Ying_Others16 rep A; time point 2
Group:
carbon source
Media:
SDM_noCarbon + 1X Ying_Others16
Culturing: MT058_ML2, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying and Valentine on
09/01/2023
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 10 genes in this experiment
For carbon source Ying_Others16 in Pantoea sp. MT58
For carbon source Ying_Others16 across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|
| acetate and ATP formation from acetyl-CoA III | 1 | 1 | 1 |
| L-malate degradation II | 1 | 1 | 1 |
| pyruvate fermentation to (R)-lactate | 1 | 1 | 1 |
| acetate conversion to acetyl-CoA | 1 | 1 | 1 |
| 4-aminobutanoate degradation III | 2 | 2 | 1 |
| malate/L-aspartate shuttle pathway | 2 | 2 | 1 |
| 4-aminobutanoate degradation I | 2 | 2 | 1 |
| chitin deacetylation | 4 | 3 | 2 |
| D-lactate to cytochrome bo oxidase electron transfer | 2 | 1 | 1 |
| L-arginine degradation II (AST pathway) | 5 | 5 | 2 |
| spermine and spermidine degradation I | 5 | 2 | 2 |
| superpathway of acetate utilization and formation | 3 | 3 | 1 |
| L-alanine degradation II (to D-lactate) | 3 | 3 | 1 |
| ethanol degradation II | 3 | 3 | 1 |
| ethanol degradation IV | 3 | 3 | 1 |
| 2-chloroacrylate degradation I | 3 | 3 | 1 |
| ethanol degradation III | 3 | 2 | 1 |
| L-isoleucine biosynthesis V | 3 | 2 | 1 |
| superpathway of 4-aminobutanoate degradation | 3 | 2 | 1 |
| vancomycin resistance I | 3 | 2 | 1 |
| 4-aminobutanoate degradation IV | 3 | 1 | 1 |
| L-carnitine degradation II | 3 | 1 | 1 |
| N-methylpyrrolidone degradation | 3 | 1 | 1 |
| GABA shunt I | 4 | 3 | 1 |
| GABA shunt II | 4 | 2 | 1 |
| putrescine degradation III | 4 | 2 | 1 |
| 2-methylcitrate cycle I | 5 | 2 | 1 |
| L-lysine degradation IV | 5 | 2 | 1 |
| C4 photosynthetic carbon assimilation cycle, NAD-ME type | 11 | 8 | 2 |
| glyoxylate cycle | 6 | 6 | 1 |
| TCA cycle VIII (Chlamydia) | 6 | 5 | 1 |
| L-isoleucine biosynthesis IV | 6 | 4 | 1 |
| L-lysine degradation X | 6 | 3 | 1 |
| methylgallate degradation | 6 | 2 | 1 |
| L-alanine degradation VI (reductive Stickland reaction) | 6 | 2 | 1 |
| 2-methylcitrate cycle II | 6 | 2 | 1 |
| L-lysine degradation III | 6 | 2 | 1 |
| superpathway of bitter acids biosynthesis | 18 | 3 | 3 |
| lupulone and humulone biosynthesis | 6 | 1 | 1 |
| β-alanine biosynthesis II | 6 | 1 | 1 |
| adlupulone and adhumulone biosynthesis | 6 | 1 | 1 |
| colupulone and cohumulone biosynthesis | 6 | 1 | 1 |
| gluconeogenesis I | 13 | 12 | 2 |
| anaerobic energy metabolism (invertebrates, cytosol) | 7 | 5 | 1 |
| incomplete reductive TCA cycle | 7 | 3 | 1 |
| L-lysine degradation I | 7 | 3 | 1 |
| pyruvate fermentation to propanoate I | 7 | 2 | 1 |
| mixed acid fermentation | 16 | 14 | 2 |
| lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales) | 8 | 4 | 1 |
| protocatechuate degradation I (meta-cleavage pathway) | 8 | 3 | 1 |
| superpathway of anaerobic energy metabolism (invertebrates) | 17 | 10 | 2 |
| TCA cycle V (2-oxoglutarate synthase) | 9 | 7 | 1 |
| TCA cycle II (plants and fungi) | 9 | 7 | 1 |
| superpathway of fermentation (Chlamydomonas reinhardtii) | 9 | 7 | 1 |
| TCA cycle IV (2-oxoglutarate decarboxylase) | 9 | 6 | 1 |
| reductive glycine pathway of autotrophic CO2 fixation | 9 | 5 | 1 |
| superpathway of L-alanine fermentation (Stickland reaction) | 9 | 4 | 1 |
| cis-geranyl-CoA degradation | 9 | 1 | 1 |
| TCA cycle I (prokaryotic) | 10 | 9 | 1 |
| TCA cycle III (animals) | 10 | 8 | 1 |
| superpathway of coenzyme A biosynthesis II (plants) | 10 | 5 | 1 |
| anaerobic energy metabolism (invertebrates, mitochondrial) | 10 | 5 | 1 |
| superpathway of vanillin and vanillate degradation | 10 | 3 | 1 |
| superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation | 11 | 8 | 1 |
| reductive TCA cycle I | 11 | 6 | 1 |
| L-glutamate degradation VIII (to propanoate) | 11 | 2 | 1 |
| superpathway of glyoxylate bypass and TCA | 12 | 11 | 1 |
| gluconeogenesis III | 12 | 9 | 1 |
| reductive TCA cycle II | 12 | 5 | 1 |
| syringate degradation | 12 | 3 | 1 |
| superpathway of L-arginine and L-ornithine degradation | 13 | 10 | 1 |
| formaldehyde assimilation I (serine pathway) | 13 | 8 | 1 |
| (S)-lactate fermentation to propanoate, acetate and hydrogen | 13 | 5 | 1 |
| peptidoglycan recycling I | 14 | 14 | 1 |
| superpathway of glyoxylate cycle and fatty acid degradation | 14 | 11 | 1 |
| superpathway of glucose and xylose degradation | 17 | 16 | 1 |
| heterolactic fermentation | 18 | 16 | 1 |
| methylaspartate cycle | 19 | 9 | 1 |
| superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle | 22 | 18 | 1 |
| superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass | 26 | 25 | 1 |
| superpathway of L-lysine degradation | 43 | 12 | 1 |
| Methanobacterium thermoautotrophicum biosynthetic metabolism | 56 | 21 | 1 |