Experiment set10IT063 for Cupriavidus basilensis FW507-4G11

Protocatechuic Acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Protocatechuic Acid (10 mM)
Culturing: cupriavidus_4G11_ML11_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 3.2 generations
By: Allie Pearson on 08/26/2019
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 24 genes in this experiment

For carbon source Protocatechuic Acid in Cupriavidus basilensis FW507-4G11

For carbon source Protocatechuic Acid across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter oligopeptide (TC 3.A.1.5.1)	3
Salicylate and gentisate catabolism	3
Gentisare degradation	2
Homogentisate pathway of aromatic compound degradation	2
Protocatechuate branch of beta-ketoadipate pathway	2
Benzoate degradation	1
Copper homeostasis	1
Glycine cleavage system	1
Leucine Degradation and HMG-CoA Metabolism	1
Photorespiration (oxidative C2 cycle)	1
Proteolysis in bacteria, ATP-dependent	1
TCA Cycle	1
p-Hydroxybenzoate degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Benzoate degradation via hydroxylation
• Tyrosine metabolism
• 2,4-Dichlorobenzoate degradation
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Bile acid biosynthesis
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Pyruvate metabolism
• Toluene and xylene degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Fluorene degradation
• Styrene degradation
• Sulfur metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• 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
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
methylsalicylate degradation	2	2	2
salicylate degradation I	1	1	1
gentisate degradation I	3	3	2
assimilatory sulfate reduction III	3	3	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
glycine cleavage	3	3	1
glycine biosynthesis II	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
4-hydroxymandelate degradation	6	3	2
D-phenylglycine degradation	3	1	1
chlorosalicylate degradation	7	3	2
protocatechuate degradation II (ortho-cleavage pathway)	4	4	1
assimilatory sulfate reduction I	4	4	1
gentisate degradation II	4	4	1
4-chlorobenzoate degradation	4	2	1
4-sulfocatechol degradation	4	2	1
4-methylphenol degradation to protocatechuate	4	1	1
L-tyrosine degradation I	5	5	1
3-phenylpropanoate degradation	10	6	2
salicylate degradation IV	5	2	1
mandelate degradation I	5	2	1
bisphenol A degradation	5	2	1
4-coumarate degradation (aerobic)	5	2	1
toluene degradation III (aerobic) (via p-cresol)	11	7	2
5-nitroanthranilate degradation	6	3	1
2,5-xylenol and 3,5-xylenol degradation	13	5	2
superpathway of salicylate degradation	7	7	1
indole-3-acetate degradation II	7	2	1
spongiadioxin C biosynthesis	7	2	1
polybrominated dihydroxylated diphenyl ethers biosynthesis	8	2	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	25	4
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
aromatic compounds degradation via β-ketoadipate	9	9	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	7	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	21	4
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
naphthalene degradation to acetyl-CoA	12	6	1
superpathway of aerobic toluene degradation	30	19	2
mandelate degradation to acetyl-CoA	18	15	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	1