Experiment set2IT069 for Cupriavidus basilensis FW507-4G11

4-Hydroxybenzoic Acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 4-Hydroxybenzoic Acid (20 mM), pH=7
Culturing: cupriavidus_4G11_ML11, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Jayashree on 3/3/2015
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 11 genes in this experiment

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

For carbon source 4-Hydroxybenzoic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Protocatechuate branch of beta-ketoadipate pathway	4
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	2
Catechol branch of beta-ketoadipate pathway	1
Chloroaromatic degradation pathway	1
Folate Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
One-carbon metabolism by tetrahydropterines	1
Serine-glyoxylate 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
• 2,4-Dichlorobenzoate degradation
• Geraniol degradation
• Aminophosphonate metabolism
• High-mannose type N-glycan biosynthesis
• Nucleotide sugars metabolism
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• One carbon pool by folate

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
protocatechuate degradation II (ortho-cleavage pathway)	4	4	2
3-oxoadipate degradation	2	2	1
toluene degradation III (aerobic) (via p-cresol)	11	7	4
aromatic compounds degradation via β-ketoadipate	9	9	3
cardiolipin biosynthesis II	3	3	1
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas)	4	3	1
4-sulfocatechol degradation	4	2	1
4-chlorobenzoate degradation	4	2	1
4-methylphenol degradation to protocatechuate	4	1	1
adipate degradation	5	5	1
adipate biosynthesis	5	5	1
bisphenol A degradation	5	2	1
4-coumarate degradation (aerobic)	5	2	1
catechol degradation III (ortho-cleavage pathway)	6	6	1
4-hydroxymandelate degradation	6	3	1
superpathway of salicylate degradation	7	7	1
4-methylcatechol degradation (ortho cleavage)	7	5	1
spongiadioxin C biosynthesis	7	2	1
superpathway of aerobic toluene degradation	30	19	4
polybrominated dihydroxylated diphenyl ethers biosynthesis	8	2	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	25	4
folate transformations III (E. coli)	9	9	1
folate transformations II (plants)	11	10	1
folate transformations I	13	9	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
mandelate degradation to acetyl-CoA	18	15	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	21	1