Experiment set7IT066 for Phaeobacter inhibens DSM 17395

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marine broth with Polymyxin B sulfate 0.0032 mg/ml

Group: stress
Media: marine_broth_2216 + Polymyxin B sulfate (0.0032 mg/ml)
Culturing: Phaeo_ML1, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Adam on marchapr14
Media components: 5 g/L Bacto Peptone, 1 g/L Yeast Extract, 0.1 g/L Ferric citrate, 19.45 g/L Sodium Chloride, 5.9 g/L Magnesium chloride hexahydrate, 3.24 g/L Magnesium sulfate, 1.8 g/L Calcium chloride, 0.55 g/L Potassium Chloride, 0.16 g/L Sodium bicarbonate, 0.08 g/L Potassium bromide, 34 mg/L Strontium chloride, 22 mg/L Boric Acid, 4 mg/L Sodium metasilicate, 2.4 mg/L sodium fluoride, 8 mg/L Disodium phosphate
Growth plate: 896 D5,D6

Specific Phenotypes

For 5 genes in this experiment

For stress Polymyxin B sulfate in Phaeobacter inhibens DSM 17395

For stress Polymyxin B sulfate across organisms

SEED Subsystems

Subsystem #Specific
Acetyl-CoA fermentation to Butyrate 1
Butanol Biosynthesis 1
Isoleucine degradation 1
Lipopolysaccharide-related cluster in Alphaproteobacteria 1
Polyhydroxybutyrate metabolism 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
benzoyl-CoA biosynthesis 3 3 3
fatty acid β-oxidation III (unsaturated, odd number) 1 1 1
fatty acid β-oxidation I (generic) 7 5 5
oleate β-oxidation 35 30 24
adipate degradation 5 5 3
adipate biosynthesis 5 4 3
fatty acid β-oxidation II (plant peroxisome) 5 3 3
glutaryl-CoA degradation 5 3 3
fatty acid β-oxidation IV (unsaturated, even number) 5 3 3
2-methyl-branched fatty acid β-oxidation 14 10 8
valproate β-oxidation 9 6 5
pyruvate fermentation to hexanol (engineered) 11 7 6
fatty acid salvage 6 6 3
oleate β-oxidation (thioesterase-dependent, yeast) 2 2 1
3-oxoadipate degradation 2 2 1
L-isoleucine degradation I 6 4 3
pyruvate fermentation to butanol II (engineered) 6 4 3
propanoate fermentation to 2-methylbutanoate 6 3 3
acetoacetate degradation (to acetyl CoA) 2 1 1
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 5 5
pyruvate fermentation to butanoate 7 3 3
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 3
benzoyl-CoA degradation I (aerobic) 7 3 3
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 5 2
5,6-dehydrokavain biosynthesis (engineered) 10 6 4
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) 10 4 4
fatty acid β-oxidation V (unsaturated, odd number, di-isomerase-dependent) 5 2 2
4-hydroxybenzoate biosynthesis III (plants) 5 2 2
pyruvate fermentation to butanol I 8 3 3
ketolysis 3 3 1
phenylacetate degradation I (aerobic) 9 6 3
polyhydroxybutanoate biosynthesis 3 2 1
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 5 3
methyl ketone biosynthesis (engineered) 6 3 2
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 3
oleate β-oxidation (reductase-dependent, yeast) 3 1 1
L-glutamate degradation V (via hydroxyglutarate) 10 4 3
3-phenylpropanoate degradation 10 4 3
superpathway of phenylethylamine degradation 11 6 3
(2S)-ethylmalonyl-CoA biosynthesis 4 3 1
L-valine degradation I 8 5 2
L-glutamate degradation VII (to butanoate) 12 4 3
2-methylpropene degradation 8 2 2
oleate β-oxidation (isomerase-dependent, yeast) 4 1 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 5 3
superpathway of glyoxylate cycle and fatty acid degradation 14 10 3
ketogenesis 5 3 1
L-tryptophan degradation III (eukaryotic) 15 5 3
androstenedione degradation I (aerobic) 25 6 5
methyl tert-butyl ether degradation 10 2 2
ethylbenzene degradation (anaerobic) 5 1 1
fatty acid β-oxidation VII (yeast peroxisome) 5 1 1
isopropanol biosynthesis (engineered) 5 1 1
pyruvate fermentation to acetone 5 1 1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 1 1
glycerol degradation to butanol 16 9 3
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 4 3
superpathway of testosterone and androsterone degradation 28 6 5
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 7 3
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 4 3
catechol degradation III (ortho-cleavage pathway) 6 4 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 11 3
6-gingerol analog biosynthesis (engineered) 6 2 1
toluene degradation VI (anaerobic) 18 4 3
superpathway of cholesterol degradation I (cholesterol oxidase) 42 8 7
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) 12 2 2
10-cis-heptadecenoyl-CoA degradation (yeast) 12 2 2
4-ethylphenol degradation (anaerobic) 6 1 1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast) 6 1 1
jasmonic acid biosynthesis 19 4 3
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 2
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 9 7
androstenedione degradation II (anaerobic) 27 4 4
superpathway of salicylate degradation 7 5 1
acetyl-CoA fermentation to butanoate 7 4 1
4-methylcatechol degradation (ortho cleavage) 7 4 1
mevalonate pathway I (eukaryotes and bacteria) 7 2 1
mevalonate pathway II (haloarchaea) 7 2 1
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 2
Spodoptera littoralis pheromone biosynthesis 22 3 3
2-deoxy-D-ribose degradation II 8 3 1
isoprene biosynthesis II (engineered) 8 2 1
mevalonate pathway IV (archaea) 8 2 1
mevalonate pathway III (Thermoplasma) 8 2 1
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 2 2
platensimycin biosynthesis 26 6 3
aromatic compounds degradation via β-ketoadipate 9 7 1
1-butanol autotrophic biosynthesis (engineered) 27 19 3
4-oxopentanoate degradation 9 2 1
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) 10 5 1
L-lysine fermentation to acetate and butanoate 10 3 1
ethylmalonyl-CoA pathway 11 7 1
toluene degradation III (aerobic) (via p-cresol) 11 7 1
gallate degradation III (anaerobic) 11 3 1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) 22 3 2
superpathway of cholesterol degradation III (oxidase) 49 5 4
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 20 2
mandelate degradation to acetyl-CoA 18 7 1
sitosterol degradation to androstenedione 18 1 1
superpathway of ergosterol biosynthesis I 26 4 1
superpathway of aerobic toluene degradation 30 11 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 14 1
superpathway of cholesterol biosynthesis 38 4 1
superpathway of L-lysine degradation 43 10 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 21 1