Experiment set4S71 for Rhodopseudomonas palustris CGA009

PM with p-Coumaric acid carbon source

Group: carbon source
Media: PM + p-Coumaric acid (3 mM) + Sodium bicarbonate (10 mM)
Culturing: RPal_CGA009_ML8, Anaerobic, at 30 (C), shaken=0 rpm
By: Yasu on 23-Mar-23
Media components: 12.5 mM Disodium phosphate, 12.5 mM Potassium phosphate monobasic, 1 g/L Ammonium Sulfate, 0.1 mM Sodium thiosulfate pentahydrate, 0.002 g/L 4-Aminobenzoic acid, UW concentrated base (0.02 g/L Nitrilotriacetic acid, 0.0289 g/L Magnesium sulfate, 0.00667 g/L Calcium chloride dihydrate, 1.85e-05 g/L ammonium molybdate tetrahydrate, 0.000698 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L EDTA, 0.001095 g/L Zinc sulfate heptahydrate, 0.000154 g/L Manganese (II) sulfate monohydrate, 3.92e-05 g/L Copper (II) sulfate pentahydrate, 2.5e-05 g/L Cobalt(II) nitrate hexahydrate, 1.77e-05 g/L sodium tetraborate decahydrate)

Specific Phenotypes

For 8 genes in this experiment

For carbon source p-Coumaric acid in Rhodopseudomonas palustris CGA009

For carbon source p-Coumaric acid across organisms

SEED Subsystems

Subsystem	#Specific
Benzoate transport and degradation cluster	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Nitric oxide synthase	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Benzoate degradation via CoA ligation
• Ubiquinone and menaquinone biosynthesis
• Tryptophan metabolism
• Biosynthesis of plant hormones
• Ascorbate and aldarate metabolism
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Biosynthesis of steroids
• Bile acid biosynthesis
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine degradation
• gamma-Hexachlorocyclohexane degradation
• Benzoxazinone biosynthesis
• Sphingolipid metabolism
• 2,4-Dichlorobenzoate degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Phenylpropanoid biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
benzoate degradation II (aerobic and anaerobic)	1	1	1
4-hydroxybenzoate biosynthesis III (plants)	5	5	3
benzoyl-CoA biosynthesis	3	3	1
4-coumarate degradation (anaerobic)	6	5	2
umbelliferone biosynthesis	3	2	1
ferulate degradation	3	1	1
phenol degradation II (anaerobic)	4	2	1
4-chlorobenzoate degradation	4	2	1
propane degradation I	4	1	1
naringenin biosynthesis (engineered)	4	1	1
xanthohumol biosynthesis	4	1	1
oleate β-oxidation	35	28	8
valproate β-oxidation	9	5	2
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	4	2
2-methyl-branched fatty acid β-oxidation	14	10	3
adipate degradation	5	5	1
adipate biosynthesis	5	5	1
4-coumarate degradation (aerobic)	5	4	1
glutaryl-CoA degradation	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	3	1
chlorogenic acid biosynthesis II	5	1	1
flavonoid biosynthesis	5	1	1
phaselate biosynthesis	5	1	1
pyruvate fermentation to hexanol (engineered)	11	7	2
fatty acid salvage	6	6	1
L-isoleucine degradation I	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
6-gingerol analog biosynthesis (engineered)	6	3	1
methyl ketone biosynthesis (engineered)	6	3	1
propanoate fermentation to 2-methylbutanoate	6	3	1
benzoyl-CoA degradation I (aerobic)	7	5	1
fatty acid β-oxidation I (generic)	7	5	1
pyruvate fermentation to butanoate	7	4	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
pyruvate fermentation to butanol I	8	3	1
2-methylpropene degradation	8	2	1
chlorogenic acid biosynthesis I	8	1	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	7	2
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	6	1
phenylacetate degradation I (aerobic)	9	5	1
avenanthramide biosynthesis	9	1	1
3-phenylpropanoate degradation	10	4	1
L-glutamate degradation V (via hydroxyglutarate)	10	4	1
rosmarinic acid biosynthesis I	10	2	1
methyl tert-butyl ether degradation	10	2	1
curcuminoid biosynthesis	10	1	1
superpathway of phenylethylamine degradation	11	6	1
L-glutamate degradation VII (to butanoate)	12	5	1
androstenedione degradation I (aerobic)	25	6	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
coumarins biosynthesis (engineered)	13	3	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	8	2
androstenedione degradation II (anaerobic)	27	4	2
superpathway of glyoxylate cycle and fatty acid degradation	14	12	1
superpathway of testosterone and androsterone degradation	28	6	2
superpathway of cholesterol degradation I (cholesterol oxidase)	42	8	3
superpathway of rosmarinic acid biosynthesis	14	2	1
flavonoid di-C-glucosylation	15	3	1
L-tryptophan degradation III (eukaryotic)	15	3	1
monolignol biosynthesis	15	1	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	9	3
glycerol degradation to butanol	16	9	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	5	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	12	1
toluene degradation VI (anaerobic)	18	5	1
suberin monomers biosynthesis	20	3	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	3	1
superpathway of cholesterol degradation III (oxidase)	49	5	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	20	1
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	21	1