Experiment set57IT034 for Escherichia coli BW25113

Ying_Others16 rep A; time point 2

Group: carbon source
Media: SDM_noCarbon + 1X Ying_Others16
Culturing: Keio_ML9a, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying on 19-Oct-22
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_Others16 1x includes: 160 uM Gamma-Aminobutyric Acid Hydrochloride, 160 uM Ectoine, 160 uM Betaine, 160 uM N-Acetyl-L-glutamic acid, 160 uM Nicotinamide, 160 uM L-Ornithine, 160 uM Shikimic Acid, 160 uM spermidine, 160 uM Taurine, 160 uM Trigonelline HCl, 160 uM L-Carnitine hydrochloride, 160 uM Choline, 160 uM N-alpha-Acetyl-L-glutamate, 160 uM n-Acetyl-lysine, 160 uM n-Acetyl-muramic acid, 160 uM sn-glycero-3-phosphocholine

Specific Phenotypes

For 24 genes in this experiment

For carbon source Ying_Others16 in Escherichia coli BW25113

For carbon source Ying_Others16 across organisms

SEED Subsystems

Subsystem	#Specific
Curli production	5
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	1
CBSS-214092.1.peg.3450	1
CytR regulation	1
D-ribose utilization	1
DNA-binding regulatory proteins, strays	1
Deoxyribose and Deoxynucleoside Catabolism	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Nitrate and nitrite ammonification	1
Polyamine Metabolism	1
Transcription factors bacterial	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Fatty acid biosynthesis
• Urea cycle and metabolism of amino groups
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ribose phosphorylation	2	2	1
spermine and spermidine degradation I	5	2	2
2-deoxy-D-ribose degradation I	3	3	1
putrescine degradation III	4	2	1