Selected organism

Reactions on models are mapped to KEGG and BioCyc databases, either to the entire database or to a subgroup that represents a specific organism.

Model	Selected organism on KEGG	Selected organism on BioCyc
e_coli_core	Entire database	MetaCyc (Tier 1)

Compartments

Model compartments are typically used to differentiate the extracellular from the intracellular environment, and can be used to further define intracellular compartments.

Model	Number of compartments
e_coli_core	2

Metabolites

Two sources are checked for finding synonyms: the "annotation" field of each metabolite in the SBML model, and, using the metabolite ID, the MNXref database is queried. The synonyms found using both methods are consolidated.

Model	Total	bigg	biocyc	cas	chebi	chemspider	drugbank	envipath	hmdb	inchi	inchi_key	kegg	knapsack	lipidmaps	metabolights	metacyc	metanetx	nci	pubchem	reactome	rhea	sabiork	seed	slm	No synonyms
e_coli_core	72	72	70	0	72	0	0	32	69	0	72	71	0	10	0	70	72	0	0	61	0	70	72	3	0

Reactions

Reactions Types

Reactions in the models are classified into six categories:
Metabolic reactions: convert internal metabolites into other internal metabolites. Examples: A(internal) <-> B(internal); A(internal) -> B(internal)
Exchange reactions: provide (or remove) metabolites to the extracellular compartment, simulating the external media. Examples: A (external) <-> NULL; NULL -> A (external)
Sink reactions: Similar to the exchange reactions, but the metabolites are made available directly in the intracellular compartment. Examples: A (internal) <-> NULL; NULL -> A (internal)
Transport reactions: responsible for the transport of metabolites across compartments. Examples: A (external) <-> A (internal); A (internal) -> A (external)
Demand reactions: Remove metabolites from the system. Example: A (internal) -> NULL
Deactivated reactions: can not carry flux because their minimum and maximum flux boundaries are set to zero.

Model	Total	Metabolic rxns	Exchange rxns	Sink rxns	Transport rxns	Demand rxns	Deactivated rxns
e_coli_core	95	50	7	0	25	13	0

Metabolic reactions blocked

Blocked reactions can not carry flux because the model cannot produce the reaction's substrate. It is dependent on the defined external media. The growth media in this analysis consists of: the default media in the model, plus all carbon, nitrogen, phosphorus, and sulfur media used in Biolog experiments.
e_coli_core: 0

Metabolic reactions synonyms on other databases

For finding synonyms for a reaction/enzyme, the reaction ID from every reaction is used to query the MNXref database, and synonyms on the “annotation” field are extracted.

Model	Total	bigg	biocyc	cas	chebi	chemspider	drugbank	envipath	hmdb	inchi	inchi_key	kegg	knapsack	lipidmaps	metabolights	metacyc	metanetx	nci	pubchem	reactome	rhea	sabiork	seed	slm	No synonyms
e_coli_core	50	50	38	0	0	0	0	0	0	0	0	46	0	0	0	33	50	0	0	19	46	40	46	0	0

The table below shows how reactions in the model maps with reactions and conversion steps on KEGG Pathway Modules. The result is divided into six categories for each module:
Organism expected: The number of processing steps in the database present in the model (completness of pathway). With mouse over: the reactions in the model mapped to KEGG, and the number of reactions.
Organism missing: The number of reactions in the database not present in the model. With mouse over: the reactions present in the model mapped to KEGG, and the number of reactions.
Unpredicted: for some organisms, the reference database expects only part of a module to be present. This category receives the number of processing steps present in the module, but not expected according to the database.
Entire module: Sum of 'Organism expected' and 'Unpredicted'.
Blocked: number of blocked reactions in pathway.
Essentials: number of essential reactions in pathway.
By clicking on the table's links, the KEGG reactions and metabolites present in the model are highlighted in a KEGG Module map.
Units used in the table: The entry "Annotated: 2 (67%)" can be read as "2 conversion steps (67% pathway completeness)". "Processing steps" is usually equivalent to "reactions". However, in some cases, different reactions, or a combination of reactions, can be used to perform the same conversion step. For example, in the TCA cycle, 2-Oxoglutarate should be produced using Isocitrate as the substrate. This single reaction step can be performed by reactions R00709, or R00267, or (R01899 and R00268).
Regarding reactions mapping: For mapping model reactions against KEGG reactions, two sources are used: (i) checking for information on KEGG reaction synonyms stored in the SBML model, and (ii) the MNXref database. Synonyms found in (i) and (ii) are consolidated.
Color code:
Green ▶: Complete pathways, or pathways where all conversion steps predicted by the database are present in the model.
Yellow ▶: Incomplete pathways, but with at least one conversion step present in the model.
Pink ▶: Incomplete pathways, with no conversion steps present in the model.
Blue ▶: Pathways not present in the selected organism, but MinPath suggested its presence.
White: Pathways suggested to exist in another model.

