Experiment set11S556 for Pantoea sp. MT58

Ying_all64 rep C; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_all64
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_all64 1x includes: 40 uM Sucrose, 40 uM D-Glucose, 40 uM D-Trehalose dihydrate, 40 uM m-Inositol, 40 uM D-Xylose, 40 uM D-Mannitol, 40 uM N-Acetyl-D-Glucosamine, 40 uM Sodium L-Lactate, 40 uM D,L-Malic Acid, 40 uM Citric Acid, 40 uM Succinic Acid, 40 uM Sodium pyruvate, 40 uM a-Ketoglutaric acid disodium salt hydrate, 40 uM L-Citrulline, 40 uM 5-methyluridine, 40 uM Adenine, 40 uM Adenosine, 40 uM Cytidine, 40 uM Cytosine, 40 uM Guanine, 40 uM Guanosine, 40 uM Hypoxanthine, 40 uM Inosine, 40 uM Thymine, 40 uM Uracil, 40 uM Uridine, 40 uM Xanthine, 40 uM Xanthosine, 40 uM L-Alanine, 40 uM L-Arginine, 40 uM L-Asparagine, 40 uM L-Aspartic Acid, 40 uM L-Cysteine, 40 uM L-Glutamic acid, 40 uM L-Glutamine, 40 uM Glycine, 40 uM L-Histidine, 40 uM L-Isoleucine, 40 uM L-Leucine, 40 uM L-Lysine, 40 uM L-Methionine, 40 uM L-Phenylalanine, 40 uM L-Proline, 40 uM L-Serine, 40 uM L-Threonine, 40 uM L-Tryptophan, 40 uM L-tyrosine, 40 uM L-Valine, 40 uM Gamma-Aminobutyric Acid Hydrochloride, 40 uM Ectoine, 40 uM Betaine, 40 uM N-Acetyl-L-glutamic acid, 40 uM Nicotinamide, 40 uM L-Ornithine, 40 uM Shikimic Acid, 40 uM spermidine, 40 uM Taurine, 40 uM Trigonelline HCl, 40 uM L-Carnitine hydrochloride, 40 uM Choline, 40 uM N-alpha-Acetyl-L-glutamate, 40 uM n-Acetyl-lysine, 40 uM n-Acetyl-muramic acid, 40 uM sn-glycero-3-phosphocholine

Specific Phenotypes

For 3 genes in this experiment

For carbon source Ying_all64 in Pantoea sp. MT58

For carbon source Ying_all64 across organisms

SEED Subsystems

Subsystem	#Specific
D-ribose utilization	1
Deoxyribose and Deoxynucleoside Catabolism	1
Glycine and Serine Utilization	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Redox-dependent regulation of nucleus processes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Lysine biosynthesis
• Glutathione metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Sphingolipid metabolism
• 1,4-Dichlorobenzene degradation
• Nicotinate and nicotinamide metabolism
• Caprolactam degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ribose phosphorylation	2	2	1
2-deoxy-D-ribose degradation I	3	3	1