-methionine S-oxide transport via ABC system (periplasm)" groups:idRef="R_METSOX1abcpp"/>
+          <groups:member groups:name="2-Acyl-sn-glycero-3-phosphoglycerol (n-C14:0) transporter via facilitated diffusion (periplasm)" groups:idRef="R_2AGPG140tipp"/>
+          <groups:member groups:name="Cyanate transport via proton symport (periplasm)" groups:idRef="R_CYNTt2pp"/>
+          <groups:member groups:name="2-dehydro-3-deoxy-D-gluconate transport via proton symport, reversible (periplasm)" groups:idRef="R_DDGLCNt2rpp"/>
+          <groups:member groups:name="Cholate transport via proton antiport" groups:idRef="R_CHOLATEtpp"/>
           <groups:member groups:name="L-glutamate transport via ABC system (periplasm)" groups:idRef="R_GLUabcpp"/>
-          <groups:member groups:name="Cytidine transport in via proton symport (periplasm)" groups:idRef="R_CYTDt2pp_copy1"/>
-          <groups:member groups:name="Glutathione export via ABC system (cytoplasm to periplasm)" groups:idRef="R_GTHRDabc2pp"/>
-          <groups:member groups:name="L-carnitine transport via ABC system (periplasm)" groups:idRef="R_CRNabcpp"/>
-          <groups:member groups:name="L-arginine transport out via proton antiport (cytoplasm to periplasm)" groups:idRef="R_ARGt3pp"/>
+          <groups:member groups:name="Uridine transport in via proton symport (periplasm)" groups:idRef="R_URIt2pp_copy1"/>
           <groups:member groups:name="Adenine transport via proton symport (reversible) (periplasm)" groups:idRef="R_ADEt2rpp"/>
+          <groups:member groups:name="L-fucose transport via proton symport (periplasm)" groups:idRef="R_FUCtpp"/>
+          <groups:member groups:name="L-lysine transport in via proton symport (periplasm)" groups:idRef="R_LYSt2pp"/>
+          <groups:member groups:name="Beta-alanine transport in via proton symport (periplasm)" groups:idRef="R_BALAt2pp"/>
+          <groups:member groups:name="Phenylacetaldehyde reversible transport via proton symport (periplasm)" groups:idRef="R_PACALDt2rpp"/>
+          <groups:member groups:name="Na+/Propionate symporter (periplasm)" groups:idRef="R_PPAt4pp"/>
+          <groups:member groups:name="L-cysteine uptake via ABC system (periplasm)" groups:idRef="R_CYSabcpp"/>
+          <groups:member groups:name="Phosphatidate transport via ABC system (n-C16:0, periplasm)" groups:idRef="R_PA160abcpp"/>
+          <groups:member groups:name="L-serine reversible transport via proton symport (periplasm)" groups:idRef="R_SERt2rpp"/>
+          <groups:member groups:name="L-cysteine export via facilitated transport" groups:idRef="R_CYStpp"/>
+          <groups:member groups:name="Phosphatidate transport via ABC system (n-C14:1, periplasm)" groups:idRef="R_PA141abcpp"/>
+          <groups:member groups:name="3-hydroxycinnamic acid transport via proton symport, reversible (periplasm)" groups:idRef="R_HCINNMt2rpp"/>
+          <groups:member groups:name="Sucrose transport via PEP:Pyr  (periplasm)" groups:idRef="R_SUCptspp"/>
+          <groups:member groups:name="Phosphatidylglycerol transport via ABC system (n-C16:1, periplasm)" groups:idRef="R_PG161abcpp"/>
+          <groups:member groups:name="Sn-glycerol-3-phosphoglycerol transport via ABC system (periplasm)" groups:idRef="R_G3PGabcpp"/>
+          <groups:member groups:name="Formate transport via proton symport (uptake only, periplasm)" groups:idRef="R_FORt2pp"/>
+          <groups:member groups:name="L-leucine transport out via proton antiport (periplasm)" groups:idRef="R_LEUt3pp"/>
+          <groups:member groups:name="Phosphatidylglycerol transport via ABC system (n-C16:0, periplasm)" groups:idRef="R_PG160abcpp"/>
+          <groups:member groups:name="Succinate transport via diffusion in (periplasm)" groups:idRef="R_SUCCt1pp"/>
+          <groups:member groups:name="Succinate transport via proton symport (2 H) (periplasm)" groups:idRef="R_SUCCt2_2pp"/>
+          <groups:member groups:name="Pyridoxine import" groups:idRef="R_PYDXNtpp"/>
           <groups:member groups:name="Guanine transport via diffusion (periplasm)" groups:idRef="R_GUAtpp"/>
+          <groups:member groups:name="D-glucose transport via PEP:Pyr PTS (periplasm)" groups:idRef="R_GLCptspp"/>
+          <groups:member groups:name="L-tryptophan transport out (periplasm)" groups:idRef="R_TRPtipp"/>
+          <groups:member groups:name="M-diaminopimelic acid ABC transport (periplasm)" groups:idRef="R_DAPabcpp"/>
+          <groups:member groups:name="L-histidine transport via ABC system (periplasm)" groups:idRef="R_HISabcpp"/>
+          <groups:member groups:name="L-leucine transport via ABC system (periplasm)" groups:idRef="R_LEUabcpp"/>
+          <groups:member groups:name="L-idonate transport via proton symport, reversible (periplasm)" groups:idRef="R_IDONt2rpp"/>
+          <groups:member groups:name="L-leucine reversible transport via proton symport (periplasm)" groups:idRef="R_LEUt2rpp"/>
+          <groups:member groups:name="Phosphatidylethanolamine transport via ABC system (n-C14:0, periplasm)" groups:idRef="R_PE140abcpp"/>
+          <groups:member groups:name="4-aminobutyrate/glutamate antiport (periplasm)" groups:idRef="R_GLUABUTt7pp"/>
+          <groups:member groups:name="Succinate:D-tartrate antiporter (periplasm)" groups:idRef="R_SUCTARTtpp"/>
+          <groups:member groups:name="D-glucose transport via ABC system (periplasm)" groups:idRef="R_GLCabcpp"/>
+          <groups:member groups:name="Malate transport via proton symport (3 H) (periplasm)" groups:idRef="R_MALt2_3pp"/>
+          <groups:member groups:name="L-lysine transport via ABC system (periplasm)" groups:idRef="R_LYSabcpp"/>
+          <groups:member groups:name="Deoxyuridine transport in via proton symport (periplasm)" groups:idRef="R_DURIt2pp"/>
+          <groups:member groups:name="Malate transport via proton symport (2 H) (periplasm)" groups:idRef="R_MALt2_2pp"/>
+          <groups:member groups:name="Autoinducer-2 ABC transporter" groups:idRef="R_AI2abcpp"/>
+          <groups:member groups:name="Glycerol-3-phosphate : phosphate antiporter (periplasm)" groups:idRef="R_GLYC3Pt6pp"/>
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-          <groups:member groups:name="Hexadecenoate transport via facilitated irreversible diffusion (extracellular to periplasm)" groups:idRef="R_HDCEAtexi"/>
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-          <groups:member groups:name="Cesium transport via diffusion" groups:idRef="R_CS1tex"/>
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           <groups:member groups:name="Copper transport out via proton antiport" groups:idRef="R_CUt3"/>
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+          <groups:member groups:name="Hexadecenoate transport via facilitated irreversible diffusion (extracellular to periplasm)" groups:idRef="R_HDCEAtexi"/>
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           <groups:member groups:name="Novobiocin transport via TolC system" groups:idRef="R_NOVBCNtpp"/>
-          <groups:member groups:name="MaltotetraoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible" groups:idRef="R_MALTTTRtexi"/>
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-          <groups:member groups:name="P-aminobenzoyl glutamate transport via diffusion (extracellular to periplasm)" groups:idRef="R_4ABZGLUtex"/>
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           <groups:member groups:name="Cobinamide transport via ton system (extermal)" groups:idRef="R_CBItonex"/>
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+          <groups:member groups:name="Deoxycytidine transport via diffusion (extracellular to periplasm)" groups:idRef="R_DCYTtex"/>
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-          <groups:member groups:name="MaltopentaoseMaltotriose transport via diffusion (extracellular to periplasm) irreversible" groups:idRef="R_MALTPTtexi"/>
+          <groups:member groups:name="Cesium transport via diffusion" groups:idRef="R_CS1tex"/>
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           <groups:member groups:name="Ferric-dicitrate transport via ton system (extracellular)" groups:idRef="R_FE3DCITtonex"/>
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       </groups:group>
       <groups:group metaid="meta_G_group36" sboTerm="SBO:0000633" groups:id="G_group36" groups:name="Transport, Outer Membrane Porin" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="L-isoleucine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ILEtex"/>
+          <groups:member groups:name="Pantothenate transport via diffusion (extracellular to periplasm)" groups:idRef="R_PNTOtex"/>
+          <groups:member groups:name="Oxygen transport via diffusion (extracellular to periplasm)" groups:idRef="R_O2tex"/>
+          <groups:member groups:name="D-glucosamine 6-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GAMAN6Ptex"/>
+          <groups:member groups:name="Deoxyinosine transport via diffusion (extracellular to periplasm)" groups:idRef="R_DINStex"/>
+          <groups:member groups:name="H2O transport via diffusion (extracellular to periplasm)" groups:idRef="R_H2Otex"/>
+          <groups:member groups:name="Lipoate transport via diffusion (extracellular to periplasm)" groups:idRef="R_LIPOtex"/>
+          <groups:member groups:name="Glycerol-2-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYC2Ptex"/>
           <groups:member groups:name="UDP-N-acetyl-D-galactosamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_UDPACGALtex"/>
-          <groups:member groups:name="Glycero-3-phospho-1-inositol transport via diffusion (extracellular to periplasm)" groups:idRef="R_G3PItex"/>
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-          <groups:member groups:name="23cGMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_23CGMPtex"/>
-          <groups:member groups:name="Methanol transport via diffusion (extracellular to periplasm)" groups:idRef="R_MEOHtex"/>
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-          <groups:member groups:name="Dopamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_DOPAtex"/>
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-          <groups:member groups:name="Glucose 6-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_G6Ptex"/>
-          <groups:member groups:name="UMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_UMPtex"/>
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-          <groups:member groups:name="Shikimate transport via diffusion (extracellular to periplasm)" groups:idRef="R_SKMtex"/>