	Carbohydrate metabolism
	Central carbohydrate metabolism						Other carbohydrate metabolism
	Pentose phosphate pathway, oxidative phase, glucose 6P => ribulose 5P	Glycolysis, core module involving three-carbon compounds	Pyruvate oxidation, pyruvate => acetyl-CoA	Pentose phosphate pathway, non-oxidative phase, fructose 6P => ribose 5P	Gluconeogenesis, oxaloacetate => fructose-6P	Citrate cycle (TCA cycle, Krebs cycle)	Methylaspartate cycle	Glyoxylate cycle
e_coli_core	Entire module: 2R01528, R02035 (2 reactions) (67%) Blocked rxns: 0 Essential rxns: 0	Entire module: 6R01015, R00200, R01512, R01518, R01061, R00658 (6 reactions) (86%) Blocked rxns: 0 Essential rxns: 4R01512, R01061, R00658, R01518	Entire module: 1R00209 (1 reactions) (20%) Blocked rxns: 0 Essential rxns: 0	Entire module: 4R01827, R01529, R01830, R01056 (4 reactions) (80%) Blocked rxns: 0 Essential rxns: 1R01056	Entire module: 6R01015, R01512, R01518, R00341, R01061, R00658 (6 reactions) (75%) Blocked rxns: 0 Essential rxns: 4R01512, R01061, R00658, R01518	Entire module: 6R01325, R01082, R00405, R00342, R00351, R01900, R00267 (7 reactions) (54%) (R01325, R01900 are present but can not be highlighted on KEGG map) Blocked rxns: 0 Essential rxns: 4R01325, R01900, R00267, R00351	Entire module: 5R01325, R00248, R00342, R00351, R01900 (5 reactions) (36%) Blocked rxns: 0 Essential rxns: 3R01325, R01900, R00351	Entire module: 6R01325, R00479, R00342, R00351, R00472, R01900 (6 reactions) (100%) Blocked rxns: 0 Essential rxns: 3R01325, R01900, R00351

	Energy metabolism
	Carbon fixation							Methane metabolism
	Reductive pentose phosphate cycle, glyceraldehyde-3P => ribulose-5P	CAM (Crassulacean acid metabolism), light	C4-dicarboxylic acid cycle, NAD - malic enzyme type	CAM (Crassulacean acid metabolism), dark	Reductive citrate cycle (Arnon-Buchanan cycle)	Phosphate acetyltransferase-acetate kinase pathway, acetyl-CoA => acetate	Incomplete reductive citrate cycle, acetyl-CoA => oxoglutarate	Formaldehyde assimilation, ribulose monophosphate pathway
e_coli_core	Entire module: 4R00762, R01056, R01067, R01068 (4 reactions) (57%) Blocked rxns: 0 Essential rxns: 1R01056	Entire module: 1R00216 (1 reactions) (50%) Blocked rxns: 0 Essential rxns: 0	Entire module: 3R00342, R00214, R00345 (3 reactions) (38%) Blocked rxns: 0 Essential rxns: 0	Entire module: 2R00342, R00345 (2 reactions) (100%) Blocked rxns: 0 Essential rxns: 0	Entire module: 9R01325, R01082, R00405, R00345, R00342, R00199, R01900, R00402, R00267 (9 reactions) (60%) Blocked rxns: 0 Essential rxns: 3R01325, R01900, R00267	Entire module: 2R00315, R00230 (2 reactions) (100%) Blocked rxns: 0 Essential rxns: 0	Entire module: 4R01082, R10660, R00342, R00405 (4 reactions) (57%) Blocked rxns: 0 Essential rxns: 0	Entire module: 2R00756, R01068 (2 reactions) (25%) Blocked rxns: 0 Essential rxns: 0

	Nucleotide metabolism
	Purine metabolism
	Adenine ribonucleotide biosynthesis, IMP => ADP,ATP
e_coli_core	Entire module: 2R00127, R00200 (2 reactions) (50%) Blocked rxns: 0 Essential rxns: 0

	Xenobiotics biodegradation
	Aromatics degradation
	Catechol meta-cleavage, catechol => acetyl-CoA / 4-methylcatechol => propanoyl-CoA
e_coli_core	Entire module: 1R00228 (1 reactions) (6%) Blocked rxns: 0 Essential rxns: 0

Are shown only KEGG Modules with four or more processing steps and at least 50% completion.

