Experiment set6IT051 for Sphingomonas koreensis DSMZ 15582

Compare to:

D-Glucose carbon source; no added vitamins

Group: nutrient
Media: RCH2_defined_noCarbon_noVitamins + D-Glucose (5 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 36 genes in this experiment

For nutrient D-Glucose in Sphingomonas koreensis DSMZ 15582

For nutrient D-Glucose across organisms

SEED Subsystems

Subsystem #Specific
ABC transporter peptide (TC 3.A.1.5.5) 1
Acetyl-CoA fermentation to Butyrate 1
Bacterial Chemotaxis 1
Butanol Biosynthesis 1
Flagellar motility 1
Heat shock dnaK gene cluster extended 1
Isoleucine degradation 1
Methionine Biosynthesis 1
Oxidative stress 1
Polyhydroxybutyrate metabolism 1
Protein chaperones 1
Purine conversions 1
Pyruvate Alanine Serine Interconversions 1
Type 4 secretion and conjugative transfer 1
Universal GTPases 1
Valine degradation 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
L-alanine degradation IV 1 1 1
long-chain fatty acid activation 1 1 1
benzoyl-CoA biosynthesis 3 3 2
fatty acid β-oxidation IV (unsaturated, even number) 5 3 3
fatty acid β-oxidation I (generic) 7 5 4
superoxide radicals degradation 2 2 1
oleate β-oxidation (thioesterase-dependent, yeast) 2 2 1
fatty acid salvage 6 5 3
γ-linolenate biosynthesis II (animals) 2 1 1
linoleate biosynthesis II (animals) 2 1 1
seleno-amino acid detoxification and volatilization I 2 1 1
dimethyl sulfide biosynthesis from methionine 2 1 1
oleate β-oxidation 35 30 17
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
valproate β-oxidation 9 6 3
L-isoleucine degradation I 6 4 2
pyruvate fermentation to butanol II (engineered) 6 4 2
alkane biosynthesis II 3 2 1
seleno-amino acid detoxification and volatilization III 3 2 1
3-methyl-branched fatty acid α-oxidation 6 3 2
methyl ketone biosynthesis (engineered) 6 3 2
propanoate fermentation to 2-methylbutanoate 6 3 2
6-gingerol analog biosynthesis (engineered) 6 3 2
oleate biosynthesis I (plants) 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
Ac/N-end rule pathway 21 6 6
benzoyl-CoA degradation I (aerobic) 7 2 2
reactive oxygen species degradation 4 4 1
phytol degradation 4 4 1
L-valine degradation I 8 5 2
homocysteine and cysteine interconversion 4 2 1
wax esters biosynthesis II 4 2 1
pyruvate fermentation to butanol I 8 3 2
phosphatidylcholine acyl editing 4 1 1
long chain fatty acid ester synthesis (engineered) 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
sporopollenin precursors biosynthesis 18 4 4
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 5 1
4-hydroxybenzoate biosynthesis III (plants) 5 4 1
L-methionine biosynthesis I 5 4 1
3-phenylpropanoate degradation 10 6 2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) 10 4 2
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
L-glutamate degradation V (via hydroxyglutarate) 10 4 2
octane oxidation 5 2 1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 1 1
superpathway of phenylethylamine degradation 11 4 2
L-methionine biosynthesis II 6 5 1
stearate biosynthesis II (bacteria and plants) 6 4 1
superpathway of L-cysteine biosynthesis (fungi) 6 4 1
stearate biosynthesis IV 6 3 1
L-glutamate degradation VII (to butanoate) 12 4 2
stearate biosynthesis I (animals) 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
ethene biosynthesis III (microbes) 7 5 1
capsaicin biosynthesis 7 3 1
hypoglycin biosynthesis 14 4 2
ceramide degradation by α-oxidation 7 2 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 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
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 4 2
2-methylpropene degradation 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 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
3-hydroxypropanoate/4-hydroxybutanate cycle 18 12 2
toluene degradation VI (anaerobic) 18 4 2
superpathway of seleno-compound metabolism 19 8 2
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) 10 8 1
suberin monomers biosynthesis 20 4 2
methyl tert-butyl ether degradation 10 2 1
superpathway of fatty acid biosynthesis II (plant) 43 37 4
gallate degradation III (anaerobic) 11 3 1
10-cis-heptadecenoyl-CoA degradation (yeast) 12 2 1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, 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
Arg/N-end rule pathway (eukaryotic) 14 8 1
superpathway of testosterone and androsterone degradation 28 6 2
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
palmitate biosynthesis II (type II fatty acid synthase) 31 29 2
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 9 3
cutin biosynthesis 16 1 1
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 2 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 17 1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) 22 3 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 fatty acids biosynthesis (E. coli) 53 48 2
palmitate biosynthesis III 29 21 1