Experiment set6IT050 for Sphingomonas koreensis DSMZ 15582

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D-Cellobiose carbon source; no added vitamins

Group: nutrient
Media: RCH2_defined_noCarbon_noVitamins + 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)

Specific Phenotypes

For 29 genes in this experiment

For nutrient D-Cellobiose in Sphingomonas koreensis DSMZ 15582

For nutrient D-Cellobiose across organisms

SEED Subsystems

Subsystem #Specific
N-heterocyclic aromatic compound degradation 2
Acetyl-CoA fermentation to Butyrate 1
Beta-Glucoside Metabolism 1
Beta-lactamase 1
Butanol Biosynthesis 1
Glycerol and Glycerol-3-phosphate Uptake and Utilization 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Isoleucine degradation 1
Methionine Biosynthesis 1
Polyhydroxybutyrate metabolism 1
Potassium homeostasis 1
Queuosine-Archaeosine Biosynthesis 1
Respiratory dehydrogenases 1 1
Rhamnose containing glycans 1
Tn552 1
Valine degradation 1
dTDP-rhamnose synthesis 1
linker unit-arabinogalactan synthesis 1
n-Phenylalkanoic acid 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
fatty acid β-oxidation III (unsaturated, odd number) 1 1 1
benzoyl-CoA biosynthesis 3 3 2
neolinustatin bioactivation 3 2 2
fatty acid β-oxidation IV (unsaturated, even number) 5 3 3
fatty acid β-oxidation I (generic) 7 5 4
glycerol-3-phosphate to cytochrome bo oxidase electron transfer 2 2 1
glycerophosphodiester degradation 2 2 1
glycerol-3-phosphate shuttle 2 2 1
oleate β-oxidation (thioesterase-dependent, yeast) 2 2 1
linustatin bioactivation 4 2 2
glycerol-3-phosphate to fumarate electron transfer 2 1 1
glycerol 3-phosphate to cytochrome aa3 oxidase electron transfer 2 1 1
linamarin degradation 2 1 1
seleno-amino acid detoxification and volatilization I 2 1 1
lotaustralin degradation 2 1 1
nitrate reduction IX (dissimilatory) 2 1 1
dimethyl sulfide biosynthesis from methionine 2 1 1
glycerol-3-phosphate to hydrogen peroxide electron transport 2 1 1
oleate β-oxidation 35 30 16
adipate biosynthesis 5 4 2
adipate degradation 5 4 2
glutaryl-CoA degradation 5 3 2
fatty acid β-oxidation II (plant peroxisome) 5 3 2
fatty acid β-oxidation V (unsaturated, odd number, di-isomerase-dependent) 5 2 2
pyruvate fermentation to hexanol (engineered) 11 7 4
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 6 4
2-methyl-branched fatty acid β-oxidation 14 9 5
L-threonine degradation I 6 5 2
fatty acid salvage 6 5 2
valproate β-oxidation 9 6 3
pyruvate fermentation to butanol II (engineered) 6 4 2
L-isoleucine degradation I 6 4 2
seleno-amino acid detoxification and volatilization III 3 2 1
glycerol degradation I 3 2 1
methyl ketone biosynthesis (engineered) 6 3 2
propanoate fermentation to 2-methylbutanoate 6 3 2
cellulose degradation II (fungi) 3 1 1
sn-glycerol 3-phosphate anaerobic respiration 3 1 1
oleate β-oxidation (reductase-dependent, yeast) 3 1 1
L-isoleucine biosynthesis I (from threonine) 7 7 2
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 2
pyruvate fermentation to butanoate 7 3 2
benzoyl-CoA degradation I (aerobic) 7 2 2
glycerol and glycerophosphodiester degradation 4 3 1
L-valine degradation I 8 5 2
homocysteine and cysteine interconversion 4 2 1
pyruvate fermentation to butanol I 8 3 2
muropeptide degradation 4 1 1
dTDP-6-deoxy-α-D-allose biosynthesis 4 1 1
dTDP-β-D-fucofuranose biosynthesis 4 1 1
dTDP-N-acetylthomosamine biosynthesis 4 1 1
dTDP-N-acetylviosamine biosynthesis 4 1 1
oleate β-oxidation (isomerase-dependent, yeast) 4 1 1
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 5 2
phenylacetate degradation I (aerobic) 9 3 2
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 2
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 5 1
L-methionine biosynthesis I 5 4 1
4-hydroxybenzoate biosynthesis III (plants) 5 4 1
3-phenylpropanoate degradation 10 6 2
