Experiment set22IT080 for Pseudomonas fluorescens SBW25-INTG

Sodium propionate 20 mM carbon source

Group: carbon source
Media: MME_noNitrogen_noCarbon + Sodium propionate (20 mM) + Ammonium chloride (10 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on 8-Mar-22
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 30 genes in this experiment

For carbon source Sodium propionate in Pseudomonas fluorescens SBW25-INTG

For carbon source Sodium propionate across organisms

SEED Subsystems

Subsystem	#Specific
Isoleucine degradation	2
Methylcitrate cycle	2
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	2
Propionate-CoA to Succinate Module	2
Valine degradation	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Acetyl-CoA fermentation to Butyrate	1
Butanol Biosynthesis	1
Cluster-based Subsystem Grouping Hypotheticals - perhaps Proteosome Related	1
Flavodoxin	1
Glutathione: Redox cycle	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
HMG CoA Synthesis	1
Lactate utilization	1
Leucine Degradation and HMG-CoA Metabolism	1
Polyhydroxybutyrate metabolism	1
Twin-arginine translocation system	1
Ubiquinone Biosynthesis	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:

• Propanoate metabolism
• Tryptophan metabolism
• Biosynthesis of plant hormones
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Benzoate degradation via CoA ligation
• Porphyrin and chlorophyll metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Citrate cycle (TCA cycle)
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Benzoxazinone biosynthesis
• beta-Alanine metabolism
• Cyanoamino acid metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Glyoxylate and dicarboxylate metabolism
• Styrene degradation
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• 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

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
2-methylcitrate cycle I	5	5	3
acrylonitrile degradation I	2	2	1
indole-3-acetate biosynthesis III (bacteria)	2	2	1
indole-3-acetate biosynthesis IV (bacteria)	2	2	1
2-methylcitrate cycle II	6	5	3
monoacylglycerol metabolism (yeast)	4	2	2
adipate degradation	5	5	2
fatty acid salvage	6	6	2
benzoyl-CoA biosynthesis	3	3	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
glyoxylate cycle	6	5	2
triacylglycerol degradation	3	2	1
oleate biosynthesis III (cyanobacteria)	3	2	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
glutathione-peroxide redox reactions	3	2	1
superpathway of acrylonitrile degradation	3	2	1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	1	1
2-methyl-branched fatty acid β-oxidation	14	11	4
oleate β-oxidation	35	33	9
partial TCA cycle (obligate autotrophs)	8	8	2
CDP-diacylglycerol biosynthesis II	4	4	1
CDP-diacylglycerol biosynthesis I	4	4	1
nitrogen remobilization from senescing leaves	8	6	2
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle VI (Helicobacter)	9	7	2
TCA cycle VII (acetate-producers)	9	7	2
superpathway of glyoxylate cycle and fatty acid degradation	14	12	3
TCA cycle I (prokaryotic)	10	9	2
fatty acid β-oxidation II (plant peroxisome)	5	4	1
fatty acid β-oxidation IV (unsaturated, even number)	5	4	1
adipate biosynthesis	5	4	1
TCA cycle III (animals)	10	7	2
phosphatidate biosynthesis (yeast)	5	3	1
glutaryl-CoA degradation	5	3	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	2	1
pyruvate fermentation to hexanol (engineered)	11	7	2
reductive TCA cycle I	11	6	2
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
superpathway of glyoxylate bypass and TCA	12	11	2
superpathway of phospholipid biosynthesis III (E. coli)	12	10	2
phosphatidylglycerol biosynthesis I	6	5	1
phosphatidylglycerol biosynthesis II	6	5	1
pyruvate fermentation to butanol II (engineered)	6	4	1
methyl ketone biosynthesis (engineered)	6	4	1
L-isoleucine degradation I	6	4	1
propanoate fermentation to 2-methylbutanoate	6	3	1
reductive TCA cycle II	12	5	2
palmitoyl ethanolamide biosynthesis	6	2	1
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
fatty acid β-oxidation I (generic)	7	6	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	5	1
diacylglycerol and triacylglycerol biosynthesis	7	3	1
benzoyl-CoA degradation I (aerobic)	7	3	1
pyruvate fermentation to butanoate	7	3	1
stigma estolide biosynthesis	7	2	1
L-valine degradation I	8	6	1
mixed acid fermentation	16	11	2
pyruvate fermentation to butanol I	8	4	1
anandamide biosynthesis II	8	2	1
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis	8	1	1
valproate β-oxidation	9	6	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
phenylacetate degradation I (aerobic)	9	4	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
methylaspartate cycle	19	9	2
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
3-phenylpropanoate degradation	10	5	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
superpathway of phenylethylamine degradation	11	6	1
gallate degradation III (anaerobic)	11	3	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
indole-3-acetate biosynthesis II	12	5	1
anandamide biosynthesis I	12	3	1
L-glutamate degradation VII (to butanoate)	12	3	1
ethene biosynthesis V (engineered)	25	18	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	3	1
superpathway of phospholipid biosynthesis II (plants)	28	9	2
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
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1