Experiment set6S17 for Pseudomonas sp. RS175

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 12 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
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Lysine degradation	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
Phenylalanine and Tyrosine Branches from Chorismate	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:

• Phenylalanine, tyrosine and tryptophan biosynthesis
• Biosynthesis of phenylpropanoids
• Tyrosine metabolism
• Phenylalanine metabolism
• Novobiocin biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of alkaloids derived from shikimate pathway
• Fatty acid metabolism
• Methionine metabolism
• Lysine biosynthesis
• Histidine metabolism
• Alkaloid biosynthesis I
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
long-chain fatty acid activation	1	1	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
3-dehydroquinate biosynthesis I	2	2	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
linoleate biosynthesis II (animals)	2	1	1
fatty acid salvage	6	6	2
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
oleate biosynthesis I (plants)	3	1	1
alkane biosynthesis II	3	1	1
L-phenylalanine biosynthesis II	4	3	1
L-tyrosine biosynthesis III	4	3	1
phytol degradation	4	3	1
L-tyrosine degradation III	4	2	1
L-tyrosine biosynthesis II	4	2	1
L-phenylalanine degradation III	4	2	1
phosphatidylcholine acyl editing	4	1	1
wax esters biosynthesis II	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
sporopollenin precursors biosynthesis	18	4	4
superpathway of L-tyrosine biosynthesis	10	10	2
superpathway of L-phenylalanine biosynthesis	10	10	2
adipate degradation	5	5	1
L-tyrosine degradation I	5	5	1
octane oxidation	5	4	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
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
superpathway of aromatic amino acid biosynthesis	18	18	3
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	3	1
stearate biosynthesis I (animals)	6	1	1
chorismate biosynthesis I	7	7	1
capsaicin biosynthesis	7	4	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
2-deoxy-D-ribose degradation II	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
oleate β-oxidation	35	30	4
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
Escherichia coli serotype O:8 O antigen biosynthesis	9	2	1
L-histidine 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
(S)-reticuline biosynthesis I	11	1	1
tropane alkaloids biosynthesis	11	1	1
superpathway of L-tryptophan biosynthesis	13	13	1
2-methyl-branched fatty acid β-oxidation	14	10	1
superpathway of rosmarinic acid biosynthesis	14	2	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 chorismate metabolism	59	43	3
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 histidine, purine, and pyrimidine biosynthesis	46	44	1