+          <groups:member groups:name="Glycerol-3-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYC3Ptex"/>
+          <groups:member groups:name="5-Dehydro-D-gluconate transport via diffusion (extracellular to periplasm)" groups:idRef="R_5DGLCNtex"/>
+          <groups:member groups:name="L-ascorbate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ASCBtex"/>
+          <groups:member groups:name="L-alanyl-L-glutamate transport via diffusion (extracellular to periplasm)" groups:idRef="R_LALALGLUtex"/>
+          <groups:member groups:name="Magnesium (Mg+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_MG2tex"/>
+          <groups:member groups:name="Nitrate transport via diffusion (extracellular to periplasm)" groups:idRef="R_NO3tex"/>
+          <groups:member groups:name="L-threonine transport via diffusion (extracellular to periplasm)" groups:idRef="R_THRtex"/>
+          <groups:member groups:name="N-acetylmuramate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACMUMtex"/>
+          <groups:member groups:name="L-alanine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ALAtex"/>
+          <groups:member groups:name="Putrescine transport via diffusion (extracellular to periplasm)" groups:idRef="R_PTRCtex"/>
           <groups:member groups:name="Selenite transport via diffusion (extracellular to periplasm)" groups:idRef="R_SLNTtex"/>
-          <groups:member groups:name="Tungstate transport via diffusion (extracellular to periplasm)" groups:idRef="R_TUNGStex"/>
-          <groups:member groups:name="N-acetyl-D-galactosamine 1-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACGAL1Ptex"/>
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-          <groups:member groups:name="L-glutamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLNtex"/>
-          <groups:member groups:name="D-glucuronat transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLCURtex"/>
+          <groups:member groups:name="L-lysine transport via diffusion (extracellular to periplasm)" groups:idRef="R_LYStex"/>
+          <groups:member groups:name="Thiamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_THMtex"/>
+          <groups:member groups:name="CO2 transport via diffusion (extracellular to periplasm)" groups:idRef="R_CO2tex"/>
+          <groups:member groups:name="Dimethyl sulfoxide transport via diffusion (extracellular to periplasm)" groups:idRef="R_DMSOtex"/>
+          <groups:member groups:name="Fluoride transport via diffusion" groups:idRef="R_Ftex"/>
+          <groups:member groups:name="L-serine transport via diffusion (extracellular to periplasm)" groups:idRef="R_SERtex"/>
+          <groups:member groups:name="Glutathione (ox) transport via diffusion (extracellular to periplasm)" groups:idRef="R_GTHOXtex"/>
+          <groups:member groups:name="L-Lyxose transport via diffusion (extracellular to periplasm)" groups:idRef="R_LYXtex"/>
+          <groups:member groups:name="D-xylose transport via diffusion (extracellular to periplasm)" groups:idRef="R_XYLtex"/>
+          <groups:member groups:name="Phosphonate transport via diffusion (extracellular to periplasm)" groups:idRef="R_PPTtex"/>
+          <groups:member groups:name="Dimethyl sulfide transport via diffusion (extracellular to periplasm)" groups:idRef="R_DMStex"/>
+          <groups:member groups:name="Phospho-L-threonine transport via diffusion (extracellular to periplasm)" groups:idRef="R_THRPtex"/>
+          <groups:member groups:name="Indole transport via diffusion (extracellular to periplasm)" groups:idRef="R_INDOLEtex"/>
+          <groups:member groups:name="Tyramine transport via diffusion (extracellular to periplasm)" groups:idRef="R_TYMtex"/>
+          <groups:member groups:name="Allose transport via diffusion (extracellular to periplasm)" groups:idRef="R_ALLtex"/>
+          <groups:member groups:name="Glycine betaine transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYBtex"/>
+          <groups:member groups:name="Pyridoxal transport via diffusion (extracellular)" groups:idRef="R_PYDXtex"/>
+          <groups:member groups:name="L-methionine R-oxide diffusion (extracellular)" groups:idRef="R_METSOX2tex"/>
+          <groups:member groups:name="Selenate transport via diffusion (extracellular to periplasm)" groups:idRef="R_SELtex"/>
+          <groups:member groups:name="3-(3-hydroxyphenyl)propionate transport via diffusion (extracellular to periplasm)" groups:idRef="R_HPPPNtex"/>
+          <groups:member groups:name="S-methyl-L-methionine transport via diffusion (extracellular to periplasm)" groups:idRef="R_MMETtex"/>
+          <groups:member groups:name="Nitrious oxide transport via diffusion (extracellular to periplasm)" groups:idRef="R_N2Otex"/>
           <groups:member groups:name="D-serine transport via diffusion (extracellular to periplasm)" groups:idRef="R_DSERtex"/>
-          <groups:member groups:name="GDP transport via diffusion (extracellular to periplasm)" groups:idRef="R_GDPtex"/>
-          <groups:member groups:name="Propanal transport via diffusion (extracellular to periplasm)" groups:idRef="R_PPALtex"/>
-          <groups:member groups:name="3CMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_3CMPtex"/>
-          <groups:member groups:name="Spermidine transport via diffusion (extracellular to periplasm)" groups:idRef="R_SPMDtex"/>
-          <groups:member groups:name="Zinc (Zn+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_Zn2tex"/>
-          <groups:member groups:name="Glycero-3-phosphoethanolamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_G3PEtex"/>
-          <groups:member groups:name="H2O transport via diffusion (extracellular to periplasm)" groups:idRef="R_H2Otex"/>
-          <groups:member groups:name="D-methionine transport via diffusion (extracellular to periplasm)" groups:idRef="R_METDtex"/>
-          <groups:member groups:name="N-acetyl-D-glucosamine 1-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACGAM1Ptex"/>
+          <groups:member groups:name="L-idonate transport via diffusion (extracellular to periplasm)" groups:idRef="R_IDONtex"/>
+          <groups:member groups:name="L-Prolinylglycine transport via diffusion (extracellular to periplasm)" groups:idRef="R_PROGLYtex"/>
+          <groups:member groups:name="L-methionine S-oxide diffusion (extracellular)" groups:idRef="R_METSOX1tex"/>
+          <groups:member groups:name="N-acetyl-D-galactosamine 1-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACGAL1Ptex"/>
+          <groups:member groups:name="Thymidine transport via diffusion (extracellular to periplasm)" groups:idRef="R_THMDtex"/>
           <groups:member groups:name="Copper (Cu+1) transport via diffusion (extracellular to periplasm)" groups:idRef="R_CUtex"/>
-          <groups:member groups:name="Minocycline transport via diffusion (extracellular to periplasm)" groups:idRef="R_MINCYCtex"/>
+          <groups:member groups:name="L-tyrosine transport via diffusion (extracellular to periplasm)" groups:idRef="R_TYRtex"/>
+          <groups:member groups:name="L cystine transport via diffusion extracellular to periplasm" groups:idRef="R_CYSItex"/>
+          <groups:member groups:name="D-glucuronate 1-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLCUR1Ptex"/>
           <groups:member groups:name="L-Cysteinylglycine transport via diffusion (extracellular to periplasm)" groups:idRef="R_CGLYtex"/>
-          <groups:member groups:name="L-threonine transport via diffusion (extracellular to periplasm)" groups:idRef="R_THRtex"/>
-          <groups:member groups:name="Cobalt (Co+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_COBALT2tex"/>
+          <groups:member groups:name="Manganese (Mn+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_MNtex"/>
           <groups:member groups:name="Cyanate transport via diffusion (extracellular to periplasm)" groups:idRef="R_CYNTtex"/>
-          <groups:member groups:name="Iron (III) transport via diffusion (extracellular to periplasm)" groups:idRef="R_FE3tex"/>
-          <groups:member groups:name="CMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_CMPtex"/>
-          <groups:member groups:name="Glyceraldehyde transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYALDtex"/>
-          <groups:member groups:name="UDPglucose transport via diffusion (extracellular to periplasm)" groups:idRef="R_UDPGtex"/>
-          <groups:member groups:name="Molybdate transport via diffusion (extracellular to periplasm)" groups:idRef="R_MOBDtex"/>
-          <groups:member groups:name="Tetracycline transport via diffusion (extracellular to periplasm)" groups:idRef="R_TTRCYCtex"/>
-          <groups:member groups:name="Calcium (Ca+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_CA2tex"/>
-          <groups:member groups:name="Hydrogen peroxide transport via diffusion (external)" groups:idRef="R_H2O2tex"/>
-          <groups:member groups:name="Psicoselysine transporter via diffusion (extracellular)" groups:idRef="R_PSCLYStex"/>
-          <groups:member groups:name="L-cysteine transport via diffusion (extracellular to periplasm)" groups:idRef="R_CYStex"/>
+          <groups:member groups:name="Decanoate transport via diffusion (extracellular to periplasm)" groups:idRef="R_DCAtex"/>
           <groups:member groups:name="L-fucose transport via diffusion (extracellular to periplasm)" groups:idRef="R_FUCtex"/>
-          <groups:member groups:name="Orotate transport via diffusion (extracellular to periplasm)" groups:idRef="R_OROTtex"/>
-          <groups:member groups:name="L-arabinose transport via diffusion (extracellular to periplasm)" groups:idRef="R_ARBtex"/>
-          <groups:member groups:name="Phospho-L-threonine transport via diffusion (extracellular to periplasm)" groups:idRef="R_THRPtex"/>
+          <groups:member groups:name="Glycine transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYtex"/>
+          <groups:member groups:name="Ribose 5-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_R5Ptex"/>
+          <groups:member groups:name="Iron (II) transport via diffusion (extracellular to periplasm)" groups:idRef="R_FE2tex"/>
           <groups:member groups:name="D-galacturonate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GALURtex"/>
-          <groups:member groups:name="DTMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_DTMPtex"/>
-          <groups:member groups:name="L-glutamate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLUtex"/>
-          <groups:member groups:name="Methanesulfonate transport via diffusion (extracellular to periplasm)" groups:idRef="R_MSO3tex"/>
