Experiment set11IT062 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 33 (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 47 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	2
Glycogen metabolism	2
Iron acquisition in Vibrio	2
Maltose and Maltodextrin Utilization	2
Transport of Iron	2
ABC transporter alkylphosphonate (TC 3.A.1.9.1)	1
Acetyl-CoA fermentation to Butyrate	1
Arginine and Ornithine Degradation	1
Bacterial Chemotaxis	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Butanol Biosynthesis	1
CBSS-262719.3.peg.410	1
Campylobacter Iron Metabolism	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Flagellar motility	1
Glutathione-regulated potassium-efflux system and associated functions	1
Heat shock dnaK gene cluster extended	1
Isoleucine degradation	1
Lipid A modifications	1
Nitric oxide synthase	1
Oxidative stress	1
Polyhydroxybutyrate metabolism	1
Potassium homeostasis	1
Pyruvate Alanine Serine Interconversions	1
Queuosine-Archaeosine Biosynthesis	1
SigmaB stress responce regulation	1
Transcription initiation, bacterial sigma factors	1
Trehalose Biosynthesis	1
Two-component regulatory systems in Campylobacter	1
Valine degradation	1
cAMP signaling in bacteria	1
n-Phenylalkanoic acid 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
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• Propanoate metabolism
• Caprolactam degradation
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Galactose metabolism
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Alanine and aspartate metabolism
• Methionine metabolism
• Geraniol degradation
• Lysine biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Benzoxazinone biosynthesis
• Aminophosphonate metabolism
• Streptomycin biosynthesis
• alpha-Linolenic acid metabolism
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• mTOR signaling pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
trehalose biosynthesis IV	1	1	1
starch degradation V	4	3	3
glycogen degradation I	8	6	5
putrescine degradation V	2	2	1
superoxide radicals degradation	2	2	1
β-alanine degradation II	2	2	1
UDP-α-D-glucose biosynthesis	2	2	1
glycogen degradation II	6	5	3
starch degradation III	4	2	2
4-coumarate degradation (aerobic)	5	3	2
sucrose biosynthesis II	8	6	3
benzoyl-CoA biosynthesis	3	3	1
trehalose degradation V	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
4-coumarate degradation (anaerobic)	6	2	2
reactive oxygen species degradation	4	4	1
sucrose degradation IV (sucrose phosphorylase)	4	3	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	2
2-methyl-branched fatty acid β-oxidation	14	11	3
dTDP-β-L-rhamnose biosynthesis	5	5	1
adipate degradation	5	5	1
L-arginine degradation II (AST pathway)	5	5	1
fatty acid β-oxidation II (plant peroxisome)	5	4	1
adipate biosynthesis	5	4	1
sucrose degradation II (sucrose synthase)	5	4	1
glucose and glucose-1-phosphate degradation	5	4	1
4-hydroxybenzoate biosynthesis III (plants)	5	4	1
fatty acid β-oxidation IV (unsaturated, even number)	5	4	1
glutaryl-CoA degradation	5	3	1
D-galactose degradation I (Leloir pathway)	5	3	1
glucosylglycerol biosynthesis	5	2	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	2	1
CDP-6-deoxy-D-gulose biosynthesis	5	1	1
pyruvate fermentation to hexanol (engineered)	11	7	2
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
oleate β-oxidation	35	33	6
fatty acid salvage	6	6	1
β-alanine biosynthesis II	6	5	1
L-isoleucine degradation I	6	4	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
methyl ketone biosynthesis (engineered)	6	4	1
propanoate fermentation to 2-methylbutanoate	6	3	1
ethene biosynthesis III (microbes)	7	6	1
fatty acid β-oxidation I (generic)	7	6	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	5	1
pyruvate fermentation to butanoate	7	3	1
benzoyl-CoA degradation I (aerobic)	7	3	1
L-valine degradation I	8	6	1
pyruvate fermentation to butanol I	8	4	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
valproate β-oxidation	9	6	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
chitin biosynthesis	9	5	1
phenylacetate degradation I (aerobic)	9	4	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
starch degradation II	9	1	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
peptidoglycan recycling II	10	8	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
3-phenylpropanoate degradation	10	5	1
starch biosynthesis	10	5	1
colanic acid building blocks biosynthesis	11	11	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
superpathway of phenylethylamine degradation	11	6	1
gallate degradation III (anaerobic)	11	3	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
L-glutamate degradation VII (to butanoate)	12	3	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	3	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	1
peptidoglycan recycling I	14	11	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	3	1
L-tryptophan degradation III (eukaryotic)	15	6	1
glycerol degradation to butanol	16	10	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	4	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	4	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	8	1
toluene degradation VI (anaerobic)	18	4	1
streptomycin biosynthesis	18	2	1
superpathway of anaerobic sucrose degradation	19	14	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	1
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1