Experiment set9IT065 for Sinorhizobium meliloti 1021

Myristic acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Myristic acid (10 mM)
Culturing: Smeli_ML6_JBEI, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Catharine Adams on 11/8/20
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 23 genes in this experiment

For carbon source Myristic acid in Sinorhizobium meliloti 1021

For carbon source Myristic acid across organisms

SEED Subsystems

Subsystem	#Specific
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	2
Serine-glyoxylate cycle	2
Bacterial Chemotaxis	1
Biotin biosynthesis	1
Phosphate metabolism	1
Propionyl-CoA to Succinyl-CoA Module	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:

• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Nucleotide sugars metabolism
• Benzoate degradation via CoA ligation
• Fructose and mannose metabolism
• Ubiquinone and menaquinone biosynthesis
• C21-Steroid hormone metabolism
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Bisphenol A degradation
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Linoleic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• Glyoxylate and dicarboxylate metabolism
• Propanoate metabolism
• Butanoate metabolism
• Retinol metabolism
• Brassinosteroid biosynthesis
• Caprolactam degradation
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide products
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
long-chain fatty acid activation	1	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
linoleate biosynthesis II (animals)	2	1	1
propanoyl CoA degradation I	3	3	1
fatty acid salvage	6	5	2
3-methyl-branched fatty acid α-oxidation	6	3	2
alkane biosynthesis II	3	1	1
conversion of succinate to propanoate	3	1	1
oleate biosynthesis I (plants)	3	1	1
phytol degradation	4	3	1
2-oxobutanoate degradation I	4	3	1
wax esters biosynthesis II	4	1	1
phosphatidylcholine acyl editing	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
sporopollenin precursors biosynthesis	18	4	4
adipate degradation	5	5	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
glyoxylate cycle	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	2	1
stearate biosynthesis I (animals)	6	1	1
pyruvate fermentation to propanoate I	7	4	1
ceramide degradation by α-oxidation	7	2	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
2-deoxy-D-ribose degradation II	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
oleate β-oxidation	35	29	4
anaerobic energy metabolism (invertebrates, mitochondrial)	10	7	1
suberin monomers biosynthesis	20	2	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
L-glutamate degradation VIII (to propanoate)	11	4	1
superpathway of glyoxylate bypass and TCA	12	11	1
3-hydroxypropanoate cycle	13	7	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	7	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	1
2-methyl-branched fatty acid β-oxidation	14	9	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	3	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
superpathway of L-methionine salvage and degradation	16	9	1
cutin biosynthesis	16	1	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	10	1
superpathway of the 3-hydroxypropanoate cycle	18	7	1
methylaspartate cycle	19	12	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
superpathway of fatty acids biosynthesis (E. coli)	53	49	2
palmitate biosynthesis III	29	28	1