Experiment set12IT025 for Paraburkholderia graminis OAS925

RCH2_defined_glucose_5mM with Cinnamic acid 5 mM

Group: stress
Media: RCH2_defined_glucose_5mM + Cinnamic acid (5 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Burkholderia_OAS925_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Albina on 15-Mar-22
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 5 mM D-Glucose, 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 15 genes in this experiment

For stress Cinnamic acid in Paraburkholderia graminis OAS925

For stress Cinnamic acid across organisms

SEED Subsystems

Subsystem	#Specific
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Isoprenoid Biosynthesis	1
Phosphonate metabolism	1
Phosphorylcholine incorporation in LPS	1
Ribosome biogenesis bacterial	1
polyprenyl synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Aminophosphonate metabolism
• Methionine metabolism
• Lysine biosynthesis
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Pyrimidine metabolism
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Nucleotide sugars metabolism
• Glycerophospholipid metabolism
• Terpenoid biosynthesis
• Caprolactam degradation
• Alkaloid biosynthesis I
• 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
2-aminoethylphosphonate biosynthesis	3	3	3
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
2-aminoethylphosphonate degradation II	2	2	1
methylphosphonate biosynthesis	4	2	2
atromentin biosynthesis	2	1	1
pseudouridine degradation	2	1	1
L-tyrosine degradation II	2	1	1
cardiolipin biosynthesis II	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
cardiolipin biosynthesis I	3	2	1
cardiolipin biosynthesis III	3	2	1
2-aminoethylphosphonate degradation I	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
fosfomycin biosynthesis	7	2	2
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
methylerythritol phosphate pathway II	9	8	2
methylerythritol phosphate pathway I	9	7	2
L-tyrosine degradation I	5	5	1
isoprene biosynthesis I	10	7	2
superpathway of plastoquinol biosynthesis	5	2	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
phosphatidylglycerol biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis II	6	6	1
superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP)	12	10	2
rhizocticin A and B biosynthesis	12	2	2
taxadiene biosynthesis (engineered)	13	10	2
dehydrophos biosynthesis	13	2	2
superpathway of aromatic amino acid biosynthesis	18	18	2
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
L-histidine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	2	1
FR-900098 and FR-33289 antibiotics biosynthesis	10	1	1
(S)-reticuline biosynthesis I	11	1	1
tropane alkaloids biosynthesis	11	1	1
superpathway of phospholipid biosynthesis III (E. coli)	12	10	1
phosphinothricin tripeptide biosynthesis	25	6	2
phosalacine biosynthesis	25	6	2
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
superpathway of ergosterol biosynthesis II	26	11	2
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	5	1
superpathway of phospholipid biosynthesis II (plants)	28	10	1
superpathway of chorismate metabolism	59	42	2
superpathway of histidine, purine, and pyrimidine biosynthesis	46	44	1