The table below shows how reactions in the model maps with reactions on BioCyc Pathways. The result is divided into six categories for each module:
Organism expected: The number of reactions in the database present in the model (completness of pathway). With mouse over: the reactions in the model mapped to BioCyc.
Organism missing: The number of reactions in the database not present in the model. With mouse over: the reactions present in the model mapped to BioCyc.
Unpredicted: for some organisms, the reference database expects only part of a module to be present. This category receives the number of reactions present in the module, but not expected according to the database.
Entire module: Sum of 'Organism expected' and 'Unpredicted'.
Blocked: number of blocked reactions in pathway.
Essentials: number of essential reactions in pathway.
By clicking on the table's links, the BioCyc reactions and metabolites present in the model are highlighted in a BioCyc Module map.
Units used in the table: The entry "Annotated: 2 (50%)" can be read as "2 reactions (50% pathway completeness)".
Regarding reactions mapping: For mapping model reactions against BioCyc reactions, two sources are used: (i) checking for information on BioCyc reaction synonyms stored in the SBML model, and (ii) the MNXref database. Synonyms found in (i) and (ii) are consolidated.
Color code:
Green ▶: Complete pathways, or pathways where all reactions predicted by the database are present in the model.
Yellow ▶: Incomplete pathways, but with at least one reaction present in the model.
Pink ▶: Incomplete pathways, with no reactions present in the model.
Blue ▶: Pathways not present in the selected organism, but MinPath suggested its presence.
White: Pathways suggested to exist in another model.

	ammonia assimilation cycle III	Calvin-Benson-Bassham cycle	gluconeogenesis I	L-glutamine degradation I	L-glutamine degradation II	superpathway of glycol metabolism and degradation	superpathway of glycolysis and the Entner-Doudoroff pathway	superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	glyoxylate cycle	pentose phosphate pathway (oxidative branch) I
e_coli_core	Entire module: 2 (100%)GLUTAMATESYN-RXN, GLUTAMINESYN-RXN Blocked rxns: 0 Essential rxns: 1GLUTAMINESYN-RXN	Entire module: 6 (46%)F16BDEPHOS-RXN, PHOSGLYPHOS-RXN, 2TRANSKETO-RXN, TRIOSEPISOMERIZATION-RXN, F16ALDOLASE-RXN, RIBULP3EPIM-RXN Blocked rxns: 0 Essential rxns: 1PHOSGLYPHOS-RXN	Entire module: 13 (100%)GAPOXNPHOSPHN-RXN, F16BDEPHOS-RXN, PGLUCISOM-RXN, 1.1.1.39-RXN, PHOSGLYPHOS-RXN, PEPCARBOXYKIN-RXN, TRIOSEPISOMERIZATION-RXN, MALIC-NADP-RXN, F16ALDOLASE-RXN, 2PGADEHYDRAT-RXN, MALATE-DEH-RXN, PEPSYNTH-RXN, 3PGAREARR-RXN Blocked rxns: 0 Essential rxns: 42PGADEHYDRAT-RXN, GAPOXNPHOSPHN-RXN, PHOSGLYPHOS-RXN, 3PGAREARR-RXN	Entire module: 1 (100%)GLUTAMIN-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 1 (100%)GLUTAMATESYN-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 1 (14%)MALSYN-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 14 (88%)PEPSYNTH-RXN, RXN-15513, F16BDEPHOS-RXN, PGLUCISOM-RXN, PHOSGLYPHOS-RXN, 6PFRUCTPHOS-RXN, TRIOSEPISOMERIZATION-RXN, 6PGLUCONOLACT-RXN, GLU6PDEHYDROG-RXN, F16ALDOLASE-RXN, 2PGADEHYDRAT-RXN, GAPOXNPHOSPHN-RXN, PEPDEPHOS-RXN, 3PGAREARR-RXN Blocked rxns: 0 Essential rxns: 5RXN-15513, PHOSGLYPHOS-RXN, 2PGADEHYDRAT-RXN, GAPOXNPHOSPHN-RXN, 3PGAREARR-RXN	Entire module: 20 (80%)RXN-15513, PHOSGLYPHOS-RXN, 6PFRUCTPHOS-RXN, CITSYN-RXN, PYRUVDEH-RXN, ACONITATEDEHYDR-RXN, 2PGADEHYDRAT-RXN, PEPSYNTH-RXN, 3PGAREARR-RXN, MALSYN-RXN, GAPOXNPHOSPHN-RXN, PGLUCISOM-RXN, SUCCCOASYN-RXN, F16BDEPHOS-RXN, TRIOSEPISOMERIZATION-RXN, F16ALDOLASE-RXN, FUMHYDR-RXN, 2OXOGLUTARATEDEH-RXN, MALATE-DEH-RXN, PEPDEPHOS-RXN Blocked rxns: 0 Essential rxns: 7RXN-15513, PHOSGLYPHOS-RXN, CITSYN-RXN, ACONITATEDEHYDR-RXN, 2PGADEHYDRAT-RXN, GAPOXNPHOSPHN-RXN, 3PGAREARR-RXN	Entire module: 4 (67%)MALSYN-RXN, CITSYN-RXN, MALATE-DEH-RXN, ACONITATEDEHYDR-RXN Blocked rxns: 0 Essential rxns: 2CITSYN-RXN, ACONITATEDEHYDR-RXN	Entire module: 3 (100%)GLU6PDEHYDROG-RXN, RXN-9952, 6PGLUCONOLACT-RXN Blocked rxns: 0 Essential rxns: 0

