Experiment set6S18 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 10 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 degradation	1
Methicillin resistance in Staphylococci	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
Phenylalanine and Tyrosine Branches from Chorismate	1
Teichoic and lipoteichoic acids 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:

• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• High-mannose type N-glycan biosynthesis
• Sphingolipid metabolism
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Fructose and mannose metabolism
• Fatty acid metabolism
• Methionine metabolism
• Lysine biosynthesis
• Histidine metabolism
• Aminophosphonate metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Nucleotide sugars metabolism
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Glycerophospholipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis I
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

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
L-tyrosine degradation II	2	1	1
γ-linolenate 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
oleate biosynthesis I (plants)	3	1	1
alkane biosynthesis II	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-phenylalanine biosynthesis II	4	3	1
phytol degradation	4	3	1
L-tyrosine biosynthesis III	4	3	1
L-tyrosine biosynthesis II	4	2	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	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
L-tyrosine degradation I	5	5	1
adipate degradation	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
Salmonella enterica serotype O:54 O antigen biosynthesis	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
enterobacterial common antigen biosynthesis	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
Escherichia coli serotype O:15 O antigen biosynthesis	5	1	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	3	1
Escherichia coli serotype O:77/Salmonella enterica serotype O:6,14 O antigen biosynthesis	6	1	1
Salmonella enterica serotype O:13 O antigen biosynthesis	6	1	1
Escherichia coli serotype O:177 O antigen biosynthesis	6	1	1
Escherichia coli serotype O:56 O antigen biosynthesis	6	1	1
Escherichia coli serotype O:149/Shigella boydii serotype O1 O antigen biosynthesis	6	1	1
Escherichia coli serotype O:50 O antigen biosynthesis	6	1	1
stearate biosynthesis I (animals)	6	1	1
capsaicin biosynthesis	7	4	1
ceramide degradation by α-oxidation	7	2	1
Salmonella enterica serotype O:18 O antigen biosynthesis	7	1	1
Escherichia coli serotype O:7 O antigen biosynthesis	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
Escherichia coli serotype O:2 O antigen biosynthesis	7	1	1
Escherichia coli serotype O:152 O antigen biosynthesis	7	1	1
Salmonella enterica serotype O:6,7 O antigen biosynthesis	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
Escherichia coli serotype O:71/Salmonella enterica serotype O:28ac O antigen biosynthesis	7	1	1
Salmonella enterica serotype O:39 O antigen biosynthesis	7	1	1
Escherichia coli serotype O:1B/Salmonella enterica serotype O:42 O antigen biosynthesis	7	1	1
Escherichia coli serotype O:85/Salmonella enterica serotype O:17 O antigen biosynthesis	7	1	1
Escherichia coli serotype O:157/Salmonella enterica serotype O:30 O antigen biosynthesis	7	1	1
Escherichia coli serotype O:111/Salmonella enterica serotype O:35 O antigen biosynthesis	7	1	1
2-deoxy-D-ribose degradation II	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
Escherichia coli serotype O:86 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:128 O antigen biosynthesis	8	1	1
Shigella boydii serotype 6 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:55/Salmonella enterica serotype O:50 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:49 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:104 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:127 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:52 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:107 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:21/Salmonella enterica serotype O:38 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:117 O antigen biosynthesis	8	1	1
Escherichia coli serotype O:51/Salmonella enterica serotype O:57 O antigen biosynthesis	8	1	1
oleate β-oxidation	35	30	4
superpathway of aromatic amino acid biosynthesis	18	18	2
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
Escherichia coli serotype O:8 O antigen biosynthesis	9	2	1
Escherichia coli serotype O:169 O antigen biosynthesis	9	1	1
Escherichia coli serotype O:183/Shigella boydii serotype O:10 O antigen biosynthesis	9	1	1
L-histidine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of enterobacterial common antigen biosynthesis	10	4	1
rosmarinic acid biosynthesis I	10	2	1
suberin monomers biosynthesis	20	3	2
Escherichia coli serotype O:9 O antigen biosynthesis	10	1	1
Escherichia coli serotype O:9a O antigen biosynthesis	10	1	1
poly(3-O-β-D-glucopyranosyl-N-acetylgalactosamine 1-phosphate) wall teichoic acid biosynthesis	10	1	1
superpathway of fatty acid biosynthesis II (plant)	43	38	4
poly(glycerol phosphate) wall teichoic acid biosynthesis	11	1	1
(S)-reticuline biosynthesis I	11	1	1
tropane alkaloids biosynthesis	11	1	1
poly(ribitol phosphate) wall teichoic acid biosynthesis I (B. subtilis)	12	1	1
2-methyl-branched fatty acid β-oxidation	14	10	1
superpathway of rosmarinic acid biosynthesis	14	2	1
poly(ribitol phosphate) wall teichoic acid biosynthesis II (S. aureus)	14	1	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
H. pylori 26695 O-antigen biosynthesis	21	1	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