Experiment set19IT088 for Pseudomonas fluorescens SBW25-INTG

p-Coumaric acid (C) and Ammonium chloride (N); with MOPS

Group: no stress control
Media: MME_noNitrogen_noCarbon + p-Coumaric acid (5 mM) + Ammonium chloride (10 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on September 1, 2021
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 15 genes in this experiment

For no stress control p-Coumaric acid in Pseudomonas fluorescens SBW25-INTG

For no stress control p-Coumaric acid across organisms

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	2
Alginate metabolism	1
Arginine and Ornithine Degradation	1
Cinnamic Acid Degradation	1
D-Galacturonate and D-Glucuronate Utilization	1
Gentisare degradation	1
LMPTP YfkJ cluster	1
LMPTP YwlE cluster	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:

• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Purine metabolism
• Pyrimidine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Benzoate degradation via CoA ligation
• Styrene degradation
• Nicotinate and nicotinamide metabolism
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
putrescine biosynthesis II	3	3	2
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	2
indole-3-acetate biosynthesis IV (bacteria)	2	2	1
indole-3-acetate biosynthesis III (bacteria)	2	2	1
polyphosphate metabolism	2	2	1
acrylonitrile degradation I	2	2	1
superpathway of acrylonitrile degradation	3	2	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
NAD salvage pathway III (to nicotinamide riboside)	3	2	1
UTP and CTP dephosphorylation I	7	5	2
purine nucleotides degradation II (aerobic)	11	11	3
inosine 5'-phosphate degradation	4	4	1
guanosine nucleotides degradation III	4	4	1
guanosine nucleotides degradation II	4	4	1
adenosine nucleotides degradation I	8	7	2
purine nucleotides degradation I (plants)	12	10	3
superpathway of polyamine biosynthesis II	8	6	2
guanosine nucleotides degradation I	4	3	1
adenosine nucleotides degradation II	5	5	1
adipate degradation	5	5	1
fatty acid salvage	6	6	1
superpathway of guanosine nucleotides degradation (plants)	6	5	1
superpathway of purines degradation in plants	18	14	3
ureide biosynthesis	7	6	1
tunicamycin biosynthesis	9	2	1
NAD salvage (plants)	11	5	1
oleate β-oxidation	35	33	3
indole-3-acetate biosynthesis II	12	5	1
2-methyl-branched fatty acid β-oxidation	14	11	1