	pyruvate fermentation to propanoate I	Bifidobacterium shunt	reductive TCA cycle I	pentose phosphate pathway	2-aminoethylphosphonate degradation I	sulfoacetaldehyde degradation I	formaldehyde assimilation I (serine pathway)	L-carnitine degradation III	NAD/NADH phosphorylation and dephosphorylation	superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle
e_coli_core	Entire module: 2 (29%)MALATE-DEH-RXN, FUMHYDR-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 9 (60%)PGLUCISOM-RXN, PHOSGLYPHOS-RXN, RIBULP3EPIM-RXN, ACETATEKIN-RXN, 2PGADEHYDRAT-RXN, GAPOXNPHOSPHN-RXN, PEPDEPHOS-RXN, TRANSALDOL-RXN, 3PGAREARR-RXN Blocked rxns: 0 Essential rxns: 42PGADEHYDRAT-RXN, GAPOXNPHOSPHN-RXN, PHOSGLYPHOS-RXN, 3PGAREARR-RXN	Entire module: 5 (42%)SUCCCOASYN-RXN, ACONITATEDEHYDR-RXN, MALATE-DEH-RXN, FUMHYDR-RXN, PEPSYNTH-RXN Blocked rxns: 0 Essential rxns: 1ACONITATEDEHYDR-RXN	Entire module: 6 (75%)RXN-9952, 2TRANSKETO-RXN, 6PGLUCONOLACT-RXN, GLU6PDEHYDROG-RXN, RIBULP3EPIM-RXN, TRANSALDOL-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 1 (33%)ACETALD-DEHYDROG-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 1 (50%)PHOSACETYLTRANS-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 3 (23%)2PGADEHYDRAT-RXN, MALATE-DEH-RXN, RXN-15513 Blocked rxns: 0 Essential rxns: 22PGADEHYDRAT-RXN, RXN-15513	Entire module: 1 (33%)1.1.1.39-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 1 (17%)PYRNUTRANSHYDROGEN-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 14 (64%)PHOSGLYPHOS-RXN, 6PFRUCTPHOS-RXN, 2OXOGLUTARATEDEH-RXN, CITSYN-RXN, MALATE-DEH-RXN, TRIOSEPISOMERIZATION-RXN, ACONITATEDEHYDR-RXN, SUCCCOASYN-RXN, F16ALDOLASE-RXN, 2PGADEHYDRAT-RXN, GAPOXNPHOSPHN-RXN, FUMHYDR-RXN, PEPDEPHOS-RXN, 3PGAREARR-RXN Blocked rxns: 0 Essential rxns: 6PHOSGLYPHOS-RXN, CITSYN-RXN, ACONITATEDEHYDR-RXN, 2PGADEHYDRAT-RXN, GAPOXNPHOSPHN-RXN, 3PGAREARR-RXN

	pyruvate fermentation to acetate II	pyruvate fermentation to acetate IV	reductive monocarboxylic acid cycle	superpathway of glyoxylate cycle and fatty acid degradation	acetyl-CoA fermentation to butanoate II	Rubisco shunt	vancomycin resistance I	methylaspartate cycle	ammonia assimilation cycle I	ammonia assimilation cycle II
e_coli_core	Entire module: 3 (100%)PHOSACETYLTRANS-RXN, PYRUVDEH-RXN, ACETATEKIN-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 3 (100%)PHOSACETYLTRANS-RXN, ACETATEKIN-RXN, PYRUVFORMLY-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 1 (50%)PYRUVFORMLY-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 6 (43%)PEPCARBOXYKIN-RXN, CITSYN-RXN, ACONITATEDEHYDR-RXN, FUMHYDR-RXN, MALSYN-RXN, MALATE-DEH-RXN Blocked rxns: 0 Essential rxns: 2CITSYN-RXN, ACONITATEDEHYDR-RXN	Entire module: 2 (29%)PHOSACETYLTRANS-RXN, ACETATEKIN-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 6 (60%)2TRANSKETO-RXN, 2PGADEHYDRAT-RXN, RIBULP3EPIM-RXN, PEPDEPHOS-RXN, TRANSALDOL-RXN, 3PGAREARR-RXN Blocked rxns: 0 Essential rxns: 22PGADEHYDRAT-RXN, 3PGAREARR-RXN	Entire module: 1 (33%)DLACTDEHYDROGNAD-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 5 (26%)CITSYN-RXN, SUCCCOASYN-RXN, ACONITATEDEHYDR-RXN, MALATE-DEH-RXN, FUMHYDR-RXN Blocked rxns: 0 Essential rxns: 2CITSYN-RXN, ACONITATEDEHYDR-RXN	Entire module: 1 (50%)GLUTAMINESYN-RXN Blocked rxns: 0 Essential rxns: 1GLUTAMINESYN-RXN	Entire module: 1 (50%)GLUTAMINESYN-RXN Blocked rxns: 0 Essential rxns: 1GLUTAMINESYN-RXN

