Experiment set6S16 for Pseudomonas sp. RS175

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Sodium octanoate carbon source

Group: carbon source
Media: MME_noCarbon + Sodium octanoate (10 mM)
Culturing: Pseudomonas_RS175_ML2, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C)
By: Andrew Frank on 1/31/23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 9 genes in this experiment

For carbon source Sodium octanoate in Pseudomonas sp. RS175

For carbon source Sodium octanoate across organisms

SEED Subsystems

Subsystem #Specific
ABC transporter dipeptide (TC 3.A.1.5.2) 1
Bacterial Chemotaxis 1
Biotin biosynthesis 1
Lysine Biosynthesis DAP Pathway 1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 1
Phenylalanine and Tyrosine Branches from Chorismate 1
Threonine and Homoserine Biosynthesis 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
long-chain fatty acid activation 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
L-phenylalanine biosynthesis III (cytosolic, plants) 2 2 1
atromentin biosynthesis 2 1 1
linoleate biosynthesis II (animals) 2 1 1
γ-linolenate biosynthesis II (animals) 2 1 1
L-tyrosine degradation II 2 1 1
fatty acid salvage 6 6 2
L-phenylalanine biosynthesis I 3 3 1
L-tyrosine biosynthesis I 3 3 1
L-homoserine biosynthesis 3 3 1
L-phenylalanine degradation II (anaerobic) 3 2 1
3-methyl-branched fatty acid α-oxidation 6 3 2
oleate biosynthesis I (plants) 3 1 1
alkane biosynthesis II 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
dipicolinate biosynthesis 4 3 1
L-phenylalanine biosynthesis II 4 3 1
spermidine biosynthesis II 4 3 1
L-tyrosine biosynthesis III 4 3 1
phytol degradation 4 3 1
L-phenylalanine degradation III 4 2 1
L-tyrosine degradation III 4 2 1
L-tyrosine biosynthesis II 4 2 1
L-methionine biosynthesis IV 4 2 1
long chain fatty acid ester synthesis (engineered) 4 1 1
phosphatidylcholine acyl editing 4 1 1
wax esters biosynthesis II 4 1 1
sporopollenin precursors biosynthesis 18 4 4
adipate degradation 5 5 1
L-tyrosine degradation I 5 5 1
octane oxidation 5 4 1
ectoine biosynthesis 5 3 1
superpathway of L-phenylalanine and L-tyrosine biosynthesis 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
superpathway of plastoquinol biosynthesis 5 2 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
superpathway of L-threonine biosynthesis 6 6 1
stearate biosynthesis II (bacteria and plants) 6 5 1
norspermidine biosynthesis 6 4 1
stearate biosynthesis IV 6 4 1
6-gingerol analog biosynthesis (engineered) 6 3 1
stearate biosynthesis I (animals) 6 1 1
L-lysine biosynthesis VI 7 6 1
L-lysine biosynthesis III 7 6 1
capsaicin biosynthesis 7 4 1
3-dehydroquinate biosynthesis II (archaea) 7 3 1
cremeomycin biosynthesis 7 2 1
ceramide degradation by α-oxidation 7 2 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
superpathway of L-homoserine and L-methionine biosynthesis 8 6 1
superpathway of polyamine biosynthesis III 8 5 1
2-deoxy-D-ribose degradation II 8 4 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
grixazone biosynthesis 8 2 1
oleate β-oxidation 35 30 4
superpathway of aromatic amino acid biosynthesis 18 18 2
L-lysine biosynthesis I 9 9 1
superpathway of S-adenosyl-L-methionine biosynthesis 9 7 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 7 1
L-lysine biosynthesis II 9 6 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 5 1
L-histidine biosynthesis 10 10 1
superpathway of L-tyrosine biosynthesis 10 10 1
superpathway of L-phenylalanine biosynthesis 10 10 1
rosmarinic acid biosynthesis I 10 2 1
suberin monomers biosynthesis 20 3 2
superpathway of fatty acid biosynthesis II (plant) 43 38 4
tropane alkaloids biosynthesis 11 1 1
(S)-reticuline biosynthesis I 11 1 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 12 1
chorismate biosynthesis II (archaea) 12 8 1
superpathway of L-isoleucine biosynthesis I 13 13 1
2-methyl-branched fatty acid β-oxidation 14 10 1
superpathway of rosmarinic acid biosynthesis 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 hyoscyamine (atropine) and scopolamine biosynthesis 16 3 1
cutin biosynthesis 16 1 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
aspartate superpathway 25 22 1
platensimycin biosynthesis 26 6 1
superpathway of fatty acids biosynthesis (E. coli) 53 49 2
anaerobic aromatic compound degradation (Thauera aromatica) 27 4 1
palmitate biosynthesis III 29 28 1
superpathway of chorismate metabolism 59 43 2
superpathway of histidine, purine, and pyrimidine biosynthesis 46 44 1