Experiment set5S283 for Lysobacter sp. OAE881

Ying_AminoAcid20 rep C; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_AminoAcid20
Culturing: Lysobacter_OAE881_ML4, 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_AminoAcid20 1x includes: 128 uM L-Alanine, 128 uM L-Arginine, 128 uM L-Asparagine, 128 uM L-Aspartic Acid, 128 uM L-Cysteine, 128 uM L-Glutamic acid, 128 uM L-Glutamine, 128 uM Glycine, 128 uM L-Histidine, 128 uM L-Isoleucine, 128 uM L-Leucine, 128 uM L-Lysine, 128 uM L-Methionine, 128 uM L-Phenylalanine, 128 uM L-Proline, 128 uM L-Serine, 128 uM L-Threonine, 128 uM L-Tryptophan, 128 uM L-tyrosine, 128 uM L-Valine

Specific Phenotypes

For 15 genes in this experiment

For carbon source Ying_AminoAcid20 in Lysobacter sp. OAE881

For carbon source Ying_AminoAcid20 across organisms

SEED Subsystems

Subsystem	#Specific
Isoleucine degradation	3
Leucine Degradation and HMG-CoA Metabolism	3
Valine degradation	3
Alanine biosynthesis	1
Biogenesis of c-type cytochromes	1
Branched-Chain Amino Acid Biosynthesis	1
Copper homeostasis	1
Heat shock dnaK gene cluster extended	1
Leucine Biosynthesis	1
Methionine Biosynthesis	1
Methionine Degradation	1
Pyruvate Alanine Serine Interconversions	1
Ton and Tol transport systems	1
Universal GTPases	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
• Valine, leucine and isoleucine biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Methionine metabolism
• gamma-Hexachlorocyclohexane degradation
• Selenoamino acid metabolism
• Pyruvate metabolism
• Toluene and xylene degradation
• Naphthalene and anthracene degradation
• Butanoate metabolism
• Pantothenate and CoA biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
chlorinated phenols degradation	4	4	4
phenol degradation I (aerobic)	1	1	1
L-alanine biosynthesis I	2	2	1
phosphatidylcholine biosynthesis VII	2	1	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
pyruvate decarboxylation to acetyl CoA I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-leucine degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
S-adenosyl-L-methionine salvage II	3	2	1
L-methionine degradation I (to L-homocysteine)	3	2	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
superpathway of L-alanine biosynthesis	4	4	1
L-valine biosynthesis	4	4	1
cis-alkene biosynthesis	4	3	1
L-phenylalanine degradation III	4	2	1
phosphatidylcholine acyl editing	4	2	1
superpathway of L-cysteine biosynthesis (mammalian)	5	4	1
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
superpathway of branched chain amino acid biosynthesis	17	17	3
L-leucine biosynthesis	6	6	1
L-leucine degradation I	6	5	1
L-isoleucine biosynthesis IV	6	4	1
L-isoleucine degradation I	6	4	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
L-isoleucine biosynthesis II	8	5	1
L-valine degradation I	8	3	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
superpathway of L-phenylalanine biosynthesis	10	9	1
superpathway of L-isoleucine biosynthesis I	13	13	1
representative whole plasma arachidonate-derived icosanoids I	13	1	1
superpathway of L-methionine salvage and degradation	16	8	1
superpathway of aromatic amino acid biosynthesis	18	16	1
superpathway of L-threonine metabolism	18	12	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	1	1
even iso-branched-chain fatty acid biosynthesis	34	24	1
odd iso-branched-chain fatty acid biosynthesis	34	24	1
anteiso-branched-chain fatty acid biosynthesis	34	24	1
superpathway of chorismate metabolism	59	38	1