L-glutamate degradation V (via hydroxyglutarate) 10 4 2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) 10 4 2
dTDP-β-L-rhamnose biosynthesis 5 2 1
coumarin biosynthesis (via 2-coumarate) 5 2 1
dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis 5 1 1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 1 1
dTDP-α-D-mycaminose biosynthesis 5 1 1
dTDP-3-acetamido-α-D-fucose biosynthesis 5 1 1
dTDP-4-O-demethyl-β-L-noviose biosynthesis 5 1 1
superpathway of phenylethylamine degradation 11 4 2
L-methionine biosynthesis II 6 5 1
superpathway of L-cysteine biosynthesis (fungi) 6 4 1
6-gingerol analog biosynthesis (engineered) 6 3 1
L-glutamate degradation VII (to butanoate) 12 4 2
dTDP-D-desosamine biosynthesis 6 1 1
dTDP-L-daunosamine biosynthesis 6 1 1
dTDP-sibirosamine biosynthesis 6 1 1
α-tomatine degradation 6 1 1
dTDP-α-D-ravidosamine and dTDP-4-acetyl-α-D-ravidosamine biosynthesis 6 1 1
superpathway of L-isoleucine biosynthesis I 13 13 2
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 4 2
superpathway of glyoxylate cycle and fatty acid degradation 14 12 2
hypoglycin biosynthesis 14 4 2
dTDP-β-L-digitoxose biosynthesis 7 2 1
dTDP-β-L-olivose biosynthesis 7 2 1
dTDP-β-L-mycarose biosynthesis 7 1 1
Spodoptera littoralis pheromone biosynthesis 22 4 3
L-tryptophan degradation III (eukaryotic) 15 6 2
superpathway of L-homoserine and L-methionine biosynthesis 8 7 1
glycerol degradation to butanol 16 10 2
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 4 2
2-methylpropene degradation 8 2 1
dTDP-β-L-4-epi-vancosamine biosynthesis 8 2 1
dTDP-β-L-megosamine biosynthesis 8 2 1
superpathway of branched chain amino acid biosynthesis 17 17 2
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 6 2
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 4 2
superpathway of L-methionine biosynthesis (transsulfuration) 9 8 1
superpathway of S-adenosyl-L-methionine biosynthesis 9 8 1
superpathway of L-threonine metabolism 18 14 2
3-hydroxypropanoate/4-hydroxybutanate cycle 18 12 2
toluene degradation VI (anaerobic) 18 4 2
dTDP-α-D-olivose, dTDP-α-D-oliose and dTDP-α-D-mycarose biosynthesis 9 2 1
dTDP-α-D-forosamine biosynthesis 9 2 1
superpathway of seleno-compound metabolism 19 8 2
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) 10 8 1
peptidoglycan recycling II 10 3 1
methyl tert-butyl ether degradation 10 2 1
superpathway of enterobacterial common antigen biosynthesis 10 1 1
O-antigen building blocks biosynthesis (E. coli) 11 7 1
gallate degradation III (anaerobic) 11 3 1
peptidoglycan maturation (meso-diaminopimelate containing) 12 4 1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) 12 2 1
10-cis-heptadecenoyl-CoA degradation (yeast) 12 2 1
androstenedione degradation I (aerobic) 25 6 2
platensimycin biosynthesis 26 6 2
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 1
1-butanol autotrophic biosynthesis (engineered) 27 19 2
androstenedione degradation II (anaerobic) 27 4 2
peptidoglycan recycling I 14 9 1
superpathway of testosterone and androsterone degradation 28 6 2
firefly bioluminescence 14 3 1
superpathway of cholesterol degradation I (cholesterol oxidase) 42 8 3
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 1
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 9 3
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 2 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 17 1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis 19 2 1
superpathway of novobiocin biosynthesis 19 2 1
superpathway of erythromycin biosynthesis 19 1 1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) 22 3 1
superpathway of megalomicin A biosynthesis 22 2 1
superpathway of dTDP-glucose-derived antibiotic building blocks biosynthesis 23 2 1
superpathway of cholesterol degradation III (oxidase) 49 5 2
aspartate superpathway 25 24 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 20 1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis 33 9 1