Experiment set32S545 for Pseudomonas simiae WCS417

Fraxetin 3 mM; solid stress

Group: solid stress
Media: + Fraxetin (3 mM)
Culturing: fluoroDangl_ML3b
By: Max Stassen on 29-Mar-24

Specific Phenotypes

For 28 genes in this experiment

For solid stress Fraxetin in Pseudomonas simiae WCS417

For solid stress Fraxetin across organisms

SEED Subsystems

Subsystem	#Specific
Transport of Iron	4
Iron acquisition in Vibrio	3
Serine-glyoxylate cycle	2
Biotin biosynthesis	1
Copper homeostasis	1
DNA repair, bacterial	1
Entner-Doudoroff Pathway	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutathione-dependent pathway of formaldehyde detoxification	1
Glycolysis and Gluconeogenesis	1
Lipid A modifications	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
Oxidative stress	1
Photorespiration (oxidative C2 cycle)	1
Propionate-CoA to Succinate Module	1
Ribosome biogenesis bacterial	1
TCA Cycle	1
Transport of Manganese	1
ZZ gjo need homes	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:

• Tryptophan metabolism
• Nucleotide sugars metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• 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
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Benzoxazinone biosynthesis
• Starch and sucrose metabolism
• Streptomycin biosynthesis
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Glyoxylate and dicarboxylate metabolism
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Diterpenoid biosynthesis
• Nitrogen metabolism
• Biosynthesis of siderophore group nonribosomal peptides

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
long-chain fatty acid activation	1	1	1
L-glutamate degradation I	1	1	1
superoxide radicals degradation	2	2	1
trehalose degradation I (low osmolarity)	2	2	1
linoleate biosynthesis II (animals)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
trehalose degradation II (cytosolic)	2	1	1
methanol oxidation to formaldehyde IV	2	1	1
L-alanine degradation II (to D-lactate)	3	3	1
ethanol degradation IV	3	3	1
glyoxylate cycle	6	5	2
trehalose degradation V	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
alkane biosynthesis II	3	1	1
trehalose degradation IV	3	1	1
ethene biosynthesis IV (engineered)	3	1	1
oleate biosynthesis I (plants)	3	1	1
partial TCA cycle (obligate autotrophs)	8	8	2
reactive oxygen species degradation	4	4	1
nitrogen remobilization from senescing leaves	8	6	2
sucrose degradation III (sucrose invertase)	4	3	1
phytol degradation	4	3	1
phosphatidylcholine acyl editing	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
wax esters biosynthesis II	4	1	1
TCA cycle VII (acetate-producers)	9	7	2
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle VI (Helicobacter)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	6	2
sporopollenin precursors biosynthesis	18	4	4
TCA cycle I (prokaryotic)	10	9	2
glucose and glucose-1-phosphate degradation	5	4	1
octane oxidation	5	4	1
TCA cycle III (animals)	10	7	2
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
reductive TCA cycle I	11	6	2
fatty acid salvage	6	6	1
superpathway of glyoxylate bypass and TCA	12	11	2
glycogen degradation II	6	5	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
reductive TCA cycle II	12	5	2
6-gingerol analog biosynthesis (engineered)	6	2	1
stearate biosynthesis I (animals)	6	1	1
methylaspartate cycle	19	10	3
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
ceramide degradation by α-oxidation	7	2	1
4-aminobutanoate degradation V	7	2	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
2-deoxy-D-ribose degradation II	8	7	1
mixed acid fermentation	16	12	2
glycogen degradation I	8	6	1
sucrose biosynthesis II	8	6	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
chitin biosynthesis	9	5	1
1,3-propanediol biosynthesis (engineered)	9	4	1
peptidoglycan recycling II	10	8	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
suberin monomers biosynthesis	20	2	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
glycolysis III (from glucose)	11	9	1
homolactic fermentation	12	9	1
ethene biosynthesis V (engineered)	25	18	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2
peptidoglycan recycling I	14	11	1
Bifidobacterium shunt	15	12	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
heterolactic fermentation	18	14	1
superpathway of fatty acids biosynthesis (E. coli)	53	49	2
palmitate biosynthesis III	29	21	1
oleate β-oxidation	35	30	1