	chitin biosynthesis	adenosine ribonucleotides de novo biosynthesis	superpathway of adenosine nucleotides de novo biosynthesis I	NAD/NADP-NADH/NADPH cytosolic interconversion (yeast)	1,3-propanediol biosynthesis (engineered)	nitrate reduction VI (assimilatory)	ethanol degradation II	formaldehyde oxidation I	TCA cycle I (prokaryotic)
e_coli_core	Entire module: 1 (11%)PGLUCISOM-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 1 (33%)ADENYL-KIN-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 1 (20%)ADENYL-KIN-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 1 (20%)GLU6PDEHYDROG-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 3 (33%)6PFRUCTPHOS-RXN, PGLUCISOM-RXN, F16ALDOLASE-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 2 (50%)GLUTAMINESYN-RXN, GLUTDEHYD-RXN Blocked rxns: 0 Essential rxns: 1GLUTAMINESYN-RXN	Entire module: 1 (33%)ALCOHOL-DEHYDROG-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 3 (50%)6PGLUCONOLACT-RXN, PGLUCISOM-RXN, GLU6PDEHYDROG-RXN Blocked rxns: 0 Essential rxns: 0	Entire module: 6 (60%)CITSYN-RXN, ACONITATEDEHYDR-RXN, FUMHYDR-RXN, 2OXOGLUTARATEDEH-RXN, SUCCCOASYN-RXN, MALATE-DEH-RXN Blocked rxns: 0 Essential rxns: 2CITSYN-RXN, ACONITATEDEHYDR-RXN

Are shown only BioCyc Pathways with four or more reactions, and at least 30% completion in superpathways, or 50% in regular pathways.

Growth of metabolic models is tested for 383 different culture media: 190 carbon sources, 95 nitrogen sources, 59 phosphorus sources, 35 sulfur sources, and 4 negative controls. 4 Biolog Phenotype Microarray Plates inspired the media selection below.
The color labels are:

Growth. The darker the purple, the higher is the flux through the objective function;

No growth;

The model has no reactions that can use the media-specific metabolite as a substrate, making the media growth phenotype identical to the negative control.

FBA fail.

Model: e_coli_core.xml
Objective reaction: BIOMASS_Ecoli_core_w_GAM
Extra metabolites, present in the objective reaction, included on every external media: []
Extra metabolites, not present in the objective reaction, included on every external media: ['co2 (carbon dioxide)', 'o2 (oxygen)']
Extra metabolites included in the external media when testing carbon sources: []
Extra metabolites included in the external media when testing nitrogen sources: []
Extra metabolites included in the external media when testing phosphorus sources: []
Extra metabolites included in the external media when testing sulfur sources: []

The inclusion of oxygen in the external media might have caused growth in a negative control media.

Overview about the growth phenotype analisis

No growth on negative control	Total growth	Growth without media-specific metabolites	Total no growth	No growth without media-specific metabolites	FBA failed	True positive (if *E. coli model)	True negative (if *E. coli model)	True negative without media-specific metabolites (if *E. coli model)	False positive (if *E. coli model)	False negative (if *E. coli model)	False negative without media-specific metabolites (if *E. coli model)	Phenotype accuracy (if *E. coli model)
3 out of 4	51	35	332	320	0	36	145	140	5	151	144	53.7 %

Growth phenotype on carbon sources

No growth on negative control	Total growth	Growth without media-specific metabolites	Total no growth	No growth without media-specific metabolites	FBA failed	True positive (if *E. coli model)	True negative (if *E. coli model)	True negative without media-specific metabolites (if *E. coli model)	False positive (if *E. coli model)	False negative (if *E. coli model)	False negative without media-specific metabolites (if *E. coli model)	Phenotype accuracy (if *E. coli model)
Yes	6	0	185	176	0	5	100	97	0	77	71	57.7 %

Growth phenotype on nitrogen sources

No growth on negative control	Total growth	Growth without media-specific metabolites	Total no growth	No growth without media-specific metabolites	FBA failed	True positive (if *E. coli model)	True negative (if *E. coli model)	True negative without media-specific metabolites (if *E. coli model)	False positive (if *E. coli model)	False negative (if *E. coli model)	False negative without media-specific metabolites (if *E. coli model)	Phenotype accuracy (if *E. coli model)
Yes	3	0	93	92	0	2	39	38	0	30	30	57.7 %

