Experiment set10IT058 for Cupriavidus basilensis FW507-4G11

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Pimelic acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Pimelic acid (10 mM)
Culturing: cupriavidus_4G11_ML11_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 3.3 generations
By: Allie Pearson on 08/26/2019
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 19 genes in this experiment

For carbon source Pimelic acid in Cupriavidus basilensis FW507-4G11

For carbon source Pimelic acid across organisms

SEED Subsystems

Subsystem #Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 5
Benzoate transport and degradation cluster 2
Homogentisate pathway of aromatic compound degradation 2
Heat shock dnaK gene cluster extended 1
Heme and Siroheme Biosynthesis 1
Methionine Biosynthesis 1
Queuosine-Archaeosine Biosynthesis 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
long-chain fatty acid activation 1 1 1
L-homocysteine biosynthesis 2 2 1
linoleate biosynthesis II (animals) 2 1 1
γ-linolenate biosynthesis II (animals) 2 1 1
superpathway of L-cysteine biosynthesis (fungi) 6 3 2
3-methyl-branched fatty acid α-oxidation 6 3 2
oleate biosynthesis I (plants) 3 1 1
alkane biosynthesis II 3 1 1
L-methionine biosynthesis III 4 4 1
phytol degradation 4 3 1
wax esters biosynthesis II 4 1 1
homocysteine and cysteine interconversion 4 1 1
long chain fatty acid ester synthesis (engineered) 4 1 1
phosphatidylcholine acyl editing 4 1 1
sporopollenin precursors biosynthesis 18 8 4
octane oxidation 5 4 1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) 10 7 2
L-methionine biosynthesis I 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III 5 1 1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II 5 1 1
stearate biosynthesis II (bacteria and plants) 6 5 1
L-methionine biosynthesis II 6 5 1
fatty acid salvage 6 5 1
stearate biosynthesis IV 6 4 1
6-gingerol analog biosynthesis (engineered) 6 3 1
methylthiopropanoate degradation I (cleavage) 6 2 1
stearate biosynthesis I (animals) 6 2 1
ceramide degradation by α-oxidation 7 2 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
capsaicin biosynthesis 7 1 1
superpathway of L-homoserine and L-methionine biosynthesis 8 6 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
superpathway of dimethylsulfoniopropanoate degradation 8 2 1
superpathway of S-adenosyl-L-methionine biosynthesis 9 7 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 7 1
suberin monomers biosynthesis 20 5 2
superpathway of fatty acid biosynthesis II (plant) 43 38 4
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 12 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
cutin biosynthesis 16 3 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
aspartate superpathway 25 23 1
superpathway of fatty acids biosynthesis (E. coli) 53 50 2
palmitate biosynthesis III 29 21 1
oleate β-oxidation 35 29 1