-          <groups:member groups:name="Inositol transport via diffusion (extracellular to periplasm)" groups:idRef="R_INSTtex"/>
-          <groups:member groups:name="Pyruvate transport via diffusion (extracellular to periplasm)" groups:idRef="R_PYRtex"/>
+          <groups:member groups:name="D-glycerate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYCAtex"/>
+          <groups:member groups:name="Glycerol transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYCtex"/>
+          <groups:member groups:name="Octanoate transport via diffusion (extracellular to periplasm)" groups:idRef="R_OCTAtex"/>
+          <groups:member groups:name="5-Methylthio-D-ribose transport via proton diffusion (extracellular to periplasm)" groups:idRef="R_5MTRtex"/>
+          <groups:member groups:name="Ethanesulfonate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ETHSO3tex"/>
+          <groups:member groups:name="Thiocyanate transport via diffusion (extracellular to periplasm)" groups:idRef="R_TCYNTtex"/>
+          <groups:member groups:name="Molybdate transport via diffusion (extracellular to periplasm)" groups:idRef="R_MOBDtex"/>
+          <groups:member groups:name="4-aminobutyrate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ABUTtex"/>
           <groups:member groups:name="Quinate transport via diffusion (extracellular to periplasm)" groups:idRef="R_QUIN2tex"/>
-          <groups:member groups:name="O-Acetyl-L-serine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACSERtex"/>
-          <groups:member groups:name="Glutathione transport via diffusion (extracellular to periplasm)" groups:idRef="R_GTHRDtex"/>
-          <groups:member groups:name="Propionate transport via diffusion" groups:idRef="R_PPAtex"/>
-          <groups:member groups:name="Pyridoxamine transport via diffusion (extracellular)" groups:idRef="R_PYDAMtex"/>
-          <groups:member groups:name="Taurine transport via diffusion (extracellular to periplasm)" groups:idRef="R_TAURtex"/>
-          <groups:member groups:name="Lipoate transport via diffusion (extracellular to periplasm)" groups:idRef="R_LIPOtex"/>
-          <groups:member groups:name="Dihydroxyphenylacetaldehyde transport via diffusion (extracellular to periplasm)" groups:idRef="R_34dhpactex"/>
-          <groups:member groups:name="Cytosine transport via diffusion (extracellular to periplasm)" groups:idRef="R_CSNtex"/>
-          <groups:member groups:name="H2s transport via diffusion (extracellular to periplasm)" groups:idRef="R_H2Stex"/>
-          <groups:member groups:name="Thiosulfate transport via diffusion (extracellular to periplasm)" groups:idRef="R_TSULtex"/>
-          <groups:member groups:name="D-tartrate transport via diffusion (extracellular to periplasm)" groups:idRef="R_TARTRDtex"/>
-          <groups:member groups:name="Oxygen transport via diffusion (extracellular to periplasm)" groups:idRef="R_O2tex"/>
-          <groups:member groups:name="L-leucine transport via diffusion (extracellular to periplasm)" groups:idRef="R_LEUtex"/>
-          <groups:member groups:name="L-homoserine transport via diffusion (extracellular to periplasm)" groups:idRef="R_HOMtex"/>
-          <groups:member groups:name="Ornithine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ORNtex"/>
-          <groups:member groups:name="Phenethylamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_PEAMNtex"/>
-          <groups:member groups:name="Tartrate transport via diffusion (extracellular to periplasm)" groups:idRef="R_TARTRtex"/>
-          <groups:member groups:name="1,5-Diaminopentane transport via diffusion (extracellular to periplasm)" groups:idRef="R_DAPtex"/>
-          <groups:member groups:name="D-glucarate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLCRtex"/>
+          <groups:member groups:name="L-tryptophan transport via diffusion (extracellular to periplasm)" groups:idRef="R_TRPtex"/>
+          <groups:member groups:name="Psicoselysine transporter via diffusion (extracellular)" groups:idRef="R_PSCLYStex"/>
+          <groups:member groups:name="Sulfoaceate transport via diffusion (extracellular to periplasm)" groups:idRef="R_SULFACtex"/>
+          <groups:member groups:name="Trimethylamine N-oxide transport via diffusion (extracellular to periplasm)" groups:idRef="R_TMAOtex"/>
           <groups:member groups:name="Acetoacetate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACACtex"/>
-          <groups:member groups:name="UDPgalactose transport via diffusion (extracellular to periplasm)" groups:idRef="R_UDPGALtex"/>
-          <groups:member groups:name="23cUMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_23CUMPtex"/>
-          <groups:member groups:name="L-ascorbate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ASCBtex"/>
-          <groups:member groups:name="Glycerol transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYCtex"/>
-          <groups:member groups:name="DUMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_DUMPtex"/>
-          <groups:member groups:name="L-rhamnose transport via diffusion (extracellular to periplasm)" groups:idRef="R_RMNtex"/>
-          <groups:member groups:name="DIMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_DIMPtex"/>
-          <groups:member groups:name="Ethanolamine transport via diffusion (extracellular)" groups:idRef="R_ETHAtex"/>
-          <groups:member groups:name="Hydrogen transport via diffusion (extracellular to periplasm)" groups:idRef="R_H2tex"/>
-          <groups:member groups:name="N-acetylmuramate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACMUMtex"/>
+          <groups:member groups:name="D-cysteine transport via diffusion (extracellular to periplasm)" groups:idRef="R_CYSDtex"/>
+          <groups:member groups:name="L-lactate transport via diffusion (extracellular to periplasm)" groups:idRef="R_L_LACtex"/>
+          <groups:member groups:name="23cAMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_23CAMPtex"/>
+          <groups:member groups:name="D-fructose transport via diffusion (extracellular to periplasm)" groups:idRef="R_FRUtex"/>
+          <groups:member groups:name="Agmatine transport via diffusion (extracellular to periplasm)" groups:idRef="R_AGMtex"/>
+          <groups:member groups:name="Choline transport via diffusion (extracellular to periplasm)" groups:idRef="R_CHLtex"/>
+          <groups:member groups:name="2-O-alpha-mannosyl-D-glycerate transport via diffusion (extracellular to periplasm)" groups:idRef="R_MANGLYCtex"/>
+          <groups:member groups:name="Ethanol transport via diffusion (extracellular to periplasm)" groups:idRef="R_ETOHtex"/>
+          <groups:member groups:name="Methanol transport via diffusion (extracellular to periplasm)" groups:idRef="R_MEOHtex"/>
+          <groups:member groups:name="XMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_XMPtex"/>
+          <groups:member groups:name="23cCMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_23CCMPtex"/>
+          <groups:member groups:name="Fructose 6-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_F6Ptex"/>
+          <groups:member groups:name="L-xylulose transport via diffusion (extracellular to periplasm)" groups:idRef="R_XYLUtex"/>
+          <groups:member groups:name="Biotin transport via diffusion (extracellular to periplasm)" groups:idRef="R_BTNtex"/>
+          <groups:member groups:name="D-glucarate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLCRtex"/>
+          <groups:member groups:name="Xanthosine transport via diffusion (extracellular to periplasm)" groups:idRef="R_XTSNtex"/>
+          <groups:member groups:name="Phenethylamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_PEAMNtex"/>
+          <groups:member groups:name="Urea transport via diffusion (extracellular to periplasm)" groups:idRef="R_UREAtex"/>
           <groups:member groups:name="Lactose transport via diffusion (extracellular to periplasm)" groups:idRef="R_LCTStex"/>
-          <groups:member groups:name="Nickel transport via diffusion (extracellular to periplasm)" groups:idRef="R_NI2tex"/>
-          <groups:member groups:name="GTP transport via diffusion (extracellular to periplasm)" groups:idRef="R_GTPtex"/>
-          <groups:member groups:name="Hexanoate transport via diffusion (extracellular to periplasm)" groups:idRef="R_HXAtex"/>
-          <groups:member groups:name="IMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_IMPtex"/>
-          <groups:member groups:name="2-dehydro-3-deoxy-D-gluconate transport via diffusion (extracellular to periplasm)" groups:idRef="R_DDGLCNtex"/>
-          <groups:member groups:name="Iron (II) transport via diffusion (extracellular to periplasm)" groups:idRef="R_FE2tex"/>
-          <groups:member groups:name="Ammonia transport via diffusion (extracellular to periplasm)" groups:idRef="R_NH4tex"/>
-          <groups:member groups:name="3GMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_3GMPtex"/>
-          <groups:member groups:name="3UMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_3UMPtex"/>
-          <groups:member groups:name="N-Acetyl-D-glucosamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACGAtex"/>
-          <groups:member groups:name="L-aspartate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ASPtex"/>
-          <groups:member groups:name="Cytidine transport via diffusion (extracellular to periplasm)" groups:idRef="R_CYTDtex"/>
-          <groups:member groups:name="D-Malate transport via diffusion (extracellular to periplasm)" groups:idRef="R_MALDtex"/>
+          <groups:member groups:name="Adenine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ADEtex"/>
+          <groups:member groups:name="Sucrose transport transport via diffusion (extracellular to periplasm)" groups:idRef="R_SUCRtex"/>
+          <groups:member groups:name="Dopamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_DOPAtex"/>
+          <groups:member groups:name="Potassium transport via diffusion (extracellular to periplasm)" groups:idRef="R_Ktex"/>
+          <groups:member groups:name="D-methionine transport via diffusion (extracellular to periplasm)" groups:idRef="R_METDtex"/>
+          <groups:member groups:name="Acetate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACtex"/>
+          <groups:member groups:name="Spermidine transport via diffusion (extracellular to periplasm)" groups:idRef="R_SPMDtex"/>
+          <groups:member groups:name="Thiosulfate transport via diffusion (extracellular to periplasm)" groups:idRef="R_TSULtex"/>
+          <groups:member groups:name="UDP-N-acetyl-D-glucosamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_UACGAMtex"/>
