Experiment set11IT050 for Paraburkholderia graminis OAS925

shik 5mM

Group: carbon source
Media: RCH2_defined_noCarbon + Shikimic Acid (5 mM)
Culturing: Burkholderia_OAS925_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
By: Marta Torres on 26-Aug-21
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 8 genes in this experiment

For carbon source Shikimic Acid in Paraburkholderia graminis OAS925

For carbon source Shikimic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Homogentisate pathway of aromatic compound degradation	3
Aromatic amino acid degradation	2
Plastoquinone Biosynthesis	2
Tocopherol Biosynthesis	2
Bacterial hemoglobins	1
Chorismate Synthesis	1
Cinnamic Acid Degradation	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Gentisare degradation	1
Phenylpropanoid compound degradation	1
Proline, 4-hydroxyproline uptake and utilization	1
Salicylate and gentisate catabolism	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:

• Ubiquinone and menaquinone biosynthesis
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
plastoquinol-9 biosynthesis I	3	1	1
chorismate biosynthesis from 3-dehydroquinate	5	5	1
L-tyrosine degradation I	5	5	1
superpathway of plastoquinol biosynthesis	5	2	1
chorismate biosynthesis I	7	7	1
vitamin E biosynthesis (tocopherols)	7	1	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
chorismate biosynthesis II (archaea)	12	8	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of chorismate metabolism	59	42	1