Experiment set16IT020 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 8 (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 43 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
ABC transporter oligopeptide (TC 3.A.1.5.1)	6
Ammonia assimilation	1
Coenzyme A Biosynthesis	1
DNA repair, bacterial MutL-MutS system	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine cleavage system	1
Isoleucine degradation	1
KDO2-Lipid A biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Lipid A modifications	1
Lysine degradation	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
Orphan regulatory proteins	1
Peptidoglycan Biosynthesis	1
Pyruvate Alanine Serine Interconversions	1
Queuosine-Archaeosine Biosynthesis	1
Ribosome biogenesis bacterial	1
Rubrerythrin	1
Valine degradation	1
cAMP signaling in bacteria	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ascorbate and aldarate metabolism
• Valine, leucine and isoleucine degradation
• Nucleotide sugars metabolism
• Ubiquinone and menaquinone biosynthesis
• Alanine and aspartate metabolism
• beta-Alanine metabolism
• Propanoate metabolism
• Butanoate metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• C21-Steroid hormone metabolism
• Purine metabolism
• Caffeine metabolism
• Pyrimidine metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Bisphenol A degradation
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Glutathione metabolism
• Starch and sucrose metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Linoleic acid metabolism
• Tetrachloroethene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Pantothenate and CoA biosynthesis
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide products

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis V	1	1	1
UDP-α-D-glucuronate biosynthesis (from UDP-glucose)	1	1	1
L-glutamine degradation I	1	1	1
β-alanine degradation II	2	2	1
4-aminobutanoate degradation III	2	2	1
ammonia assimilation cycle II	2	2	1
L-glutamate biosynthesis I	2	2	1
4-aminobutanoate degradation I	2	2	1
4-aminobutanoate degradation II	2	2	1
GABA shunt II	4	3	2
pseudouridine degradation	2	1	1
UDP-α-D-xylose biosynthesis	2	1	1
superpathway of 4-aminobutanoate degradation	3	3	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
superpathway of ammonia assimilation (plants)	3	3	1
ammonia assimilation cycle III	3	3	1
urate conversion to allantoin I	3	2	1
L-glutamate and L-glutamine biosynthesis	7	6	2
phosphopantothenate biosynthesis I	4	4	1
queuosine biosynthesis I (de novo)	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
phosphopantothenate biosynthesis III (archaea)	4	2	1
GABA shunt I	4	2	1
L-lysine degradation IV	5	5	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	2
β-alanine biosynthesis II	6	5	1
L-leucine degradation I	6	5	1
L-lysine degradation X	6	5	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
L-lysine degradation III	6	2	1
ureide biosynthesis	7	6	1
L-lysine degradation I	7	4	1
4-aminobutanoate degradation V	7	3	1
L-citrulline biosynthesis	8	8	1
nitrogen remobilization from senescing leaves	8	6	1
superpathway of coenzyme A biosynthesis I (bacteria)	9	8	1
UDP-sugars interconversion	9	2	1
teichuronic acid biosynthesis (B. subtilis 168)	9	2	1
peptidoglycan recycling II	10	8	1
methyl tert-butyl ether degradation	10	4	1
colanic acid building blocks biosynthesis	11	11	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
superpathway of L-citrulline metabolism	12	10	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
peptidoglycan recycling I	14	11	1
nicotine degradation I (pyridine pathway)	17	5	1
superpathway of purines degradation in plants	18	14	1
superpathway of L-lysine degradation	43	17	1