Experiment set10S454 for Pantoea sp. MT58

Compare to:

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 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_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 11 genes in this experiment

For carbon source Ying_Others16 in Pantoea sp. MT58

For carbon source Ying_Others16 across organisms

SEED Subsystems

Subsystem #Specific
Arginine and Ornithine Degradation 3
Sialic Acid Metabolism 2
Ketoisovalerate oxidoreductase 1
Lactate utilization 1
Polyamine Metabolism 1
Pyruvate metabolism I: anaplerotic reactions, PEP 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Respiratory dehydrogenases 1 1

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 conversion to acetyl-CoA 1 1 1
acetate and ATP formation from acetyl-CoA III 1 1 1
pyruvate fermentation to (R)-lactate 1 1 1
L-malate degradation II 1 1 1
L-arginine degradation II (AST pathway) 5 5 3
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
spermine and spermidine degradation I 5 2 2
2-chloroacrylate degradation I 3 3 1
ethanol degradation IV 3 3 1
superpathway of acetate utilization and formation 3 3 1
ethanol degradation II 3 3 1
L-alanine degradation II (to D-lactate) 3 3 1
L-isoleucine biosynthesis V 3 2 1
vancomycin resistance I 3 2 1
ethanol degradation III 3 2 1
superpathway of 4-aminobutanoate degradation 3 2 1
N-methylpyrrolidone degradation 3 1 1
L-carnitine degradation II 3 1 1
4-aminobutanoate degradation IV 3 1 1
GABA shunt I 4 3 1
putrescine degradation III 4 2 1
GABA shunt II 4 2 1
L-lysine degradation IV 5 2 1
2-methylcitrate cycle I 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
L-lysine degradation III 6 2 1
2-methylcitrate cycle II 6 2 1
L-alanine degradation VI (reductive Stickland reaction) 6 2 1
methylgallate degradation 6 2 1
superpathway of bitter acids biosynthesis 18 3 3
lupulone and humulone biosynthesis 6 1 1
adlupulone and adhumulone biosynthesis 6 1 1
β-alanine biosynthesis II 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
gluconeogenesis I 13 12 2
anaerobic energy metabolism (invertebrates, cytosol) 7 5 1
L-lysine degradation I 7 3 1
incomplete reductive TCA cycle 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
superpathway of fermentation (Chlamydomonas reinhardtii) 9 7 1
TCA cycle II (plants and fungi) 9 7 1
TCA cycle V (2-oxoglutarate synthase) 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