Nutrient	cpd.id	rule	maxFlux	proton.balance	Comment	Category
Water	cpd00001	TRUE	100	FALSE	Core medium compound	Inorganics
Sodium	cpd00971	TRUE	10	FALSE	Core medium compound	Inorganics
K+	cpd00205	TRUE	10	FALSE	Core medium compound	Inorganics
Cl-	cpd00099	TRUE	10	FALSE	Core medium compound	Inorganics
Fe2+	cpd10515	TRUE	10	FALSE	Core medium compound	Inorganics
Fe3+	cpd10516	TRUE	0.1	FALSE	Core medium compound	Inorganics
Phosphate	cpd00009	TRUE	10	FALSE	Core medium compound	Inorganics
Co2+	cpd00149	TRUE	10	FALSE	Core medium compound	Inorganics
Mg2+	cpd00254	TRUE	10	FALSE	Core medium compound	Inorganics
Ni2+	cpd00244	TRUE	1	FALSE	Core medium compound	Inorganics
Sulfate	cpd00048	TRUE	10	FALSE	Core medium compound	Inorganics
H2S	cpd00239	TRUE	1	FALSE	Core medium compound	Inorganics
Zn2+	cpd00034	TRUE	10	FALSE	Core medium compound	Inorganics
Cu2+	cpd00058	TRUE	10	FALSE	Core medium compound	Inorganics
Mn2+	cpd00030	TRUE	10	FALSE	Core medium compound	Inorganics
Ca2+	cpd00063	TRUE	10	FALSE	Core medium compound	Inorganics
Ammonium	cpd00013	!("N2FIX-PWY" | "PWY-7576")	10	FALSE	Add ammonium if no N2 fixation pathway has been predicted	Inorganics
N2	cpd00528	"N2FIX-PWY" | "PWY-7576"	25	FALSE	Nitrogen fixation	Inorganics
O2	cpd00007	"PWY-3781" | "PWY1YI0-3" | "PWY-7279" | "PWY1YI0-6"	12.5	FALSE	aerobic respiration (1 - I (cytochrome c); 2- NDH-1 to cytochrome c oxidase via plastocyanin; 3 - II (cytochrome c); 3 - ;4- in cyanobacteria)	Inorganics
O2	cpd00007	"PWY0-1565" | "PWY0-1561" | "PWY0-1544" | "PWY-7545" | "PWY-7544" | "PWY0-1353" | "PWY0-1329"	12.5	FALSE	1 - D-Lactate to Cytochrome bo; 2 - glyc3p to cytochrome bo; 3 - Pro to Cytochom bo; 4 - Pyr to cytochrome bd; 5  - Pyr to cytochrome bo; 6 - Succ to cytochrome bd; 7  - Succ to cytochrome bo	Inorganics
O2	cpd00007	"PWY0-1334" | "PWY0-1568" | "PWY0-1335" | "PWY0-1567"	12.5	FALSE	NADH to cytochrome	Inorganics
O2	cpd00007	rxn05747 | rxn09272 | rxn08288 | rxn00145	12.5	FALSE	Reactions from respiration chain (complex I + II), a quinol oxidases and a lactate dehydrogenase (cytochrome) 	Inorganics
CO2	cpd00011	"CALVIN-PWY" | "CODH-PWY" | "PWY-5789" | "PWY-7784" | "LWP-GS" | "METHANOGENESIS-PWY"	25	FALSE	CO2 fixation, methanogenesis	Inorganics
H2	cpd11640	"CODH-PWY" | "LWP-GS" | "METHANOGENESIS-PWY" | "PWY-7867"	100	FALSE	Ljungdahl-Wood pathway, methanogenesis	Inorganics
Photons	cpd11632	"PWY-101"	50	FALSE	photosynthesis light reactions	Inorganics
PCE	cpd04166	"PCEDEG-PWY" | "PCEDEG-PWY2"	25	FALSE	Reductive dehalogenation	Inorganics
O2	cpd00007	"PCEDEG-PWY" | "PCEDEG-PWY2"	NA	FALSE	Add no oxygen for anaerobic respirations	Inorganics
						