           <groups:member groups:name="D-alanyl-D-alanine (DalaDala) transport via diffusion (extracellular to periplasm)" groups:idRef="R_ALAALAtex"/>
-          <groups:member groups:name="Arbutin transport via diffusion (extracellular to periplasm)" groups:idRef="R_ARBTtex"/>
-          <groups:member groups:name="Beta-alanine transport via diffusion (extracellular to periplasm)" groups:idRef="R_BALAtex"/>
-          <groups:member groups:name="Gamma-butyrobetaine transport via diffusion (extracellular to periplasm)" groups:idRef="R_GBBTNtex"/>
-          <groups:member groups:name="L-histidine transport via diffusion (extracellular to periplasm)" groups:idRef="R_HIStex"/>
-          <groups:member groups:name="Thiocyanate transport via diffusion (extracellular to periplasm)" groups:idRef="R_TCYNTtex"/>
-          <groups:member groups:name="N-acetyl-D-galactosamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACGALtex"/>
-          <groups:member groups:name="Fructoselysine transporter via diffusion (extracellular)" groups:idRef="R_FRULYStex"/>
-          <groups:member groups:name="Glycolate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYCLTtex"/>
-          <groups:member groups:name="L-arginine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ARGtex"/>
-          <groups:member groups:name="L-asparagine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ASNtex"/>
-          <groups:member groups:name="Dimethyl sulfoxide transport via diffusion (extracellular to periplasm)" groups:idRef="R_DMSOtex"/>
-          <groups:member groups:name="Galactitol transport via diffusion (extracellular to periplasm)" groups:idRef="R_GALTtex"/>
-          <groups:member groups:name="Melibiose transport via diffusion (extracellular to periplasm)" groups:idRef="R_MELIBtex"/>
-          <groups:member groups:name="L-methionine transport via diffusion (extracellular to periplasm)" groups:idRef="R_METtex"/>
-          <groups:member groups:name="Glycine betaine transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYBtex"/>
-          <groups:member groups:name="L-alanyl-D-glutamate transport via diffusion (extracellular to periplasm)" groups:idRef="R_LALADGLUtex"/>
-          <groups:member groups:name="Nitrate transport via diffusion (extracellular to periplasm)" groups:idRef="R_NO3tex"/>
-          <groups:member groups:name="Allose transport via diffusion (extracellular to periplasm)" groups:idRef="R_ALLtex"/>
-          <groups:member groups:name="L-alanine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ALAtex"/>
+          <groups:member groups:name="D-carnitine transport via diffusion (extracellular to periplasm)" groups:idRef="R_CRNDtex"/>
           <groups:member groups:name="Beta D-galactose transport via diffusion (extracellular to periplasm)" groups:idRef="R_GALBDtex"/>
-          <groups:member groups:name="L-alanyl-L-glutamate transport via diffusion (extracellular to periplasm)" groups:idRef="R_LALALGLUtex"/>
-          <groups:member groups:name="SO2 transport via diffusion (extracellular to periplasm)" groups:idRef="R_SO2tex"/>
+          <groups:member groups:name="Hexanoate transport via diffusion (extracellular to periplasm)" groups:idRef="R_HXAtex"/>
+          <groups:member groups:name="Proton transport via diffusion (extracellular to periplasm)" groups:idRef="R_Htex"/>
+          <groups:member groups:name="Nickel transport via diffusion (extracellular to periplasm)" groups:idRef="R_NI2tex"/>
+          <groups:member groups:name="3CMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_3CMPtex"/>
+          <groups:member groups:name="Butyrate transport via diffusion (extracellular to periplasm)" groups:idRef="R_BUTtex"/>
+          <groups:member groups:name="CMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_CMPtex"/>
+          <groups:member groups:name="(R)-Propane-1,2-diol transport via diffusion (extracellular to periplasm)" groups:idRef="R_12PPDRtex"/>
+          <groups:member groups:name="Cytosine transport via diffusion (extracellular to periplasm)" groups:idRef="R_CSNtex"/>
+          <groups:member groups:name="D-galactose 1-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GAL1Ptex"/>
+          <groups:member groups:name="Ethanolamine transport via diffusion (extracellular)" groups:idRef="R_ETHAtex"/>
+          <groups:member groups:name="Fructoselysine transporter via diffusion (extracellular)" groups:idRef="R_FRULYStex"/>
+          <groups:member groups:name="D-galactose transport via diffusion (extracellular to periplasm)" groups:idRef="R_GALtex"/>
+          <groups:member groups:name="Cyanide transport via diffusion (extracellular to periplasm)" groups:idRef="R_CYANtex"/>
+          <groups:member groups:name="DCMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_DCMPtex"/>
+          <groups:member groups:name="D-fructuronate transport via diffusion (extracellular)" groups:idRef="R_FRUURtex"/>
+          <groups:member groups:name="D-glucose 1-phosphate transport via diffusion" groups:idRef="R_G1Ptex"/>
+          <groups:member groups:name="L-glutamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLNtex"/>
+          <groups:member groups:name="GMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_GMPtex"/>
+          <groups:member groups:name="Glucose 6-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_G6Ptex"/>
+          <groups:member groups:name="D-Malate transport via diffusion (extracellular to periplasm)" groups:idRef="R_MALDtex"/>
+          <groups:member groups:name="Minocycline transport via diffusion (extracellular to periplasm)" groups:idRef="R_MINCYCtex"/>
+          <groups:member groups:name="Phenethylacetaldehyde transport via diffusion (extracellular to periplasm)" groups:idRef="R_PACALDtex"/>
           <groups:member groups:name="Succinate transport via diffusion (extracellular to periplasm)" groups:idRef="R_SUCCtex"/>
-          <groups:member groups:name="Sulfoaceate transport via diffusion (extracellular to periplasm)" groups:idRef="R_SULFACtex"/>
-          <groups:member groups:name="Tyramine transport via diffusion (extracellular to periplasm)" groups:idRef="R_TYMtex"/>
-          <groups:member groups:name="L-tryptophan transport via diffusion (extracellular to periplasm)" groups:idRef="R_TRPtex"/>
-          <groups:member groups:name="Xanthine transport via diffusion (extracellular to periplasm)" groups:idRef="R_XANtex"/>
-          <groups:member groups:name="UDP-D-glucuronate transport via diffusion (extracellular to periplasm)" groups:idRef="R_UDPGLCURtex"/>
-          <groups:member groups:name="Biotin transport via diffusion (extracellular to periplasm)" groups:idRef="R_BTNtex"/>
-          <groups:member groups:name="Mercury (Hg+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_HG2tex"/>
-          <groups:member groups:name="D-glucosamine 6-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GAMAN6Ptex"/>
-          <groups:member groups:name="L-galactonate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GALCTNLtex"/>
-          <groups:member groups:name="Putrescine transport via diffusion (extracellular to periplasm)" groups:idRef="R_PTRCtex"/>
-          <groups:member groups:name="Copper (Cu+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_CU2tex"/>
-          <groups:member groups:name="XMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_XMPtex"/>
+          <groups:member groups:name="Taurine transport via diffusion (extracellular to periplasm)" groups:idRef="R_TAURtex"/>
+          <groups:member groups:name="Trimethylamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_TMAtex"/>
+          <groups:member groups:name="Sulfate transport via diffusion (extracellular to periplasm)" groups:idRef="R_SO4tex"/>
+          <groups:member groups:name="UMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_UMPtex"/>
+          <groups:member groups:name="L-homoserine transport via diffusion (extracellular to periplasm)" groups:idRef="R_HOMtex"/>
           <groups:member groups:name="L-valine transport via diffusion (extracellular to periplasm)" groups:idRef="R_VALtex"/>
-          <groups:member groups:name="D-fructose transport via diffusion (extracellular to periplasm)" groups:idRef="R_FRUtex"/>
+          <groups:member groups:name="Glycero-3-phospho-1-inositol transport via diffusion (extracellular to periplasm)" groups:idRef="R_G3PItex"/>
+          <groups:member groups:name="L-galactonate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GALCTNLtex"/>
           <groups:member groups:name="Phopho-L-tyrosine transport via diffusion (extracellular to periplasm)" groups:idRef="R_TYRPtex"/>
-          <groups:member groups:name="Ribose 5-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_R5Ptex"/>
-          <groups:member groups:name="Uric acid transport" groups:idRef="R_URATEtex"/>
-          <groups:member groups:name="Meso-2,6-Diaminoheptanedioate transport via diffusion (extracellular to periplasm)" groups:idRef="R_26DAHtex"/>
-          <groups:member groups:name="Adenine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ADEtex"/>
-          <groups:member groups:name="Glycerophoglycerol transport via diffusion (extracellular to periplasm)" groups:idRef="R_G3PGtex"/>
-          <groups:member groups:name="Alpha-ketoglutarate transport via diffusion (extracellular to periplasm)" groups:idRef="R_AKGtex"/>
-          <groups:member groups:name="Dimethyl sulfide transport via diffusion (extracellular to periplasm)" groups:idRef="R_DMStex"/>
-          <groups:member groups:name="Cadmium (Cd+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_CD2tex"/>
-          <groups:member groups:name="L-methionine S-oxide diffusion (extracellular)" groups:idRef="R_METSOX1tex"/>
-          <groups:member groups:name="GMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_GMPtex"/>
-          <groups:member groups:name="23cCMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_23CCMPtex"/>
-          <groups:member groups:name="Pyridoxal transport via diffusion (extracellular)" groups:idRef="R_PYDXtex"/>
-          <groups:member groups:name="Glycerol-3-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYC3Ptex"/>
-          <groups:member groups:name="Nicotinic acid transport via diffusion (extracellular to periplasm)" groups:idRef="R_NACtex"/>
-          <groups:member groups:name="Trimethylamine N-oxide transport via diffusion (extracellular to periplasm)" groups:idRef="R_TMAOtex"/>
-          <groups:member groups:name="Malate transport via diffusion (extracellular to periplasm)" groups:idRef="R_MALtex"/>