Growth phenotype on phosphorus sources

No growth on negative control	Total growth	Growth without media-specific metabolites	Total no growth	No growth without media-specific metabolites	FBA failed	True positive (if *E. coli model)	True negative (if *E. coli model)	True negative without media-specific metabolites (if *E. coli model)	False positive (if *E. coli model)	False negative (if *E. coli model)	False negative without media-specific metabolites (if *E. coli model)	Phenotype accuracy (if *E. coli model)
Yes	6	0	54	52	0	6	6	5	0	44	43	21.4 %

Growth phenotype on sulfur sources

No growth on negative control	Total growth	Growth without media-specific metabolites	Total no growth	No growth without media-specific metabolites	FBA failed	True positive (if *E. coli model)	True negative (if *E. coli model)	True negative without media-specific metabolites (if *E. coli model)	False positive (if *E. coli model)	False negative (if *E. coli model)	False negative without media-specific metabolites (if *E. coli model)	Phenotype accuracy (if *E. coli model)
No	36	35	0	0	0	23	0	0	5	0	0	82.1 %

*Escherichia coli K-12 substr. MG1655

Biolog Phenotype Microarray Plate 1 - Carbon Sources

	1	2	3	4	5	6	7	8	9	10	11	12
A	Optimization result: 0.0 (No growth) E. coli experimental result: No growth Carbon negative control	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Arabinose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth N-Acetyl-D- Glucosamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Saccharic acid	Optimization result: 0.0 (No growth) E. coli experimental result: Growth Succinic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Galactose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Aspartic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Proline	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Alanine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Trehalose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Mannose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Dulcitol
B	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Serine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Sorbitol	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Glycerol	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Fucose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Glucuronic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Gluconic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth DL-α- Glycerol Phosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Xylose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Lactic acid	Optimization result: 0.0 (No growth) E. coli experimental result: No growth Formic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Mannitol	Optimization result: 20.4736 (Growth) E. coli experimental result: Inconsistent results L-Glutamic acid
C	Optimization result: 41.9381 (Growth) E. coli experimental result: Growth D-Glucose- 6-Phosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Galactonic acid-γ- Lactone	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth DL-Malic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Ribose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Tween 20	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Rhamnose	Optimization result: 35.044 (Growth) E. coli experimental result: Growth D-Fructose	Optimization result: 0.0 (No growth) E. coli experimental result: Growth Acetic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth α- D-Glucose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Maltose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Melibiose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Thymidine
D	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Asparagine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Aspartic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Glucosaminic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth 1,2-Propanediol	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Tween 40	Optimization result: 27.1669 (Growth) E. coli experimental result: Growth α- Ketoglutaric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth α- Ketobutyric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth α- Methyl-D- Galactoside	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth α- D-Lactose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Lactulose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Sucrose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Uridine
E	Optimization result: 0.0 (No growth) E. coli experimental result: Low growth L-Glutamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth M-Tartaric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Glucose- 1-Phosphate	Optimization result: 41.9381 (Growth) E. coli experimental result: Growth D-Fructose- 6-Phosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Tween 80	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth α- Hydroxyglutaric acid- γ-Lactone	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth α- Hydroxybutyric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth β- Methyl-D- Glucoside	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Adonitol	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Maltotriose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth 2-Deoxyadenosine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Adenosine
F	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Gly-Asp	Optimization result: 0.0 (No growth) E. coli experimental result: No growth Citric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth M-Inositol	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Threonine	Optimization result: 0.0 (No growth) E. coli experimental result: Growth Fumaric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Bromosuccinic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Propionic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Mucic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Glycolic acid	Optimization result: 0.0 (No growth) E. coli experimental result: Growth Glyoxylic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Cellobiose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Inosine
G	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Gly-Glu	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Tricarballylic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Serine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Threonine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Alanine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Ala-Gly	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Acetoacetic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth N-Acetyl-D- Mannosamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Low growth Mono-Methylsuccinate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Methylpyruvate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Malic acid	Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Malic acid
H	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Gly-Pro	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth p-Hydroxyphenyl Acetic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth m-Hydroxyphenyl Acetic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Tyramine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results D-Psicose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Lyxose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Glucuronamide	Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Pyruvic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Galactonic acid-γ- Lactone	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Galacturonic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Phenylethylamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth 2-Aminoethanol

