Experiment set32S539 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 31 genes in this experiment

For solid stress Fraxetin in Pseudomonas simiae WCS417

For solid stress Fraxetin across organisms

SEED Subsystems

Subsystem	#Specific
Iron acquisition in Vibrio	3
Photorespiration (oxidative C2 cycle)	3
DNA repair, bacterial	2
Glycine and Serine Utilization	2
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	2
Transport of Iron	2
Allantoin Utilization	1
Copper homeostasis	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutathione-dependent pathway of formaldehyde detoxification	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine cleavage system	1
Hemin transport system	1
Lactate utilization	1
Lipid A modifications	1
Lysine degradation	1
Oxidative stress	1
Pentose phosphate pathway	1
Serine-glyoxylate cycle	1
Ton and Tol transport systems	1
Transport of Manganese	1
Triacylglycerol metabolism	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Tryptophan metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Glyoxylate and dicarboxylate metabolism
• Methane metabolism
• Nitrogen 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
L-glutamate degradation I	1	1	1
superoxide radicals degradation	2	2	1
methanol oxidation to formaldehyde IV	2	1	1
2-O-α-mannosyl-D-glycerate degradation	2	1	1
glycine cleavage	3	3	1
glycine biosynthesis II	3	3	1
ethanol degradation IV	3	3	1
pentose phosphate pathway (oxidative branch) I	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
ethene biosynthesis IV (engineered)	3	1	1
reactive oxygen species degradation	4	4	1
D-glucarate degradation I	4	3	1
D-galactarate degradation I	4	3	1
glycolate and glyoxylate degradation I	4	3	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
superpathway of D-glucarate and D-galactarate degradation	5	4	1
superpathway of glycol metabolism and degradation	7	5	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
4-aminobutanoate degradation V	7	2	1
pentose phosphate pathway	8	8	1
2-deoxy-D-ribose degradation II	8	7	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
photorespiration I	9	5	1
photorespiration III	9	5	1
peptidoglycan recycling II	10	8	1
photorespiration II	10	6	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
formaldehyde assimilation I (serine pathway)	13	6	1
peptidoglycan recycling I	14	11	1
superpathway of glucose and xylose degradation	17	16	1
methylaspartate cycle	19	10	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	13	1