-          <groups:member groups:name="Thiamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_THMtex"/>
-          <groups:member groups:name="Fluoride transport via diffusion" groups:idRef="R_Ftex"/>
-          <groups:member groups:name="Thymidine transport via diffusion (extracellular to periplasm)" groups:idRef="R_THMDtex"/>
-          <groups:member groups:name="Glycine transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYtex"/>
-          <groups:member groups:name="Manganese (Mn+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_MNtex"/>
-          <groups:member groups:name="L-tyrosine transport via diffusion (extracellular to periplasm)" groups:idRef="R_TYRtex"/>
-          <groups:member groups:name="(R)-Propane-1,2-diol transport via diffusion (extracellular to periplasm)" groups:idRef="R_12PPDRtex"/>
-          <groups:member groups:name="2,3-diaminopropionate transport via diffusion" groups:idRef="R_23DAPPAtex"/>
-          <groups:member groups:name="Superoxide anion transport via diffusion (extracellular to periplasm)" groups:idRef="R_O2Stex"/>
+          <groups:member groups:name="L-histidine transport via diffusion (extracellular to periplasm)" groups:idRef="R_HIStex"/>
+          <groups:member groups:name="1,5-Diaminopentane transport via diffusion (extracellular to periplasm)" groups:idRef="R_DAPtex"/>
           <groups:member groups:name="Phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_PItex"/>
-          <groups:member groups:name="Phenethylacetaldehyde transport via diffusion (extracellular to periplasm)" groups:idRef="R_PACALDtex"/>
-          <groups:member groups:name="D-xylonate transport via diffusion (extracellular)" groups:idRef="R_DXYLONtex"/>
-          <groups:member groups:name="Potassium transport via diffusion (extracellular to periplasm)" groups:idRef="R_Ktex"/>
+          <groups:member groups:name="Hypoxanthine transport via diffusion (extracellular to periplasm)" groups:idRef="R_HYXNtex"/>
+          <groups:member groups:name="Shikimate transport via diffusion (extracellular to periplasm)" groups:idRef="R_SKMtex"/>
+          <groups:member groups:name="NMN transport via diffusion (extracellular to periplasm)" groups:idRef="R_NMNtex"/>
+          <groups:member groups:name="N-acetyl-D-mannosamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACMANAtex"/>
+          <groups:member groups:name="D-tartrate transport via diffusion (extracellular to periplasm)" groups:idRef="R_TARTRDtex"/>
+          <groups:member groups:name="Tungstate transport via diffusion (extracellular to periplasm)" groups:idRef="R_TUNGStex"/>
           <groups:member groups:name="Trehalose transport via diffusion (extracellular to periplasm)" groups:idRef="R_TREtex"/>
-          <groups:member groups:name="Ethanesulfonate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ETHSO3tex"/>
-          <groups:member groups:name="Octanoate transport via diffusion (extracellular to periplasm)" groups:idRef="R_OCTAtex"/>
-          <groups:member groups:name="L-methionine R-oxide diffusion (extracellular)" groups:idRef="R_METSOX2tex"/>
-          <groups:member groups:name="D-glycerate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYCAtex"/>
-          <groups:member groups:name="L cystine transport via diffusion extracellular to periplasm" groups:idRef="R_CYSItex"/>
-          <groups:member groups:name="Guanosine transport via diffusion (extracellular to periplasm)" groups:idRef="R_GSNtex"/>
-          <groups:member groups:name="Nitrious oxide transport via diffusion (extracellular to periplasm)" groups:idRef="R_N2Otex"/>
-          <groups:member groups:name="D-xylose transport via diffusion (extracellular to periplasm)" groups:idRef="R_XYLtex"/>
+          <groups:member groups:name="23cUMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_23CUMPtex"/>
           <groups:member groups:name="(S)-Propane-1,2-diol transport via diffusion (extracellular to periplasm)" groups:idRef="R_12PPDStex"/>
-          <groups:member groups:name="Glucose transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLCtex_copy2"/>
-          <groups:member groups:name="LalaDgluMdapDala (pentapeptide) transport via diffusion (extracellular to periplasm)" groups:idRef="R_4PEPTtex"/>
-          <groups:member groups:name="D-galactarte transport via diffusion (extracellular to periplasm)" groups:idRef="R_GALCTtex"/>
-          <groups:member groups:name="Dihydroxyacetone transport via diffusion (extracellular to periplasm)" groups:idRef="R_DHAtex"/>
-          <groups:member groups:name="Ethanol transport via diffusion (extracellular to periplasm)" groups:idRef="R_ETOHtex"/>
           <groups:member groups:name="Formaldehyde transport via diffusion (extracellular to periplasm)" groups:idRef="R_FALDtex"/>
-          <groups:member groups:name="AMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_AMPtex"/>
-          <groups:member groups:name="D-fructuronate transport via diffusion (extracellular)" groups:idRef="R_FRUURtex"/>
-          <groups:member groups:name="DCMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_DCMPtex"/>
-          <groups:member groups:name="Fusidic acid transport via diffusion (extracellular to periplasm)" groups:idRef="R_FUSAtex"/>
-          <groups:member groups:name="Glutathione (ox) transport via diffusion (extracellular to periplasm)" groups:idRef="R_GTHOXtex"/>
-          <groups:member groups:name="D-Alanine transport via diffusion (extracellular to periplasm)" groups:idRef="R_DALAtex"/>
-          <groups:member groups:name="D-glucuronate 1-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLCUR1Ptex"/>
-          <groups:member groups:name="2-O-alpha-mannosyl-D-glycerate transport via diffusion (extracellular to periplasm)" groups:idRef="R_MANGLYCtex"/>
+          <groups:member groups:name="Thymine transport via diffusion (extracellular to periplasm)" groups:idRef="R_THYMtex"/>
           <groups:member groups:name="4-hydroxyphenylacetaldehyde transport via diffusion (extracellular to periplasm)" groups:idRef="R_4HOXPACDtex"/>
-          <groups:member groups:name="D-carnitine transport via diffusion (extracellular to periplasm)" groups:idRef="R_CRNDtex"/>
+          <groups:member groups:name="L-aspartate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ASPtex"/>
+          <groups:member groups:name="Doxorubicin transport via diffusion (extracellular to periplasm)" groups:idRef="R_DOXRBCNtex"/>
+          <groups:member groups:name="Glycerophoglycerol transport via diffusion (extracellular to periplasm)" groups:idRef="R_G3PGtex"/>
+          <groups:member groups:name="L-leucine transport via diffusion (extracellular to periplasm)" groups:idRef="R_LEUtex"/>
+          <groups:member groups:name="L-alanyl-D-glutamate transport via diffusion (extracellular to periplasm)" groups:idRef="R_LALADGLUtex"/>
+          <groups:member groups:name="Tartrate transport via diffusion (extracellular to periplasm)" groups:idRef="R_TARTRtex"/>
+          <groups:member groups:name="Chloramphenicol transport via diffusion (extracellular to periplasm)" groups:idRef="R_CMtex"/>
+          <groups:member groups:name="L-methionine transport via diffusion (extracellular to periplasm)" groups:idRef="R_METtex"/>
+          <groups:member groups:name="Ornithine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ORNtex"/>
+          <groups:member groups:name="3GMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_3GMPtex"/>
+          <groups:member groups:name="Chitobiose transport via diffusion (extracellular to periplasm)" groups:idRef="R_CHTBStex"/>
+          <groups:member groups:name="Nitric oxide transport via diffusion (extracellular to periplasm)" groups:idRef="R_NOtex"/>
           <groups:member groups:name="Ribose transport via diffusion (extracellular to periplasm)" groups:idRef="R_RIBtex"/>
-          <groups:member groups:name="Pantothenate transport via diffusion (extracellular to periplasm)" groups:idRef="R_PNTOtex"/>
-          <groups:member groups:name="Selenate transport via diffusion (extracellular to periplasm)" groups:idRef="R_SELtex"/>
-          <groups:member groups:name="Urea transport via diffusion (extracellular to periplasm)" groups:idRef="R_UREAtex"/>
-          <groups:member groups:name="3-hydroxypropionate transport via diffusion (extracellular to periplasm)" groups:idRef="R_3HPPtex"/>
+          <groups:member groups:name="SO2 transport via diffusion (extracellular to periplasm)" groups:idRef="R_SO2tex"/>
+          <groups:member groups:name="D-lactate transport via diffusion (extracellular to periplasm)" groups:idRef="R_D_LACtex"/>
+          <groups:member groups:name="Mannose 6-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_MAN6Ptex"/>
+          <groups:member groups:name="UDPgalactose transport via diffusion (extracellular to periplasm)" groups:idRef="R_UDPGALtex"/>
           <groups:member groups:name="Acetaldehyde transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACALDtex"/>
-          <groups:member groups:name="GlcNAc-anhMurNAc transport via diffusion (extracellular to periplasm)" groups:idRef="R_ANHGMtex"/>
-          <groups:member groups:name="L-lysine transport via diffusion (extracellular to periplasm)" groups:idRef="R_LYStex"/>
-          <groups:member groups:name="Nitric oxide transport via diffusion (extracellular to periplasm)" groups:idRef="R_NOtex"/>
+          <groups:member groups:name="Formate transport via diffusion (extracellular to periplasm)" groups:idRef="R_FORtex"/>
+          <groups:member groups:name="H2s transport via diffusion (extracellular to periplasm)" groups:idRef="R_H2Stex"/>
+          <groups:member groups:name="Copper (Cu+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_CU2tex"/>
+          <groups:member groups:name="Mannitol transport via diffusion (extracellular to periplasm)" groups:idRef="R_MNLtex"/>
+          <groups:member groups:name="Superoxide anion transport via diffusion (extracellular to periplasm)" groups:idRef="R_O2Stex"/>
+          <groups:member groups:name="N-Acetyl-D-glucosamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACGAtex"/>
+          <groups:member groups:name="GDP transport via diffusion (extracellular to periplasm)" groups:idRef="R_GDPtex"/>
+          <groups:member groups:name="Glutathione transport via diffusion (extracellular to periplasm)" groups:idRef="R_GTHRDtex"/>
+          <groups:member groups:name="L-arabinose transport via diffusion (extracellular to periplasm)" groups:idRef="R_ARBtex"/>
+          <groups:member groups:name="Inositol transport via diffusion (extracellular to periplasm)" groups:idRef="R_INSTtex"/>
