Experiment set11S558 for Pantoea sp. MT58

Ying_sugar7 rep B; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_sugar7
Culturing: MT058_ML2, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying and Valentine on 1-Sep-23
Media components: 1.5 g/L Ammonium chloride, 0.6 g/L Potassium phosphate monobasic, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Ying_sugar7 1x includes: 366 uM Sucrose, 366 uM D-Glucose, 366 uM D-Trehalose dihydrate, 366 uM m-Inositol, 366 uM D-Xylose, 366 uM D-Mannitol, 366 uM N-Acetyl-D-Glucosamine

Specific Phenotypes

For 14 genes in this experiment

For carbon source Ying_sugar7 in Pantoea sp. MT58

For carbon source Ying_sugar7 across organisms

SEED Subsystems

Subsystem	#Specific
Acetyl-CoA fermentation to Butyrate	1
Butanol Biosynthesis	1
CBSS-214092.1.peg.3450	1
Heat shock dnaK gene cluster extended	1
Isoleucine degradation	1
Oxidative stress	1
Polyhydroxybutyrate metabolism	1
Protein degradation	1
Valine degradation	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:

• Lysine degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Fatty acid biosynthesis
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Propanoate metabolism
• Ethylbenzene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
N-end rule pathway I (prokaryotic)	2	2	2
benzoyl-CoA biosynthesis	3	3	1
microcin B17 biosynthesis	3	1	1
2-methyl-branched fatty acid β-oxidation	14	8	3
adipate biosynthesis	5	3	1
glutaryl-CoA degradation	5	3	1
fatty acid β-oxidation IV (unsaturated, even number)	5	3	1
adipate degradation	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
pyruvate fermentation to hexanol (engineered)	11	7	2
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	5	2
oleate β-oxidation	35	29	6
L-isoleucine degradation I	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
fatty acid salvage	6	4	1
methyl ketone biosynthesis (engineered)	6	3	1
propanoate fermentation to 2-methylbutanoate	6	3	1
fatty acid β-oxidation I (generic)	7	6	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
pyruvate fermentation to butanoate	7	3	1
benzoyl-CoA degradation I (aerobic)	7	2	1
L-valine degradation I	8	5	1
pyruvate fermentation to butanol I	8	3	1
valproate β-oxidation	9	5	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
phenylacetate degradation I (aerobic)	9	3	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
L-glutamate degradation V (via hydroxyglutarate)	10	5	1
3-phenylpropanoate degradation	10	3	1
superpathway of phenylethylamine degradation	11	4	1
gallate degradation III (anaerobic)	11	3	1
Spodoptera littoralis pheromone biosynthesis	22	3	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	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
L-tryptophan degradation III (eukaryotic)	15	3	1
glycerol degradation to butanol	16	11	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	3	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	3	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	9	1
toluene degradation VI (anaerobic)	18	3	1
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1