Experiment set21IT068 for Pseudomonas fluorescens SBW25-INTG

Citraconic acid 20 mM carbon source

Group: carbon source
Media: MME_noNitrogen_noCarbon + Citraconic acid (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 26 genes in this experiment

For carbon source Citraconic acid in Pseudomonas fluorescens SBW25-INTG

For carbon source Citraconic acid across organisms

SEED Subsystems

Subsystem	#Specific
Isoleucine degradation	7
Valine degradation	6
Leucine Degradation and HMG-CoA Metabolism	5
Methylcitrate cycle	2
Propionate-CoA to Succinate Module	2
Acetyl-CoA fermentation to Butyrate	1
Alanine biosynthesis	1
Anaerobic respiratory reductases	1
Biotin biosynthesis	1
Branched-Chain Amino Acid Biosynthesis	1
Butanol Biosynthesis	1
Coenzyme A Biosynthesis	1
Cysteine Biosynthesis	1
DNA-binding regulatory proteins, strays	1
Fructose utilization	1
HMG CoA Synthesis	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Polyhydroxybutyrate metabolism	1
Pyruvate Alanine Serine Interconversions	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Serine-glyoxylate cycle	1
Transport of Zinc	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:

• Valine, leucine and isoleucine degradation
• Propanoate metabolism
• Butanoate metabolism
• Fatty acid metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Synthesis and degradation of ketone bodies
• Glycine, serine and threonine metabolism
• Pyruvate metabolism
• Benzoate degradation via CoA ligation
• 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
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid elongation in mitochondria
• C21-Steroid hormone metabolism
• Purine metabolism
• Geraniol degradation
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Benzoate degradation via hydroxylation
• Bisphenol A degradation
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Linoleic acid metabolism
• alpha-Linolenic acid metabolism
• Tetrachloroethene degradation
• Glyoxylate and dicarboxylate metabolism
• Ethylbenzene degradation
• Reductive carboxylate cycle (CO2 fixation)
• Pantothenate and CoA biosynthesis
• Folate biosynthesis
• Retinol metabolism
• Terpenoid biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of type II polyketide products

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	3
2-methylcitrate cycle I	5	5	3
L-alanine biosynthesis I	2	2	1
2-methylcitrate cycle II	6	5	3
acetoacetate degradation (to acetyl CoA)	2	1	1
mevalonate degradation	2	1	1
5,6-dehydrokavain biosynthesis (engineered)	10	6	4
ketogenesis	5	3	2
ketolysis	3	3	1
benzoyl-CoA biosynthesis	3	3	1
glycine cleavage	3	3	1
glycine biosynthesis II	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
glyoxylate cycle	6	5	2
pyruvate fermentation to butanol II (engineered)	6	4	2
polyhydroxybutanoate biosynthesis	3	2	1
pyruvate fermentation to hexanol (engineered)	11	7	3
partial TCA cycle (obligate autotrophs)	8	8	2
phosphopantothenate biosynthesis I	4	4	1
superpathway of L-alanine biosynthesis	4	4	1
nitrogen remobilization from senescing leaves	8	6	2
phosphopantothenate biosynthesis III (archaea)	4	2	1
(2S)-ethylmalonyl-CoA biosynthesis	4	1	1
oleate β-oxidation	35	33	8
TCA cycle VI (Helicobacter)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle VII (acetate-producers)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
valproate β-oxidation	9	6	2
superpathway of glyoxylate cycle and fatty acid degradation	14	12	3
2-methyl-branched fatty acid β-oxidation	14	11	3
TCA cycle I (prokaryotic)	10	9	2
fatty acid β-oxidation II (plant peroxisome)	5	4	1
4-hydroxybenzoate biosynthesis III (plants)	5	4	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	1
TCA cycle III (animals)	10	7	2
glutaryl-CoA degradation	5	3	1
fatty acid β-oxidation VII (yeast peroxisome)	5	3	1
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	5	2
ethylbenzene degradation (anaerobic)	5	1	1
isopropanol biosynthesis (engineered)	5	1	1
pyruvate fermentation to acetone	5	1	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	2
reductive TCA cycle I	11	6	2
fatty acid salvage	6	6	1
superpathway of glyoxylate bypass and TCA	12	11	2
L-leucine degradation I	6	5	1
L-isoleucine degradation I	6	4	1
propanoate fermentation to 2-methylbutanoate	6	3	1
reductive TCA cycle II	12	5	2
4-ethylphenol degradation (anaerobic)	6	2	1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast)	6	1	1
jasmonic acid biosynthesis	19	7	3
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
acetyl-CoA fermentation to butanoate	7	3	1
mevalonate pathway I (eukaryotes and bacteria)	7	1	1
mevalonate pathway II (haloarchaea)	7	1	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	3
2-deoxy-D-ribose degradation II	8	7	1
mixed acid fermentation	16	11	2
pyruvate fermentation to butanol I	8	4	1
2-methylpropene degradation	8	2	1
mevalonate pathway IV (archaea)	8	1	1
isoprene biosynthesis II (engineered)	8	1	1
mevalonate pathway III (Thermoplasma)	8	1	1
androstenedione degradation I (aerobic)	25	6	3
superpathway of coenzyme A biosynthesis I (bacteria)	9	8	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
cis-geranyl-CoA degradation	9	4	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
4-oxopentanoate degradation	9	1	1
superpathway of testosterone and androsterone degradation	28	7	3
methylaspartate cycle	19	9	2
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
3-phenylpropanoate degradation	10	5	1
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)	10	4	1
methyl tert-butyl ether degradation	10	4	1
L-lysine fermentation to acetate and butanoate	10	3	1
superpathway of cholesterol degradation I (cholesterol oxidase)	42	8	4
ethylmalonyl-CoA pathway	11	1	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	9	4
10-cis-heptadecenoyl-CoA degradation (yeast)	12	4	1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	4	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 Clostridium acetobutylicum solventogenic fermentation	13	5	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	3	1
1-butanol autotrophic biosynthesis (engineered)	27	19	2
androstenedione degradation II (anaerobic)	27	4	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
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	8	1
toluene degradation VI (anaerobic)	18	4	1
sitosterol degradation to androstenedione	18	1	1
Spodoptera littoralis pheromone biosynthesis	22	4	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	3	1
superpathway of cholesterol degradation III (oxidase)	49	5	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
platensimycin biosynthesis	26	6	1
superpathway of ergosterol biosynthesis I	26	3	1
superpathway of cholesterol biosynthesis	38	3	1
superpathway of L-lysine degradation	43	17	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1