+          <groups:member groups:name="D-sorbitol transport via diffusion (extracellular to periplasm)" groups:idRef="R_SBTtex"/>
+          <groups:member groups:name="LalaDgluMdap (tripeptide) transport via diffusion (extracellular to periplasm)" groups:idRef="R_3PEPTtex"/>
+          <groups:member groups:name="Glycero-3-phosphoethanolamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_G3PEtex"/>
+          <groups:member groups:name="Uracil transport via diffusion (extracellular to periplasm)" groups:idRef="R_URAtex"/>
+          <groups:member groups:name="D-mannose transport via diffusion (extracellular to periplasm)" groups:idRef="R_MANtex"/>
+          <groups:member groups:name="UDP-D-glucuronate transport via diffusion (extracellular to periplasm)" groups:idRef="R_UDPGLCURtex"/>
+          <groups:member groups:name="Nicotinic acid transport via diffusion (extracellular to periplasm)" groups:idRef="R_NACtex"/>
+          <groups:member groups:name="Phospho-L-serine transport via diffusion (extracellular to periplasm)" groups:idRef="R_PSERtex"/>
+          <groups:member groups:name="Pyridoxamine transport via diffusion (extracellular)" groups:idRef="R_PYDAMtex"/>
+          <groups:member groups:name="UDPglucose transport via diffusion (extracellular to periplasm)" groups:idRef="R_UDPGtex"/>
+          <groups:member groups:name="23cGMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_23CGMPtex"/>
+          <groups:member groups:name="Allantoin transport via diffusion (extracellular to periplasm)" groups:idRef="R_ALLTNtex"/>
+          <groups:member groups:name="Isethionate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ISETACtex"/>
+          <groups:member groups:name="GTP transport via diffusion (extracellular to periplasm)" groups:idRef="R_GTPtex"/>
+          <groups:member groups:name="Malate transport via diffusion (extracellular to periplasm)" groups:idRef="R_MALtex"/>
+          <groups:member groups:name="Ammonia transport via diffusion (extracellular to periplasm)" groups:idRef="R_NH4tex"/>
+          <groups:member groups:name="Meso-2,6-Diaminoheptanedioate transport via diffusion (extracellular to periplasm)" groups:idRef="R_26DAHtex"/>
+          <groups:member groups:name="Dihydroxyacetone transport via diffusion (extracellular to periplasm)" groups:idRef="R_DHAtex"/>
+          <groups:member groups:name="D-xylonate transport via diffusion (extracellular)" groups:idRef="R_DXYLONtex"/>
+          <groups:member groups:name="Zinc (Zn+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_Zn2tex"/>
+          <groups:member groups:name="Cobalt (Co+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_COBALT2tex"/>
+          <groups:member groups:name="L-cysteine transport via diffusion (extracellular to periplasm)" groups:idRef="R_CYStex"/>
+          <groups:member groups:name="D-galactarte transport via diffusion (extracellular to periplasm)" groups:idRef="R_GALCTtex"/>
+          <groups:member groups:name="Arbutin transport via diffusion (extracellular to periplasm)" groups:idRef="R_ARBTtex"/>
+          <groups:member groups:name="Cadmium (Cd+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_CD2tex"/>
+          <groups:member groups:name="Iron (III) transport via diffusion (extracellular to periplasm)" groups:idRef="R_FE3tex"/>
+          <groups:member groups:name="Arsenite transport via diffusion (extracellular to periplasm)" groups:idRef="R_ASO3tex"/>
+          <groups:member groups:name="L-carnitine transport via diffusion (extracellular to periplasm)" groups:idRef="R_CRNtex"/>
+          <groups:member groups:name="IMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_IMPtex"/>
+          <groups:member groups:name="Fusidic acid transport via diffusion (extracellular to periplasm)" groups:idRef="R_FUSAtex"/>
+          <groups:member groups:name="D-glucuronat transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLCURtex"/>
+          <groups:member groups:name="Pyridoxine transport via diffusion (extracellular)" groups:idRef="R_PYDXNtex"/>
+          <groups:member groups:name="Glycerophosphserine transport via diffusion (extracellular to periplasm)" groups:idRef="R_G3PStex"/>
+          <groups:member groups:name="Propanal transport via diffusion (extracellular to periplasm)" groups:idRef="R_PPALtex"/>
+          <groups:member groups:name="L-rhamnose transport via diffusion (extracellular to periplasm)" groups:idRef="R_RMNtex"/>
+          <groups:member groups:name="Uric acid transport" groups:idRef="R_URATEtex"/>
+          <groups:member groups:name="Xanthine transport via diffusion (extracellular to periplasm)" groups:idRef="R_XANtex"/>
+          <groups:member groups:name="Sulfite transport via diffusion (extracellular to periplasm)" groups:idRef="R_SO3tex"/>
+          <groups:member groups:name="L-arginine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ARGtex"/>
+          <groups:member groups:name="3-hydroxycinnamic acid transport via diffusion (extracellular to periplasm)" groups:idRef="R_HCINNMtex"/>
+          <groups:member groups:name="Nitrite transport via diffusion (extracellular to periplasm)" groups:idRef="R_NO2tex"/>
+          <groups:member groups:name="DTMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_DTMPtex"/>
+          <groups:member groups:name="D-Alanine transport via diffusion (extracellular to periplasm)" groups:idRef="R_DALAtex"/>
+          <groups:member groups:name="Tetracycline transport via diffusion (extracellular to periplasm)" groups:idRef="R_TTRCYCtex"/>
+          <groups:member groups:name="Dihydroxyphenylacetaldehyde transport via diffusion (extracellular to periplasm)" groups:idRef="R_34dhpactex"/>
+          <groups:member groups:name="Orotate transport via diffusion (extracellular to periplasm)" groups:idRef="R_OROTtex"/>
+          <groups:member groups:name="Pseudouridine transport via diffusion (extracellular to periplasm)" groups:idRef="R_PSURItex"/>
+          <groups:member groups:name="3AMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_3AMPtex"/>
+          <groups:member groups:name="N-acetyl-D-glucosamine 1-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACGAM1Ptex"/>
+          <groups:member groups:name="Beta-alanine transport via diffusion (extracellular to periplasm)" groups:idRef="R_BALAtex"/>
+          <groups:member groups:name="Deoxyguanosine transport via diffusion (extracellular to periplasm)" groups:idRef="R_DGSNtex"/>
+          <groups:member groups:name="D-glucosamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_GAMtex"/>
+          <groups:member groups:name="Methanesulfonate transport via diffusion (extracellular to periplasm)" groups:idRef="R_MSO3tex"/>
+          <groups:member groups:name="3UMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_3UMPtex"/>
+          <groups:member groups:name="AMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_AMPtex"/>
+          <groups:member groups:name="Mercury (Hg+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_HG2tex"/>
+          <groups:member groups:name="Guanosine transport via diffusion (extracellular to periplasm)" groups:idRef="R_GSNtex"/>
           <groups:member groups:name="L-phenylalanine transport via diffusion (extracellular to periplasm)" groups:idRef="R_PHEtex"/>
-          <groups:member groups:name="Citrate transport via diffusion (extracellular to periplasm)" groups:idRef="R_CITtex"/>
-          <groups:member groups:name="D-lactate transport via diffusion (extracellular to periplasm)" groups:idRef="R_D_LACtex"/>
+          <groups:member groups:name="Propionate transport via diffusion" groups:idRef="R_PPAtex"/>
+          <groups:member groups:name="D-gluconate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLCNtex"/>
+          <groups:member groups:name="Melibiose transport via diffusion (extracellular to periplasm)" groups:idRef="R_MELIBtex"/>
           <groups:member groups:name="3-phenylpropionate transport via diffusion (extracellular to periplasm)" groups:idRef="R_PPPNtex"/>
-          <groups:member groups:name="D-glucosamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_GAMtex"/>
-          <groups:member groups:name="L-proline transport via diffusion (extracellular to periplasm)" groups:idRef="R_PROtex"/>
-          <groups:member groups:name="Trimethylamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_TMAtex"/>
+          <groups:member groups:name="L-asparagine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ASNtex"/>
           <groups:member groups:name="DGMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_DGMPtex"/>
-          <groups:member groups:name="L-xylulose transport via diffusion (extracellular to periplasm)" groups:idRef="R_XYLUtex"/>
-          <groups:member groups:name="Butanesulfonate transport via diffusion (extracellular to periplasm)" groups:idRef="R_BUTSO3tex"/>
-          <groups:member groups:name="Chloride (Cl-1) transport via diffusion (extracellular to periplasm)" groups:idRef="R_CLtex"/>
-          <groups:member groups:name="Proton transport via diffusion (extracellular to periplasm)" groups:idRef="R_Htex"/>
-          <groups:member groups:name="5-Dehydro-D-gluconate transport via diffusion (extracellular to periplasm)" groups:idRef="R_5DGLCNtex"/>
-          <groups:member groups:name="3-(3-hydroxyphenyl)propionate transport via diffusion (extracellular to periplasm)" groups:idRef="R_HPPPNtex"/>
-          <groups:member groups:name="L-Lyxose transport via diffusion (extracellular to periplasm)" groups:idRef="R_LYXtex"/>
           <groups:member groups:name="Glycero-3-phosphocholine transport via diffusion (extracellular to periplasm)" groups:idRef="R_G3PCtex"/>
-          <groups:member groups:name="Glycerol-2-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYC2Ptex"/>
-          <groups:member groups:name="Pseudouridine transport via diffusion (extracellular to periplasm)" groups:idRef="R_PSURItex"/>
+          <groups:member groups:name="Citrate transport via diffusion (extracellular to periplasm)" groups:idRef="R_CITtex"/>
           <groups:member groups:name="Fumarate transport via diffusion (extracellular to periplasm)" groups:idRef="R_FUMtex"/>
-          <groups:member groups:name="Isethionate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ISETACtex"/>
-          <groups:member groups:name="Sulfite transport via diffusion (extracellular to periplasm)" groups:idRef="R_SO3tex"/>
-          <groups:member groups:name="5-Methylthio-D-ribose transport via proton diffusion (extracellular to periplasm)" groups:idRef="R_5MTRtex"/>