D-Glucose	cpd00027	rxn05226 | rxn08612	5	TRUE	D-glucose transport via PEP:Pyr PTS	Saccharides
D-Glucose	cpd00027	rxn05573 | rxn08616	5	TRUE	D-glucose transport in via proton symport	Saccharides
D-Glucose	cpd00027	rxn05147 | rxn08606	5	TRUE	D-Glucose-ABC transport	Saccharides
D-Fructose	cpd00082	rxn05560 | rxn08536	5	TRUE	D-Fructose-specific PTS-System	Saccharides
Lactose	cpd00208	"LACTOSECAT-PWY" | "LACTOSEUTIL-PWY" | "BGALACT-PWY"	2.5	TRUE		Saccharides
Starch (n=27)	cpd90003	rxn90043 & rxn90034	0.18	TRUE	Pullulanase-type debranching enzyme and alpha-amylase	Saccharides
Starch (n=27)	cpd90003	"METHANOGENESIS-PWY" | "PWY-7867"	NA	TRUE	Do not add starch for methanogens, can stop methanogenesis to be predicted	Saccharides
Maltose	cpd00179	"MALTOSECAT-PWY"	2.5	TRUE		Saccharides
2'-Fucosyllactose	cpd90001	"2FLHYD"	1.67	TRUE	Alpha-fucosidase & ABC transport	Saccharides
Pectin	cpd27519	"PWY-7246" | "PWY-7248"	1.67	TRUE		Saccharides
Melitose/Raffinose	cpd00382	rxn05643 & (rxn00818 | rxn34781)	1.67	TRUE	Raffinose transporter AND galactohydrolase	Saccharides
Sucrose	cpd00076	"SUCUTIL-PWY" | "PWY-621" | "PWY-5384" | "SUCROSEUTIL2-PWY"	2.5	TRUE		Saccharides
Inulin	cpd28763	"INULIN-DEGRADATION-EXO" | "INULIN-DEGRADATION"	0.42	TRUE		Saccharides
N-acetylneuraminate	cpd00232	"PWY0-1324" & "GLUAMCAT-PWY"	5	TRUE		Saccharides
N-Acetyl-D-glucosamine	cpd00122	"GLUAMCAT-PWY" & (rxn05485 | rxn08041)	5	TRUE	Including PTS for uptake	Saccharides
Xylan-b-1-4	cpd90021	"PWY-6717"	0.01	TRUE	1,4-D-beta-Xylan (n=500) degradation, extracellular	Saccharides
Trehalose	cpd00794	"PWY0-1182" | "PWY0-1466" | "PWY-2721" | "PWY-2722" | "PWY-2723" | "TREDEGLOW-PWY"	2.5	TRUE		Saccharides
Xylose	cpd00154	"XYLCAT-PWY" | "PWY-5516" | "PWY-6760" | "PWY-7294" | "PWY-7178" | "PWY-8020" | "PWY-8330"	5	TRUE		Saccharides
Fucose	cpd00751	"FUCCAT-PWY" | "PWY-8444" | "PWY-8318"	5	TRUE		Saccharides
Rhamnose	cpd00396	"RHAMCAT-PWY" | "PWY-6713" | "PWY-6714"	5	TRUE		Saccharides
						
