Experiment set10IT083 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 3.1 generations
By: Allie Pearson on 8/26/19
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 23 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
Salicylate and gentisate catabolism	4
Gentisare degradation	3
ABC transporter oligopeptide (TC 3.A.1.5.1)	2
Protocatechuate branch of beta-ketoadipate pathway	2
Benzoate degradation	1
Cinnamic Acid Degradation	1
Copper homeostasis	1
Glycine cleavage system	1
Homogentisate pathway of aromatic compound degradation	1
Hydantoin metabolism	1
Leucine Degradation and HMG-CoA Metabolism	1
Phenylpropanoid compound degradation	1
Photorespiration (oxidative C2 cycle)	1
Polyhydroxybutyrate metabolism	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:

• Tyrosine metabolism
• Benzoate degradation via hydroxylation
• 2,4-Dichlorobenzoate degradation
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Ascorbate and aldarate metabolism
• Bile acid biosynthesis
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Glycerophospholipid metabolism
• Pyruvate metabolism
• Toluene and xylene degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Fluorene degradation
• Styrene degradation
• Butanoate metabolism
• Retinol metabolism
• Sulfur metabolism
• Alkaloid biosynthesis II
• 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-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
glycine biosynthesis II	3	3	1
glycine cleavage	3	3	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
D-phenylglycine degradation	3	1	1
chlorosalicylate degradation	7	3	2
assimilatory sulfate reduction I	4	4	1
gentisate degradation II	4	4	1
protocatechuate degradation II (ortho-cleavage pathway)	4	4	1
4-sulfocatechol degradation	4	2	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
4-hydroxymandelate degradation	6	3	1
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
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
toluene degradation III (aerobic) (via p-cresol)	11	7	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	25	3
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
naphthalene degradation to acetyl-CoA	12	6	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	21	3
mandelate degradation to acetyl-CoA	18	15	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	1
superpathway of aerobic toluene degradation	30	19	1