Biolog Phenotype Microarray Plate 2 - Carbon Sources

	1	2	3	4	5	6	7	8	9	10	11	12
A		There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Chondroitin Sulfate C	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth α- Cyclodextrin	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth β- Cyclodextrin	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth γ- Cyclodextrin	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Dextrin	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Gelatin	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Glycogen	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Inulin	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Laminarin	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Mannan	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Pectin
B	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth N-Acetyl-D- Galactosamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth N-Acetyl- Neuraminic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth β- D-Allose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Amygdalin	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Arabinose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Arabitol	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Arabitol	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Arbutin	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth 2-Deoxy- D-Ribose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth i-Erythritol	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Fucose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth 3-O-β-D- Galactopyranosyl- D-Arabinose
C	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Gentiobiose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Glucose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Lactitol	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Melezitose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Maltitol	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results α- Methyl-D- Glucoside	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth β-Methyl- D-Galactoside	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth 3-Methylglucose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth β- Methyl-D- Glucuronic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth α- Methyl-D- Mannoside	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth β- Methyl-D- Xyloside	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Palatinose
D	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Raffinose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Salicin	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Sedoheptulosan	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Sorbose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Stachyose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Tagatose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Turanose	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Xylitol	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth N-Acetyl-D- Glucosaminitol	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth γ- Amino-N- Butyric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth δ- Amino Valeric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Butyric acid
E	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Capric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Caproic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Citraconic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Citramalic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Glucosamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth 2-Hydroxybenzoic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth 4-Hydroxybenzoic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth β- Hydroxybutyric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth γ- Hydroxybutyric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results α- Keto- Valeric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Itaconic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth 5-Keto-D- Gluconic acid
F	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Lactic acid Methyl Ester	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Malonic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Melibionic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Oxalic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Oxalomalic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Quinic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Ribono- 1,4-Lactone	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Sebacic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Sorbic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Succinamic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Tartaric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Tartaric acid
G	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Acetamide	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results L-Alaninamide	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth N-Acetyl-L- Glutamic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Arginine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Glycine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Histidine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Homoserine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Hydroxy- L-Proline	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Isoleucine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Leucine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Lysine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Methionine
H	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Ornithine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Phenylalanine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Pyroglutamic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Valine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D,L-Carnitine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth sec-Butylamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D,L-Octopamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Putrescine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Dihydroxyacetone	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth 2,3-Butanediol	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth 2,3-Butanedione	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth 3-Hydroxy- 2-butanone

Biolog Phenotype Microarray Plate 3 - Nitrogen Sources

	1	2	3	4	5	6	7	8	9	10	11	12
A	Optimization result: 0.0 (No growth) E. coli experimental result: No growth nitrogen negative control	Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Ammonia	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Nitrite	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Nitrate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Urea	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Biuret	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Alanine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Arginine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Asparagine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Aspartic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results L-Cysteine	Optimization result: 26.72 (Growth) E. coli experimental result: Inconsistent results L-Glutamic acid
B	Optimization result: 24.113 (Growth) E. coli experimental result: Growth L-Glutamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Glycine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Histidine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Isoleucine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Leucine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results L-Lysine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results L-Methionine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results L-Phenylalanine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Proline	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Serine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results L-Threonine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Tryptophan
C	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Tyrosine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Valine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Alanine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results D-Asparagine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Aspartic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Glutamic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results D-Lysine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Serine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results D-Valine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Citrulline	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results L-Homoserine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth L-Ornithine
D	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth N-Acetyl-L- Glutamic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth N-Phthaloyl-L- Glutamic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth L-Pyroglutamic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Hydroxylamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Methylamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth N-Amylamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth N-Butylamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Ethylamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Ethanolamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Ethylenediamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Putrescine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Agmatine
E	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Histamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth b-Phenylethylamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Tyramine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Acetamide	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Formamide	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Glucuronamide	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth DL-Lactamide	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Glucosamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth D-Galactosamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results D-Mannosamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth N-Acetyl-D- Glucosamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth N-Acetyl-D- Galactosamine
F	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results N-Acetyl-D- Mannosamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Adenine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Adenosine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Cytidine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Cytosine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Guanine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Guanosine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Thymine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Thymidine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Uracil	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Uridine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Inosine
G	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Xanthine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Xanthosine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Uric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Alloxan	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Allantoin	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Parabanic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results DL-α- Amino-N- Butyric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results γ- Amino-N- Butyric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth ε- Amino-N- Caproic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results DL-α- Amino- Caprylic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth δ- Amino-N- Valeric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth α- Amino-N- Valeric acid
H	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Ala-Asp	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Ala-Gln	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Ala-Glu	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Ala-Gly	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Ala-His	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Ala-Leu	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Ala-Thr	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Gly-Asn	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Gly-Gln	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Gly-Glu	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Gly-Met	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Met-Ala

