Experiment set11IT017 for Agrobacterium fabrum C58

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Glutaric acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Glutaric acid (10 mM), pH=7
Culturing: Agro_ML11, 24-well plate, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 1/6/22
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 9 genes in this experiment

For carbon source Glutaric acid in Agrobacterium fabrum C58

For carbon source Glutaric acid across organisms

SEED Subsystems

Subsystem #Specific
Acetyl-CoA fermentation to Butyrate 1
Bacterial RNA-metabolizing Zn-dependent hydrolases 1
Butanol Biosynthesis 1
Conserved gene cluster associated with Met-tRNA formyltransferase 1
Entner-Doudoroff Pathway 1
Glutathione-regulated potassium-efflux system and associated functions 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Glycolate, glyoxylate interconversions 1
Methylglyoxal Metabolism 1
Polyhydroxybutyrate metabolism 1
Potassium homeostasis 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 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
mannosylfructose biosynthesis 2 2 1
putrescine degradation V 2 2 1
putrescine degradation I 2 1 1
acetoacetate degradation (to acetyl CoA) 2 1 1
ethylene glycol degradation 2 1 1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 5 2
5,6-dehydrokavain biosynthesis (engineered) 10 6 4
glutaryl-CoA degradation 5 3 2
ethanol degradation IV 3 3 1
benzoyl-CoA biosynthesis 3 3 1
ethanol degradation II 3 3 1
pyruvate fermentation to butanol II (engineered) 6 4 2
hypotaurine degradation 3 2 1
ketolysis 3 2 1
ethanol degradation III 3 2 1
putrescine degradation IV 3 2 1
polyhydroxybutanoate biosynthesis 3 2 1
histamine degradation 3 1 1
pyruvate fermentation to butanoate 7 3 2
pyruvate fermentation to hexanol (engineered) 11 7 3
oleate β-oxidation 35 27 9
phytol degradation 4 3 1
pyruvate fermentation to butanol I 8 4 2
(2S)-ethylmalonyl-CoA biosynthesis 4 2 1
L-tryptophan degradation X (mammalian, via tryptamine) 4 2 1
fatty acid α-oxidation I (plants) 4 2 1
2-methylpropene degradation 8 3 2
putrescine degradation III 4 1 1
D-arabinose degradation II 4 1 1
valproate β-oxidation 9 5 2
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 3 2
2-methyl-branched fatty acid β-oxidation 14 9 3
ketogenesis 5 3 1
mitochondrial NADPH production (yeast) 5 3 1
4-hydroxybenzoate biosynthesis III (plants) 5 3 1
fatty acid β-oxidation II (plant peroxisome) 5 3 1
L-glutamate degradation V (via hydroxyglutarate) 10 4 2
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
octane oxidation 5 2 1
methyl tert-butyl ether degradation 10 3 2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) 10 2 2
isopropanol biosynthesis (engineered) 5 1 1
ethylbenzene degradation (anaerobic) 5 1 1
dopamine degradation 5 1 1
fatty acid β-oxidation VII (yeast peroxisome) 5 1 1
pyruvate fermentation to acetone 5 1 1
fatty acid salvage 6 5 1
L-isoleucine degradation I 6 4 1
3-methyl-branched fatty acid α-oxidation 6 3 1
propanoate fermentation to 2-methylbutanoate 6 3 1
L-glutamate degradation VII (to butanoate) 12 4 2
4-ethylphenol degradation (anaerobic) 6 2 1
alkane oxidation 6 1 1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast) 6 1 1
jasmonic acid biosynthesis 19 4 3
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 5 2
noradrenaline and adrenaline degradation 13 4 2
fatty acid β-oxidation I (generic) 7 4 1
superpathway of glycol metabolism and degradation 7 4 1
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 1
serotonin degradation 7 3 1
acetyl-CoA fermentation to butanoate 7 2 1
ceramide degradation by α-oxidation 7 2 1
mevalonate pathway II (haloarchaea) 7 1 1
mevalonate pathway I (eukaryotes and bacteria) 7 1 1
limonene degradation IV (anaerobic) 7 1 1
L-tryptophan degradation III (eukaryotic) 15 4 2
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 6 1
glycerol degradation to butanol 16 11 2
superpathway of ornithine degradation 8 4 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
2-deoxy-D-ribose degradation II 8 2 1
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 3 2
aromatic biogenic amine degradation (bacteria) 8 1 1
mevalonate pathway IV (archaea) 8 1 1
isoprene biosynthesis II (engineered) 8 1 1
mevalonate pathway III (Thermoplasma) 8 1 1
androstenedione degradation I (aerobic) 25 6 3
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 5 2
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 3 2
3-hydroxypropanoate/4-hydroxybutanate cycle 18 11 2
Entner-Doudoroff pathway II (non-phosphorylative) 9 5 1
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 1
4-oxopentanoate degradation 9 2 1
toluene degradation VI (anaerobic) 18 3 2
superpathway of testosterone and androsterone degradation 28 6 3
3-phenylpropanoate degradation 10 4 1
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) 10 4 1
L-lysine fermentation to acetate and butanoate 10 2 1
superpathway of cholesterol degradation I (cholesterol oxidase) 42 8 4
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 6 1
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 6 1
ethylmalonyl-CoA pathway 11 3 1
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 8 4
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) 12 1 1
10-cis-heptadecenoyl-CoA degradation (yeast) 12 1 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 19 2
superpathway of L-arginine and L-ornithine degradation 13 8 1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 1
1-butanol autotrophic biosynthesis (engineered) 27 18 2
androstenedione degradation II (anaerobic) 27 4 2
superpathway of glyoxylate cycle and fatty acid degradation 14 12 1
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 1
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 2 1
sitosterol degradation to androstenedione 18 1 1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) 22 2 1
superpathway of cholesterol degradation III (oxidase) 49 4 2
platensimycin biosynthesis 26 6 1
superpathway of ergosterol biosynthesis I 26 3 1
superpathway of cholesterol biosynthesis 38 3 1
superpathway of pentose and pentitol degradation 42 16 1
superpathway of L-lysine degradation 43 10 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 18 1