-          <groups:member groups:name="Decanoate transport via diffusion (extracellular to periplasm)" groups:idRef="R_DCAtex"/>
-          <groups:member groups:name="Hypoxanthine transport via diffusion (extracellular to periplasm)" groups:idRef="R_HYXNtex"/>
-          <groups:member groups:name="3-hydroxycinnamic acid transport via diffusion (extracellular to periplasm)" groups:idRef="R_HCINNMtex"/>
-          <groups:member groups:name="Magnesium (Mg+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_MG2tex"/>
           <groups:member groups:name="Sodium transport via diffusion (extracellular to periplasm)" groups:idRef="R_NAtex"/>
-          <groups:member groups:name="Mannitol transport via diffusion (extracellular to periplasm)" groups:idRef="R_MNLtex"/>
-          <groups:member groups:name="L-Prolinylglycine transport via diffusion (extracellular to periplasm)" groups:idRef="R_PROGLYtex"/>
-          <groups:member groups:name="Xanthosine transport via diffusion (extracellular to periplasm)" groups:idRef="R_XTSNtex"/>
-          <groups:member groups:name="Cyanide transport via diffusion (extracellular to periplasm)" groups:idRef="R_CYANtex"/>
-          <groups:member groups:name="Glycerophosphserine transport via diffusion (extracellular to periplasm)" groups:idRef="R_G3PStex"/>
+          <groups:member groups:name="Alpha-ketoglutarate transport via diffusion (extracellular to periplasm)" groups:idRef="R_AKGtex"/>
+          <groups:member groups:name="Hydrogen transport via diffusion (extracellular to periplasm)" groups:idRef="R_H2tex"/>
+          <groups:member groups:name="Pyruvate transport via diffusion (extracellular to periplasm)" groups:idRef="R_PYRtex"/>
+          <groups:member groups:name="3-hydroxypropionate transport via diffusion (extracellular to periplasm)" groups:idRef="R_3HPPtex"/>
+          <groups:member groups:name="Glucose transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLCtex_copy2"/>
+          <groups:member groups:name="Hydrogen peroxide transport via diffusion (external)" groups:idRef="R_H2O2tex"/>
+          <groups:member groups:name="Chloride (Cl-1) transport via diffusion (extracellular to periplasm)" groups:idRef="R_CLtex"/>
+          <groups:member groups:name="2,3-diaminopropionate transport via diffusion" groups:idRef="R_23DAPPAtex"/>
+          <groups:member groups:name="O-Acetyl-L-serine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACSERtex"/>
+          <groups:member groups:name="GlcNAc-anhMurNAc transport via diffusion (extracellular to periplasm)" groups:idRef="R_ANHGMtex"/>
+          <groups:member groups:name="Butanesulfonate transport via diffusion (extracellular to periplasm)" groups:idRef="R_BUTSO3tex"/>
+          <groups:member groups:name="Calcium (Ca+2) transport via diffusion (extracellular to periplasm)" groups:idRef="R_CA2tex"/>
+          <groups:member groups:name="DUMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_DUMPtex"/>
           <groups:member groups:name="D-galactonate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GALCTNtex"/>
-          <groups:member groups:name="Allantoin transport via diffusion (extracellular to periplasm)" groups:idRef="R_ALLTNtex"/>
-          <groups:member groups:name="Deoxyinosine transport via diffusion (extracellular to periplasm)" groups:idRef="R_DINStex"/>
-          <groups:member groups:name="D-galactose 1-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GAL1Ptex"/>
-          <groups:member groups:name="Fructose 6-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_F6Ptex"/>
-          <groups:member groups:name="D-gluconate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLCNtex"/>
-          <groups:member groups:name="L-idonate transport via diffusion (extracellular to periplasm)" groups:idRef="R_IDONtex"/>
-          <groups:member groups:name="Arsenite transport via diffusion (extracellular to periplasm)" groups:idRef="R_ASO3tex"/>
-          <groups:member groups:name="D-galactose transport via diffusion (extracellular to periplasm)" groups:idRef="R_GALtex"/>
-          <groups:member groups:name="Indole transport via diffusion (extracellular to periplasm)" groups:idRef="R_INDOLEtex"/>
-          <groups:member groups:name="Chloramphenicol transport via diffusion (extracellular to periplasm)" groups:idRef="R_CMtex"/>
-          <groups:member groups:name="3AMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_3AMPtex"/>
-          <groups:member groups:name="N-acetyl-D-mannosamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACMANAtex"/>
+          <groups:member groups:name="L-glutamate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLUtex"/>
+          <groups:member groups:name="LalaDgluMdapDala (pentapeptide) transport via diffusion (extracellular to periplasm)" groups:idRef="R_4PEPTtex"/>
+          <groups:member groups:name="Glyceraldehyde transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYALDtex"/>
+          <groups:member groups:name="Glycolate transport via diffusion (extracellular to periplasm)" groups:idRef="R_GLYCLTtex"/>
+          <groups:member groups:name="N-acetyl-D-galactosamine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACGALtex"/>
+          <groups:member groups:name="2-dehydro-3-deoxy-D-gluconate transport via diffusion (extracellular to periplasm)" groups:idRef="R_DDGLCNtex"/>
+          <groups:member groups:name="Galactitol transport via diffusion (extracellular to periplasm)" groups:idRef="R_GALTtex"/>
+          <groups:member groups:name="Cytidine transport via diffusion (extracellular to periplasm)" groups:idRef="R_CYTDtex"/>
+          <groups:member groups:name="Gamma-butyrobetaine transport via diffusion (extracellular to periplasm)" groups:idRef="R_GBBTNtex"/>
+          <groups:member groups:name="L-proline transport via diffusion (extracellular to periplasm)" groups:idRef="R_PROtex"/>
+          <groups:member groups:name="L-isoleucine transport via diffusion (extracellular to periplasm)" groups:idRef="R_ILEtex"/>
+          <groups:member groups:name="DIMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_DIMPtex"/>
           <groups:member groups:name="DAMP transport via diffusion (extracellular to periplasm)" groups:idRef="R_DAMPtex"/>
-          <groups:member groups:name="Butyrate transport via diffusion (extracellular to periplasm)" groups:idRef="R_BUTtex"/>
-          <groups:member groups:name="Choline transport via diffusion (extracellular to periplasm)" groups:idRef="R_CHLtex"/>
-          <groups:member groups:name="LalaDgluMdap (tripeptide) transport via diffusion (extracellular to periplasm)" groups:idRef="R_3PEPTtex"/>
-          <groups:member groups:name="Agmatine transport via diffusion (extracellular to periplasm)" groups:idRef="R_AGMtex"/>
-          <groups:member groups:name="L-lactate transport via diffusion (extracellular to periplasm)" groups:idRef="R_L_LACtex"/>
-          <groups:member groups:name="Acetate transport via diffusion (extracellular to periplasm)" groups:idRef="R_ACtex"/>
-          <groups:member groups:name="Mannose 6-phosphate transport via diffusion (extracellular to periplasm)" groups:idRef="R_MAN6Ptex"/>
-          <groups:member groups:name="NMN transport via diffusion (extracellular to periplasm)" groups:idRef="R_NMNtex"/>
-          <groups:member groups:name="D-glucose 1-phosphate transport via diffusion" groups:idRef="R_G1Ptex"/>
-          <groups:member groups:name="Nitrite transport via diffusion (extracellular to periplasm)" groups:idRef="R_NO2tex"/>
-          <groups:member groups:name="Uracil transport via diffusion (extracellular to periplasm)" groups:idRef="R_URAtex"/>
-          <groups:member groups:name="D-cysteine transport via diffusion (extracellular to periplasm)" groups:idRef="R_CYSDtex"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group37" sboTerm="SBO:0000633" groups:id="G_group37" groups:name="Tyrosine, Tryptophan, and Phenylalanine Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
+          <groups:member groups:name="Prephenate dehydrogenase" groups:idRef="R_PPND"/>
+          <groups:member groups:name="3-dehydroquinate synthase" groups:idRef="R_DHQS"/>
           <groups:member groups:name="Tryptophanase (L-tryptophan)" groups:idRef="R_TRPAS2"/>
+          <groups:member groups:name="3-dehydroquinate dehydratase, irreversible" groups:idRef="R_DHQTi"/>
+          <groups:member groups:name="Prephenate dehydratase" groups:idRef="R_PPNDH"/>
+          <groups:member groups:name="Shikimate kinase" groups:idRef="R_SHKK"/>
+          <groups:member groups:name="Anthranilate phosphoribosyltransferase" groups:idRef="R_ANPRT"/>
+          <groups:member groups:name="Tryptophan synthase (indole)" groups:idRef="R_TRPS2"/>
           <groups:member groups:name="Indole-3-glycerol-phosphate synthase" groups:idRef="R_IGPS"/>
-          <groups:member groups:name="Quinate dehydrogenase" groups:idRef="R_QUINDH"/>
-          <groups:member groups:name="3-dehydroquinate synthase" groups:idRef="R_DHQS"/>
-          <groups:member groups:name="Phenylalanine transaminase" groups:idRef="R_PHETA1"/>
-          <groups:member groups:name="3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase" groups:idRef="R_DDPA"/>
+          <groups:member groups:name="Chorismate synthase" groups:idRef="R_CHORS"/>
           <groups:member groups:name="Phospho-L-tyrosine phosphatase (periplasmic)" groups:idRef="R_TYRPpp"/>
-          <groups:member groups:name="Tryptophan synthase (indoleglycerol phosphate)" groups:idRef="R_TRPS1"/>
-          <groups:member groups:name="Anthranilate synthase" groups:idRef="R_ANS"/>
           <groups:member groups:name="3-phosphoshikimate 1-carboxyvinyltransferase" groups:idRef="R_PSCVT"/>
           <groups:member groups:name="Quinate dehydrogenase (NADP)" groups:idRef="R_QUINDHyi"/>
-          <groups:member groups:name="Chorismate synthase" groups:idRef="R_CHORS"/>
+          <groups:member groups:name="Tryptophan synthase (indoleglycerol phosphate)" groups:idRef="R_TRPS1"/>
+          <groups:member groups:name="Tryptophan synthase (indoleglycerol phosphate)" groups:idRef="R_TRPS3"/>
+          <groups:member groups:name="Chorismate mutase" groups:idRef="R_CHORM"/>
           <groups:member groups:name="Phosphoribosylanthranilate isomerase (irreversible)" groups:idRef="R_PRAIi"/>
-          <groups:member groups:name="Shikimate kinase" groups:idRef="R_SHKK"/>
-          <groups:member groups:name="Anthranilate phosphoribosyltransferase" groups:idRef="R_ANPRT"/>
-          <groups:member groups:name="Tryptophan synthase (indole)" groups:idRef="R_TRPS2"/>