Biolog Phenotype Microarray Plate 4 - Phosphorus and Sulfur Sources

	1	2	3	4	5	6	7	8	9	10	11	12
A	Optimization result: 0.0 (No growth) E. coli experimental result: No growth phosphorus negative control	Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Phosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Pyrophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Trimetaphosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Tripolyphosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Triethyl Phosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Hypophosphite	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Adenosine 2'- Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Adenosine 3'- Monophosphate	Optimization result: 0.0 (No growth) E. coli experimental result: Growth Adenosine 5'- Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Adenosine 2', 3'-Cyclic Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Adenosine 3', 5'-Cyclic Monophosphate
B	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Thiophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Dithiophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth DL-α- Glycerol Phosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth β- Glycerol Phosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Carbamyl Phosphate	Optimization result: 38.2671 (Growth) E. coli experimental result: Growth D-2-Phospho- Glyceric acid	Optimization result: 38.2671 (Growth) E. coli experimental result: Growth D-3-Phospho- Glyceric acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Guanosine 2'- Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Guanosine 3'- Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Guanosine 5'- Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Guanosine 2', 3'-Cyclic Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Guanosine 3', 5'-Cyclic Monophosphate
C	Optimization result: 25.4756 (Growth) E. coli experimental result: Growth Phosphoenol Pyruvate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Phospho- Glycolic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Glucose- 1-Phosphate	Optimization result: 45.5028 (Growth) E. coli experimental result: Growth D-Glucose- 6-Phosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth 2-Deoxy-D- Glucose 6- Phosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Glucosamine- 6-Phosphate	Optimization result: 48.0532 (Growth) E. coli experimental result: Growth 6-Phospho- Gluconic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Cytidine 2'- Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Cytidine 3'- Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Cytidine 5'- Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Cytidine 2', 3'-Cyclic Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Cytidine 3', 5'-Cyclic Monophosphate
D	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Mannose- 1-Phosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth D-Mannose- 6-Phosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Cysteamine- S-Phosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Phospho- L-Arginine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth O-Phospho- D-Serine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth O-Phospho- L-Serine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth O-Phospho- L-Threonine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Uridine 2'- Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Uridine 3'- Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Uridine 5'- Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Uridine 2', 3'-Cyclic Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Uridine 3', 5'-Cyclic Monophosphate
E	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth O-Phospho- D-Tyrosine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth O-Phospho- L-Tyrosine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Phosphocreatine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Phosphoryl Choline	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth O-Phosphoryl- Ethanolamine	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Phosphono Acetic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results 2-Aminoethyl Phosphonic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Inconsistent results Methylene Diphosphonic acid	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Thymidine 3'- Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Thymidine 5'- Monophosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: Growth Inositol Hexaphosphate	There are no media-specific metabolites present in the model. Optimization result: 0.0 (No growth) E. coli experimental result: No growth Thymidine 3', 5'-Cyclic Monophosphate
F	Optimization result: 22.0959 (Growth) E. coli experimental result: No growth sulfur negative control	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Sulfate	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Thiosulfate	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Tetrathionate	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Thiophosphate	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Dithiophosphate	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth L-Cysteine	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth D-Cysteine	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Cys-Gly	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Inconsistent results L-Cysteic acid	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Inconsistent results Cysteamine	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth L-Cysteine Sulfinic acid
G	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: No growth N-Acetyl- L-Cysteine	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Inconsistent results S-Methyl- L-Cysteine	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Cystathionine	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Lanthionine	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Glutathione	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Inconsistent results DL-Ethionine	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth L-Methionine	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth D-Methionine	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Gly-Met	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth N-Acetyl-D, L- Methionine	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth L-Methionine Sulfoxide	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: No growth L-Methionine Sulfone
H	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth L-Djenkolic acid	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Inconsistent results Thiourea	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Inconsistent results 1-Thio- β-D- Glucose	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Inconsistent results DL-Lipoamide	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Inconsistent results Taurocholic acid	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Taurine	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Hypotaurine	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: No growth p-Aminobenzene Sulfonic acid	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Butane Sulfonic acid	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth 2-Hydroxyethane Sulfonic acid	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: Growth Methane Sulfonic acid	There are no media-specific metabolites present in the model. Optimization result: 22.0959 (Growth) E. coli experimental result: No growth Tetramethylene Sulfone

SBMLComp

Model Analysis

General characteristics

Selected organism

Compartments

Metabolites

Reactions

Reactions Types

Metabolic reactions blocked

Metabolic reactions synonyms on other databases

KEGG Pathway Modules

Tables (with clickable links)

Heatmap

BioCyc Pathways

Tables

Heatmap

Growth phenotype

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e_coli_core

Include in the model reactions annotated by KEGG and BioCyc for the selected organism

KEGG Modules

BioCyc Pathways

Remove from model reactions annotated by KEGG and BioCyc on the selected organism

KEGG Modules

BioCyc Pathways

Remove from model reactions mapped to KEGG and BioCyc pathways NOT annotated on the selected organism

KEGG Modules

BioCyc Pathways

Remove from model reactions mapped to KEGG and BioCyc pathways NOT annotated on the selected organism, and can not contribute to maximum growth

KEGG Modules

BioCyc Pathways