Experiment set6IT062 for Sphingomonas koreensis DSMZ 15582

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D-Cellobiose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Cellobiose (20 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), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 3 genes in this experiment

For carbon source D-Cellobiose in Sphingomonas koreensis DSMZ 15582

For carbon source D-Cellobiose across organisms

SEED Subsystems

Subsystem #Specific
Beta-Glucoside Metabolism 1
Oxidative stress 1
Propionyl-CoA to Succinyl-CoA Module 1
Serine-glyoxylate cycle 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
neolinustatin bioactivation 3 2 2
linustatin bioactivation 4 2 2
linamarin degradation 2 1 1
lotaustralin degradation 2 1 1
propanoyl CoA degradation I 3 3 1
conversion of succinate to propanoate 3 1 1
cellulose degradation II (fungi) 3 1 1
2-oxobutanoate degradation I 4 3 1
coumarin biosynthesis (via 2-coumarate) 5 2 1
α-tomatine degradation 6 1 1
pyruvate fermentation to propanoate I 7 4 1
anaerobic energy metabolism (invertebrates, mitochondrial) 10 6 1
L-glutamate degradation VIII (to propanoate) 11 4 1
3-hydroxypropanoate cycle 13 9 1
(S)-lactate fermentation to propanoate, acetate and hydrogen 13 7 1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered) 14 5 1
firefly bioluminescence 14 3 1
superpathway of L-methionine salvage and degradation 16 7 1
superpathway of anaerobic energy metabolism (invertebrates) 17 11 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 12 1
superpathway of the 3-hydroxypropanoate cycle 18 10 1
methylaspartate cycle 19 14 1