L-Tryptophan	cpd00065	!("TRPSYN-PWY2" | "TRPSYN-PWY")	0.1	TRUE		Amino acids
L-Histidine	cpd00119	!"HISTSYN-PWY"	0.1	TRUE		Amino acids
L-Serine	cpd00054	!"SERSYN-PWY"	0.1	TRUE		Amino acids
L-Arginine	cpd00051	!("ARGSYN-PWY" | "ARGSYNBSUB-PWY" | "PWY-5154" | "PWY-7400")	0.1	TRUE		Amino acids
L-Asparagine	cpd00132	!("ASPARAGINE-BIOSYNTHESIS" | "ASPARAGINESYN-PWY" | "PWY490-4")	0.1	TRUE		Amino acids
L-Glutamine	cpd00053	!"GLNSYN-PWY"	0.1	TRUE	EC 6.3.1.2	Amino acids
Glycine	cpd00033	!("GLYSYN-PWY" | "GLYSYN-ALA-PWY" | "GLYSYN-THR-PWY")	0.1	TRUE		Amino acids
Chorismate	cpd00216	rxn02213 + (rxn01740 | rxn01741) + (rxn01739 | rxn38708) + rxn02476 + rxn01255 < 3	0.1	TRUE	Chorismate biosynthesis from 3-dehydroquinate is <40% complete	Amino acids
L-Cysteine	cpd00084	!("CYSTSYN-PWY" | "PWY-6308" | "HOMOCYSDEGR-PWY" | "PWY-7289" | "PWY-8009" | "PWY-8010")	0.1	TRUE		Amino acids
L-Isoleucine	cpd00322	!("ILEUSYN-PWY" | "PWY-5101" | "PWY-5104")	0.1	TRUE		Amino acids
L-Leucine	cpd00107	!("LEUSYN-PWY" & (rxn00003 | rxn33164) & rxn02186 & rxn00898)	0.1	TRUE	LEUSYN-PWY and the first three steps of VALSYN-PWY	Amino acids
L-Lysine	cpd00039	!("DAPLYSINESYN-PWY" | "PWY-2941" | "PWY-2942" | "PWY-3081" | "PWY-5097")	0.1	TRUE		Amino acids
L-Methionine	cpd00060	!("HOMOSER-METSYN-PWY" | "PWY-702" | "HSERMETANA-PWY" | "PWY-7977")	0.1	TRUE		Amino acids
L-Phenylalanine	cpd00066	!((rxn01256 & rxn01000 & (rxn00493 | rxn21134 | rxn28060 | rxn38254)) | "PWY-3462" | "PWY-7432")	0.1	TRUE		Amino acids
L-Proline	cpd00129	!("PROSYN-PWY" | "PWY-3341")	0.1	TRUE		Amino acids
L-Threonine	cpd00161	!("HOMOSER-THRESYN-PWY" | "THRBIOSYN-GS")	0.1	TRUE	Either MetaCycs HOMOSER-THRESYN-PWY (from L-homoserine to Thr) or gapseq connected pathway of the same rout but together with L-Homoserine synthesis.	Amino acids
L-Tyrosine	cpd00069	!("TYRSYN" | "PWY-3461" | "PWY-6120" | "PWY-6134")	0.1	TRUE		Amino acids
L-Valine	cpd00156	!"VALSYN-PWY"	0.1	TRUE		Amino acids
						
Pantothenic acid	cpd00644	!(rxn01791 | rxn16218)	0.025	TRUE	EC 6.3.2.1 or EC 6.3.2.36	Vitamins
Thiamin	cpd00305	!(rxn02305 | rxn23042)	0.025	TRUE	EC 2.5.1.3	Vitamins
Riboflavin	cpd00220	!("RIBOSYN2-PWY" | "PWY-6167")	0.025	TRUE		Vitamins
						
L-Lactate	cpd00159	rxn90054	15	TRUE	Electron-bifurcating lactate dehydrogenase forming pyruvate (EC 1.3.1.110)	Organic acids
L-Lactate	cpd00159	"PWY-5494" | "PWY-8086" | "PWY-8086-GS"	15	TRUE	acrylate pathway or lactate fermentation to propionate, acetate and h2	Organic acids
Acetate	cpd00029	rxn00875 & rxn00225 & rxn00173 & rxn90001	20	TRUE	EC 2.8.3.8, EC 2.7.2.1, EC 2.3.1.8, EC 1.3.1.109	Organic acids
Acetate	cpd00029	"METH-ACETATE-PWY"	25	TRUE	Methanogenisis from acetate	Organic acids
Succinate	cpd00036	"PWY-5677"	10	TRUE	Succinate fermentation to butyrate	Organic acids
Succinate	cpd00036	(rxn00602 | rxn01996) & rxn90096 & rxn09174	10	TRUE	Succinate transformation to propionate (Na+ exporting). Part of PWY-8086	Organic acids
Formate	cpd00047	"PWY-7868"	20	TRUE	coenzyme B/coenzyme M regeneration V (formate-dependent) involved in methanogenesis	Organic acids
						
sulfoquinovose	cpd22614	"PWY-7446" | "PWY-7722"	10	TRUE		Secondary plant metabolites
Gallate	cpd01020	"GALLATE-DEGRADATION-II-PWY" | "GALLATE-DEGRADATION-I-PWY" | "P3-PWY"	10	TRUE		Secondary plant metabolites
Quercetin	cpd00313	"QUERCETIN-ANAERO-DEG"	10	TRUE	Key-reaction: Taxifolin isomerase (EC 5.5.1.6)	Secondary plant metabolites
Genistein	cpd03971	rxn90097	10	TRUE	Genistein reductase	Secondary plant metabolites
Daidzein	cpd07097	"PWY-6996"	10	TRUE	Anaerobic daidzein degradation to equol	Secondary plant metabolites
Dimethylsulfide	cpd00450	"PWY-5258"	10	TRUE	methanogenesis from dimethylsulfide	Secondary plant metabolites
Methanethiol	cpd00324	"PWY-5259"	10	TRUE	methanogenesis from methanethiol	Organosulfur compound
