Experiment set1S302 for Acinetobacter radioresistens SK82

L-tyrosine disodium salt carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-tyrosine disodium salt (20 mM)
Culturing: Acinetobacter_SK82_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Kiani on 5/1/24
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, 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)

Specific Phenotypes

For 8 genes in this experiment

For carbon source L-tyrosine disodium salt in Acinetobacter radioresistens SK82

For carbon source L-tyrosine disodium salt across organisms

SEED Subsystems

Subsystem	#Specific
Cysteine Biosynthesis	1
DNA-binding regulatory proteins, strays	1
DNA-replication	1
DNA Repair Base Excision	1
DNA repair, bacterial RecFOR pathway	1
Ketoisovalerate oxidoreductase	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	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:

• Benzoate degradation via CoA ligation
• Pyruvate metabolism
• Butanoate metabolism
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Fatty acid biosynthesis
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Bile acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine degradation
• Tryptophan metabolism
• alpha-Linolenic acid metabolism
• Propanoate metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• 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

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate and ATP formation from acetyl-CoA III	1	1	1
acetate conversion to acetyl-CoA	1	1	1
L-malate degradation I	1	1	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	5	3
oleate β-oxidation (thioesterase-dependent, yeast)	2	2	1
superpathway of acetate utilization and formation	3	3	1
benzoyl-CoA biosynthesis	3	3	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
L-isoleucine biosynthesis V	3	2	1
ethanol degradation III	3	2	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	2
oleate β-oxidation	35	32	9
chitin deacetylation	4	3	1
valproate β-oxidation	9	5	2
adipate degradation	5	5	1
2-methylcitrate cycle I	5	5	1
adipate biosynthesis	5	4	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
glutaryl-CoA degradation	5	3	1
4-hydroxybenzoate biosynthesis III (plants)	5	2	1
pyruvate fermentation to hexanol (engineered)	11	7	2
fatty acid salvage	6	6	1
2-methylcitrate cycle II	6	5	1
pyruvate fermentation to butanol II (engineered)	6	4	1
L-isoleucine biosynthesis IV	6	4	1
β-alanine biosynthesis II	6	3	1
methyl ketone biosynthesis (engineered)	6	3	1
methylgallate degradation	6	2	1
superpathway of bitter acids biosynthesis	18	3	3
lupulone and humulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
fatty acid β-oxidation I (generic)	7	6	1
2-methyl-branched fatty acid β-oxidation	14	10	2
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	2
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
pyruvate fermentation to butanoate	7	3	1
benzoyl-CoA degradation I (aerobic)	7	3	1
pyruvate fermentation to butanol I	8	4	1
protocatechuate degradation I (meta-cleavage pathway)	8	3	1
2-methylpropene degradation	8	2	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	3
phenylacetate degradation I (aerobic)	9	7	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
cis-geranyl-CoA degradation	9	1	1
superpathway of coenzyme A biosynthesis II (plants)	10	7	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
3-phenylpropanoate degradation	10	3	1
superpathway of vanillin and vanillate degradation	10	3	1
methyl tert-butyl ether degradation	10	2	1
superpathway of phenylethylamine degradation	11	8	1
L-glutamate degradation VII (to butanoate)	12	3	1
syringate degradation	12	3	1
androstenedione degradation I (aerobic)	25	8	2
gluconeogenesis I	13	12	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	7	1
androstenedione degradation II (anaerobic)	27	4	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
superpathway of testosterone and androsterone degradation	28	8	2
superpathway of cholesterol degradation I (cholesterol oxidase)	42	10	3
L-tryptophan degradation III (eukaryotic)	15	3	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	11	3
glycerol degradation to butanol	16	9	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	4	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	9	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	10	1
toluene degradation VI (anaerobic)	18	3	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	3	1
superpathway of cholesterol degradation III (oxidase)	49	5	2
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	18	1