Experiment set11IT013 for Pseudomonas fluorescens SBW25-INTG

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

Group: stress
Media: MME_noNitrogen_noCarbon + p-Coumaric acid (5 mM) + Ammonium chloride (10 mM) + TAPS sodium salt (20 mM) + Sodium Chloride (400 mM), pH=8.5
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1300 rpm
By: Rob Egbert on 11-May-21
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 74 genes in this experiment

For stress p-Coumaric acid in Pseudomonas fluorescens SBW25-INTG

For stress p-Coumaric acid across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	4
Bacterial Chemotaxis	2
Flagellar motility	2
Flagellum	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Glutathione-regulated potassium-efflux system and associated functions	2
Glycogen metabolism	2
Maltose and Maltodextrin Utilization	2
Multidrug Resistance Efflux Pumps	2
Ribosome biogenesis bacterial	2
Siderophore Pyoverdine	2
Two-component regulatory systems in Campylobacter	2
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	1
ATP-dependent RNA helicases, bacterial	1
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Arginine and Ornithine Degradation	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Benzoate transport and degradation cluster	1
Butanol Biosynthesis	1
CBSS-262719.3.peg.410	1
Calvin-Benson cycle	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Glutamate dehydrogenases	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerol fermenation to 1,3-propanediol	1
HMG CoA Synthesis	1
Heat shock dnaK gene cluster extended	1
Hydantoin metabolism	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
Leucine Degradation and HMG-CoA Metabolism	1
Lipid A modifications	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	1
Orphan regulatory proteins	1
Pentose phosphate pathway	1
Potassium homeostasis	1
Putative TldE-TldD proteolytic complex	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
SigmaB stress responce regulation	1
Terminal cytochrome C oxidases	1
Trehalose Biosynthesis	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Starch and sucrose metabolism
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Arginine and proline metabolism
• Pentose phosphate pathway
• Glutamate metabolism
• Tryptophan metabolism
• Benzoate degradation via CoA ligation
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Galactose metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Pyrimidine metabolism
• Geraniol degradation
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Benzoxazinone biosynthesis
• D-Glutamine and D-glutamate metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Porphyrin and chlorophyll metabolism
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of ansamycins
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• mTOR signaling pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine degradation I	1	1	1
L-glutamate degradation I	1	1	1
cis-cyclopropane fatty acid (CFA) biosynthesis	1	1	1
trehalose biosynthesis IV	1	1	1
starch degradation V	4	3	3
pentose phosphate pathway (partial)	3	3	2
glycogen degradation I	8	6	5
arsenate detoxification III	2	2	1
L-glutamate biosynthesis I	2	2	1
UDP-α-D-glucose biosynthesis	2	2	1
glycogen degradation II	6	5	3
starch degradation III	4	2	2
arsenite to oxygen electron transfer	2	1	1
sterculate biosynthesis	2	1	1
pseudouridine degradation	2	1	1
pentose phosphate pathway (non-oxidative branch) I	5	5	2
sucrose biosynthesis II	8	6	3
glycerol degradation I	3	3	1
ammonia assimilation cycle III	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
pentose phosphate pathway (non-oxidative branch) II	6	5	2
GDP-α-D-glucose biosynthesis	3	2	1
trehalose degradation V	3	2	1
D-apiose degradation I	3	2	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
ethene biosynthesis IV (engineered)	3	1	1
pentose phosphate pathway	8	8	2
glycerol and glycerophosphodiester degradation	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
aerobic respiration I (cytochrome c)	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
sucrose degradation IV (sucrose phosphorylase)	4	3	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	2
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	6	2
dTDP-β-L-rhamnose biosynthesis	5	5	1
L-arginine degradation II (AST pathway)	5	5	1
Rubisco shunt	10	8	2
glucose and glucose-1-phosphate degradation	5	4	1
sucrose degradation II (sucrose synthase)	5	4	1
D-galactose degradation I (Leloir pathway)	5	3	1
ferrichrome A biosynthesis	5	2	1
glucosylglycerol biosynthesis	5	2	1
CDP-6-deoxy-D-gulose biosynthesis	5	1	1
fatty acid salvage	6	6	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	2
L-leucine degradation I	6	5	1
arsenic detoxification (plants)	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
Fe(II) oxidation	6	3	1
Calvin-Benson-Bassham cycle	13	10	2
L-glutamate and L-glutamine biosynthesis	7	6	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
4-aminobutanoate degradation V	7	3	1
L-citrulline biosynthesis	8	8	1
superpathway of glucose and xylose degradation	17	16	2
oxygenic photosynthesis	17	11	2
sucrose biosynthesis I (from photosynthesis)	9	7	1
1-butanol autotrophic biosynthesis (engineered)	27	19	3
chitin biosynthesis	9	5	1
starch degradation II	9	1	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
starch biosynthesis	10	5	1
colanic acid building blocks biosynthesis	11	11	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
pyruvate fermentation to hexanol (engineered)	11	7	1
superpathway of L-citrulline metabolism	12	10	1
arsenic detoxification (yeast)	12	4	1
ethene biosynthesis V (engineered)	25	18	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
Bifidobacterium shunt	15	12	1
arsenic detoxification (mammals)	17	8	1
streptomycin biosynthesis	18	2	1
superpathway of anaerobic sucrose degradation	19	14	1
methylaspartate cycle	19	9	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1
oleate β-oxidation	35	33	1
mycolate biosynthesis	205	20	3
superpathway of mycolate biosynthesis	239	21	3