Experiment set6IT059 for Sphingomonas koreensis DSMZ 15582

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D-Cellobiose carbon source and 0.25mM L-Methionine; no added vitamins

Group: nutrient
Media: RCH2_defined_noCarbon_noVitamins + D-Cellobiose (20 mM) + L-Methionine (0.25 mM), pH=7
Culturing: korea_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Adam on 15-Mar-20
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate)

Specific Phenotypes

For 15 genes in this experiment

For nutrient D-Cellobiose in Sphingomonas koreensis DSMZ 15582

For nutrient D-Cellobiose across organisms

SEED Subsystems

Subsystem #Specific
Beta-Glucoside Metabolism 2
Fructooligosaccharides(FOS) and Raffinose Utilization 1
Glutathione: Non-redox reactions 1
Methionine Biosynthesis 1
Methylglyoxal Metabolism 1
N-heterocyclic aromatic compound degradation 1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-methionine degradation II 3 3 3
neolinustatin bioactivation 3 2 2
linustatin bioactivation 4 2 2
lotaustralin degradation 2 1 1
dimethyl sulfide biosynthesis from methionine 2 1 1
seleno-amino acid detoxification and volatilization I 2 1 1
linamarin degradation 2 1 1
L-threonine degradation I 6 5 2
seleno-amino acid detoxification and volatilization III 3 2 1
methylglyoxal degradation I 3 2 1
methylglyoxal degradation VIII 3 2 1
cellulose degradation II (fungi) 3 1 1
L-isoleucine biosynthesis I (from threonine) 7 7 2
homocysteine and cysteine interconversion 4 2 1
L-methionine biosynthesis I 5 4 1
coumarin biosynthesis (via 2-coumarate) 5 2 1
L-methionine biosynthesis II 6 5 1
superpathway of L-cysteine biosynthesis (fungi) 6 4 1
α-tomatine degradation 6 1 1
superpathway of L-isoleucine biosynthesis I 13 13 2
hypoglycin biosynthesis 14 4 2
superpathway of L-homoserine and L-methionine biosynthesis 8 7 1
superpathway of methylglyoxal degradation 8 3 1
superpathway of branched chain amino acid biosynthesis 17 17 2
superpathway of S-adenosyl-L-methionine biosynthesis 9 8 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 8 1
superpathway of L-threonine metabolism 18 14 2
superpathway of seleno-compound metabolism 19 8 2
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) 10 8 1
firefly bioluminescence 14 3 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 17 1
aspartate superpathway 25 24 1