Experiment set1IT034 for Burkholderia phytofirmans PsJN

LB with Paraquat dichloride 0.064 mg/ml

Group: stress
Media: LB + Paraquat dichloride (0.064 mg/ml)
Culturing: BFirm_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 3.8 generations
By: Mark on 6/2/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: BFirm_SP2 C3

Specific Phenotypes

For 4 genes in this experiment

For stress Paraquat dichloride in Burkholderia phytofirmans PsJN

For stress Paraquat dichloride across organisms

SEED Subsystems

Subsystem	#Specific
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Fatty acid metabolism
• Pyrimidine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Brassinosteroid biosynthesis
• Caprolactam degradation
• Biosynthesis of phenylpropanoids
• 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

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pseudouridine degradation	2	1	1
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 VII (acetate-producers)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
TCA cycle VI (Helicobacter)	9	6	2
2-methylcitrate cycle I	5	5	1
adipate degradation	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
fatty acid salvage	6	5	1
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
oleate β-oxidation	35	29	3
ethene biosynthesis V (engineered)	25	18	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2
2-methyl-branched fatty acid β-oxidation	14	9	1