           <groups:member groups:name="Tyrosine transaminase" groups:idRef="R_TYRTA"/>
-          <groups:member groups:name="Chorismate mutase" groups:idRef="R_CHORM"/>
-          <groups:member groups:name="Prephenate dehydratase" groups:idRef="R_PPNDH"/>
-          <groups:member groups:name="3-dehydroquinate dehydratase, irreversible" groups:idRef="R_DHQTi"/>
+          <groups:member groups:name="Phenylalanine transaminase" groups:idRef="R_PHETA1"/>
           <groups:member groups:name="Acetyl-CoA:anthranilate acetyltransferase" groups:idRef="R_ACANTHAT"/>
           <groups:member groups:name="Shikimate dehydrogenase" groups:idRef="R_SHK3Dr"/>
-          <groups:member groups:name="Tryptophan synthase (indoleglycerol phosphate)" groups:idRef="R_TRPS3"/>
-          <groups:member groups:name="Prephenate dehydrogenase" groups:idRef="R_PPND"/>
+          <groups:member groups:name="Anthranilate synthase" groups:idRef="R_ANS"/>
+          <groups:member groups:name="3-deoxy-D-arabino-heptulosonate 7-phosphate synthetase" groups:idRef="R_DDPA"/>
+          <groups:member groups:name="Quinate dehydrogenase" groups:idRef="R_QUINDH"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group38" sboTerm="SBO:0000633" groups:id="G_group38" groups:name="Unassigned" groups:kind="partonomy">
         <groups:listOfMembers>
-          <groups:member groups:name="Apolipoprotein N-acyltransferase (phosphatidylethanolamine, periplasm)" groups:idRef="R_ALPATE160pp"/>
-          <groups:member groups:name="Uricase" groups:idRef="R_URIC"/>
+          <groups:member groups:name="Cyanide sulfurtransferase" groups:idRef="R_CYANST"/>
+          <groups:member groups:name="Aconitate isomerase (spontaneous)" groups:idRef="R_ACONIs"/>
+          <groups:member groups:name="Glutathione peridoxase" groups:idRef="R_GTHPi"/>
           <groups:member groups:name="Catalase" groups:idRef="R_CAT"/>
+          <groups:member groups:name="Uricase" groups:idRef="R_URIC"/>
+          <groups:member groups:name="Phosphonate hydrogenase (periplasm)" groups:idRef="R_PPTHpp"/>
           <groups:member groups:name="Superoxide dismutase" groups:idRef="R_SPODM"/>
           <groups:member groups:name="Choline dehydrogenase" groups:idRef="R_CHOLD"/>
-          <groups:member groups:name="NADH peroxidase" groups:idRef="R_NADHPO"/>
           <groups:member groups:name="Tellurite methyltransferase" groups:idRef="R_TEO2M"/>
-          <groups:member groups:name="Trans-aconitate methyltransferase" groups:idRef="R_ACONMT"/>
-          <groups:member groups:name="DsbG:glutathione thiotransferase" groups:idRef="R_DSBGGT"/>
           <groups:member groups:name="Betaine-aldehyde dehydrogenase" groups:idRef="R_BETALDHy"/>
-          <groups:member groups:name="Glutaredoxin reductase" groups:idRef="R_GRXR"/>
-          <groups:member groups:name="Superoxide dismutase" groups:idRef="R_SPODMpp"/>
-          <groups:member groups:name="Phosphonate hydrogenase (periplasm)" groups:idRef="R_PPTHpp"/>
-          <groups:member groups:name="DsbC:glutathione thiotransferase" groups:idRef="R_DSBCGT"/>
-          <groups:member groups:name="DsbA protein reoxidation reaction (anaerobic)" groups:idRef="R_DSBAO2"/>
-          <groups:member groups:name="Flavodoxin reductase (NADPH)" groups:idRef="R_FLDR2"/>
-          <groups:member groups:name="Selenophosphate synthase" groups:idRef="R_SELNPS"/>
+          <groups:member groups:name="Apolipoprotein N-acyltransferase (phosphatidylethanolamine, periplasm)" groups:idRef="R_ALPATE160pp"/>
           <groups:member groups:name="Apolipoprotein N-acyltransferase (phosphatidylglycerol, periplasm)" groups:idRef="R_ALPATG160pp"/>
-          <groups:member groups:name="DsbD reductase" groups:idRef="R_DSBDR"/>
-          <groups:member groups:name="Glutathione peridoxase" groups:idRef="R_GTHPi"/>
-          <groups:member groups:name="Aconitate isomerase (spontaneous)" groups:idRef="R_ACONIs"/>
+          <groups:member groups:name="DsbG:glutathione thiotransferase" groups:idRef="R_DSBGGT"/>
           <groups:member groups:name="HCO3 equilibration reaction" groups:idRef="R_HCO3E"/>
           <groups:member groups:name="Hydrogen peroxide reductase (thioredoxin)" groups:idRef="R_THIORDXi"/>
-          <groups:member groups:name="Cyanide sulfurtransferase" groups:idRef="R_CYANST"/>
           <groups:member groups:name="Betaine-aldehyde dehydrogenase" groups:idRef="R_BETALDHx"/>
+          <groups:member groups:name="Selenophosphate synthase" groups:idRef="R_SELNPS"/>
+          <groups:member groups:name="DsbC:glutathione thiotransferase" groups:idRef="R_DSBCGT"/>
           <groups:member groups:name="DsbA protein reoxidation reaction (aerobic)" groups:idRef="R_DSBAO1"/>
+          <groups:member groups:name="DsbA protein reoxidation reaction (anaerobic)" groups:idRef="R_DSBAO2"/>
+          <groups:member groups:name="Glutaredoxin reductase" groups:idRef="R_GRXR"/>
+          <groups:member groups:name="Trans-aconitate methyltransferase" groups:idRef="R_ACONMT"/>
+          <groups:member groups:name="Flavodoxin reductase (NADPH)" groups:idRef="R_FLDR2"/>
+          <groups:member groups:name="Superoxide dismutase" groups:idRef="R_SPODMpp"/>
+          <groups:member groups:name="DsbD reductase" groups:idRef="R_DSBDR"/>
+          <groups:member groups:name="NADH peroxidase" groups:idRef="R_NADHPO"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group39" sboTerm="SBO:0000633" groups:id="G_group39" groups:name="Valine, Leucine, and Isoleucine Metabolism" groups:kind="partonomy">
         <groups:listOfMembers>
+          <groups:member groups:name="Ketol-acid reductoisomerase (2,3-dihydroxy-3-methylbutanoate)" groups:idRef="R_KARA1"/>
+          <groups:member groups:name="2-aceto-2-hydroxybutanoate synthase" groups:idRef="R_ACHBS"/>
           <groups:member groups:name="3-isopropylmalate dehydratase" groups:idRef="R_IPPMIa"/>
-          <groups:member groups:name="Ketol-acid reductoisomerase (2-Acetolactate)" groups:idRef="R_KARA2"/>
-          <groups:member groups:name="Valine transaminase" groups:idRef="R_VALTA"/>
-          <groups:member groups:name="Isoleucine transaminase" groups:idRef="R_ILETA"/>
-          <groups:member groups:name="Acetolactate synthase" groups:idRef="R_ACLS"/>
-          <groups:member groups:name="2-Oxo-4-methyl-3-carboxypentanoate decarboxylation" groups:idRef="R_OMCDC"/>
           <groups:member groups:name="Leucine transaminase (irreversible)" groups:idRef="R_LEUTAi"/>
-          <groups:member groups:name="Ketol-acid reductoisomerase (2,3-dihydroxy-3-methylbutanoate)" groups:idRef="R_KARA1"/>
+          <groups:member groups:name="2-Oxo-4-methyl-3-carboxypentanoate decarboxylation" groups:idRef="R_OMCDC"/>
           <groups:member groups:name="L-threonine deaminase" groups:idRef="R_THRD_L"/>
-          <groups:member groups:name="Valine-pyruvate aminotransferase" groups:idRef="R_VPAMTr"/>
           <groups:member groups:name="3-isopropylmalate dehydrogenase" groups:idRef="R_IPMD"/>
+          <groups:member groups:name="Isoleucine transaminase" groups:idRef="R_ILETA"/>
           <groups:member groups:name="2-isopropylmalate hydratase" groups:idRef="R_IPPMIb"/>
-          <groups:member groups:name="2-isopropylmalate synthase" groups:idRef="R_IPPS"/>
-          <groups:member groups:name="2-aceto-2-hydroxybutanoate synthase" groups:idRef="R_ACHBS"/>
-          <groups:member groups:name="Dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylpentanoate)" groups:idRef="R_DHAD2"/>
+          <groups:member groups:name="Valine transaminase" groups:idRef="R_VALTA"/>
+          <groups:member groups:name="Valine-pyruvate aminotransferase" groups:idRef="R_VPAMTr"/>
+          <groups:member groups:name="Ketol-acid reductoisomerase (2-Acetolactate)" groups:idRef="R_KARA2"/>
           <groups:member groups:name="Dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylbutanoate)" groups:idRef="R_DHAD1"/>
+          <groups:member groups:name="Dihydroxy-acid dehydratase (2,3-dihydroxy-3-methylpentanoate)" groups:idRef="R_DHAD2"/>
+          <groups:member groups:name="Acetolactate synthase" groups:idRef="R_ACLS"/>
+          <groups:member groups:name="2-isopropylmalate synthase" groups:idRef="R_IPPS"/>
         </groups:listOfMembers>
       </groups:group>
       <groups:group metaid="meta_G_group40" sboTerm="SBO:0000633" groups:id="G_group40" groups:name="tRNA Charging" groups:kind="partonomy">
diff --git a/model/Ecoli-GEM.yml b/model/Ecoli-GEM.yml
index 76cae28..cb426e1 100644
--- a/model/Ecoli-GEM.yml
+++ b/model/Ecoli-GEM.yml
@@ -2,8 +2,8 @@
 - metaData:
     id: "Ecoli-GEM"
     name: "The Consensus Genome-Scale Metabolic Model of Escherichia coli"
-    date: "2025-06-11"
-    version: ""
+    date: "2025-09-01"
+    version: "0.2.0"
     github: "https://github.com/SysBioChalmers/Ecoli-GEM"
 - metabolites:
   - !!omap
@@ -73286,7 +73286,7 @@
       - mlthf_c: 1.0
       - ser__L_c: -1.0
       - thf_c: -1.0
-    - lower_bound: 0
+    - lower_bound: 0.0
     - upper_bound: 1000.0
     - gene_reaction_rule: b2551
     - subsystem: Glycine and Serine Metabolism
diff --git a/model/FROG/metadata.json b/model/FROG/metadata.json
index 3b5d105..7126830 100644
--- a/model/FROG/metadata.json
+++ b/model/FROG/metadata.json
@@ -1,5 +1,5 @@
 {
-  "frog_date": "2025-04-30",
+  "frog_date": "2025-09-05",
   "frog_version": "1.0",
   "frog_curators": [],
   "frog_software": {
@@ -18,6 +18,6 @@
     "url": null
   },
   "model_filename": "model.xml",
-  "model_md5": "4b4c4df0f6501e84bb8a1240d2bb33ff",
+  "model_md5": "bbc4716ae305623fbc8ae745329f4434",
   "environment": "posix, Linux, 5.4.0-200-generic"
 }
\ No newline at end of file
diff --git a/model/README.md b/model/README.md
index 4908cca..fc0b358 100644
--- a/model/README.md
+++ b/model/README.md
@@ -8,4 +8,4 @@ The model is available as `.xml`, `.xlsx`, `.txt`, `.yml`, and `.mat`. Note that
 
 ## FROG report
 
-A FROG report generated using https://runfrog.de/ on the SBML model file is available in the `FROG` folder. This folder contains `tsv` files detailing the results of the FROG analysis as well as a `json` file describing the metadata.
+A FROG report generated using https://runfrog.de/ on the SBML model file is available in the `FROG` folder. This folder contains `tsv` files detailing the results of the FROG analysis as well as a `json` file describing the metadata. The `frog.tsv` is skipped (as in, not versioned) because its content is already duplicated in the other files.
diff --git a/version.txt b/version.txt
index 77d6f4c..0ea3a94 100644
--- a/version.txt
+++ b/version.txt
@@ -1 +1 @@
-0.0.0
+0.2.0
