Experiment set11IT024 for Burkholderia phytofirmans PsJN

Protocatechuic Acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Protocatechuic Acid (10 mM)
Culturing: BFirm_ML3_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 2.6 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 2 genes in this experiment

For carbon source Protocatechuic Acid in Burkholderia phytofirmans PsJN

For carbon source Protocatechuic Acid across organisms

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Citrate cycle (TCA cycle)
• Glyoxylate and dicarboxylate metabolism
• Propanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• 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
glyoxylate cycle	6	6	2
partial TCA cycle (obligate autotrophs)	8	7	2
nitrogen remobilization from senescing leaves	8	6	2
TCA cycle V (2-oxoglutarate synthase)	9	8	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
TCA cycle VII (acetate-producers)	9	7	2
TCA cycle VI (Helicobacter)	9	6	2
2-methylcitrate cycle I	5	5	1
TCA cycle I (prokaryotic)	10	8	2
TCA cycle III (animals)	10	7	2
reductive TCA cycle I	11	6	2
superpathway of glyoxylate bypass and TCA	12	10	2
2-methylcitrate cycle II	6	5	1
reductive TCA cycle II	12	6	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
mixed acid fermentation	16	13	2
methylaspartate cycle	19	11	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	17	2
ethene biosynthesis V (engineered)	25	18	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2