Experiment set11S561 for Pantoea sp. MT58

Compare to:

Ying_AminoAcid20 rep B; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_AminoAcid20
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_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 20 genes in this experiment

For carbon source Ying_AminoAcid20 in Pantoea sp. MT58

For carbon source Ying_AminoAcid20 across organisms

SEED Subsystems

Subsystem #Specific
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 2
Glycine and Serine Utilization 2
Histidine Degradation 2
Pyruvate metabolism I: anaplerotic reactions, PEP 2
Allantoin Utilization 1
Arginine and Ornithine Degradation 1
Biogenesis of cytochrome c oxidases 1
D-galactarate, D-glucarate and D-glycerate catabolism 1
Entner-Doudoroff Pathway 1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Glycolysis and Gluconeogenesis 1
Glycolysis and Gluconeogenesis, including Archaeal enzymes 1
Lactose and Galactose Uptake and Utilization 1
Lactose utilization 1
Methylglyoxal Metabolism 1
Orphan regulatory proteins 1
Photorespiration (oxidative C2 cycle) 1
Proline, 4-hydroxyproline uptake and utilization 1
Pyruvate Alanine Serine Interconversions 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Respiratory dehydrogenases 1 1
Serine-glyoxylate cycle 1
TCA Cycle 1
Ton and Tol transport systems 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
L-serine degradation 3 3 3
L-asparagine degradation I 1 1 1
UDP-N-acetyl-α-D-mannosaminouronate biosynthesis 1 1 1
L-malate degradation II 1 1 1
D-serine degradation 3 3 2
L-cysteine degradation II 3 2 2
L-tryptophan degradation II (via pyruvate) 3 2 2
malate/L-aspartate shuttle pathway 2 2 1
ethylene glycol degradation 2 2 1
phenylethylamine degradation II 2 1 1
2-O-α-mannosyl-D-glycerate degradation 2 1 1
proline to cytochrome bo oxidase electron transfer 2 1 1
putrescine degradation I 2 1 1
phenylethanol degradation 2 1 1
putrescine degradation V 2 1 1
phenylethylamine degradation I 2 1 1
glycine betaine degradation III 7 4 3
L-histidine degradation II 5 5 2
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis 5 2 2
glycine betaine degradation I 8 4 3
glycine degradation 3 3 1
ethanol degradation II 3 3 1
ethanol degradation IV 3 3 1
L-methionine biosynthesis II 6 5 2
TCA cycle VIII (Chlamydia) 6 5 2
L-asparagine degradation III (mammalian) 3 2 1
putrescine degradation IV 3 2 1
ethanol degradation III 3 2 1
hypotaurine degradation 3 2 1
L-phenylalanine degradation II (anaerobic) 3 2 1
L-proline degradation I 3 2 1
L-carnitine degradation II 3 1 1
L-arginine degradation I (arginase pathway) 3 1 1
histamine degradation 3 1 1
styrene degradation 3 1 1
superpathway of glycol metabolism and degradation 7 6 2
incomplete reductive TCA cycle 7 3 2
pyruvate fermentation to propanoate I 7 2 2
superpathway of L-aspartate and L-asparagine biosynthesis 4 4 1
L-histidine degradation I 4 4 1
D-glucarate degradation I 4 4 1
D-galactarate degradation I 4 4 1
phytol degradation 4 3 1
glycolate and glyoxylate degradation I 4 3 1
chitin deacetylation 4 3 1
L-mimosine degradation 8 4 2
putrescine degradation III 4 2 1
fatty acid α-oxidation I (plants) 4 2 1
glutathione-mediated detoxification I 8 3 2
ethene biosynthesis II (microbes) 4 1 1
D-arabinose degradation II 4 1 1
L-tryptophan degradation X (mammalian, via tryptamine) 4 1 1
NADPH to cytochrome c oxidase via plastocyanin (thylakoid membrane) 4 1 1
photosynthesis light reactions 4 1 1
gluconeogenesis I 13 12 3
TCA cycle V (2-oxoglutarate synthase) 9 7 2
TCA cycle II (plants and fungi) 9 7 2
Entner-Doudoroff pathway II (non-phosphorylative) 9 6 2
TCA cycle IV (2-oxoglutarate decarboxylase) 9 6 2
superpathway of D-glucarate and D-galactarate degradation 5 5 1
TCA cycle I (prokaryotic) 10 9 2
TCA cycle III (animals) 10 8 2
mitochondrial NADPH production (yeast) 5 3 1
anaerobic energy metabolism (invertebrates, mitochondrial) 10 5 2
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
N-(1-deoxy-D-fructos-1-yl)-L-asparagine degradation 5 2 1
octane oxidation 5 2 1
dopamine degradation 5 1 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 8 2
reductive TCA cycle I 11 6 2
L-glutamate degradation VIII (to propanoate) 11 2 2
superpathway of anaerobic energy metabolism (invertebrates) 17 10 3
glyoxylate cycle 6 6 1
superpathway of glyoxylate bypass and TCA 12 11 2
L-histidine degradation III 6 4 1
3-methyl-branched fatty acid α-oxidation 6 3 1
reductive TCA cycle II 12 5 2
methylgallate degradation 6 2 1
superpathway of photosynthetic hydrogen production 6 2 1
alkane oxidation 6 1 1
formaldehyde assimilation I (serine pathway) 13 8 2
(S)-lactate fermentation to propanoate, acetate and hydrogen 13 5 2
noradrenaline and adrenaline degradation 13 4 2
superpathway of glyoxylate cycle and fatty acid degradation 14 11 2
anaerobic energy metabolism (invertebrates, cytosol) 7 5 1
serotonin degradation 7 3 1
ceramide degradation by α-oxidation 7 2 1
limonene degradation IV (anaerobic) 7 1 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 2
mixed acid fermentation 16 14 2
partial TCA cycle (obligate autotrophs) 8 7 1
L-histidine degradation VI 8 7 1
superpathway of ornithine degradation 8 6 1
purine nucleobases degradation II (anaerobic) 24 16 3
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 5 1
2-deoxy-D-ribose degradation II 8 3 1
protocatechuate degradation I (meta-cleavage pathway) 8 3 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
aromatic biogenic amine degradation (bacteria) 8 1 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 25 3
TCA cycle VI (Helicobacter) 9 6 1
TCA cycle VII (acetate-producers) 9 6 1
photorespiration III 9 5 1
photorespiration I 9 5 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 4 1
methylaspartate cycle 19 9 2
superpathway of enterobacterial common antigen biosynthesis 10 8 1
glycolysis V (Pyrococcus) 10 7 1
photorespiration II 10 6 1
superpathway of vanillin and vanillate degradation 10 3 1
glycolysis II (from fructose 6-phosphate) 11 11 1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle 22 18 2
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 8 1
superpathway of phenylethylamine degradation 11 4 1
gluconeogenesis III 12 9 1
syringate degradation 12 3 1
glycolysis I (from glucose 6-phosphate) 13 13 1
superpathway of L-arginine and L-ornithine degradation 13 10 1
superpathway of glycolysis and the Entner-Doudoroff pathway 17 16 1
oxygenic photosynthesis 17 11 1
superpathway of hexitol degradation (bacteria) 18 16 1
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 8 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 21 3
superpathway of anaerobic sucrose degradation 19 17 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 17 1
superpathway of N-acetylneuraminate degradation 22 18 1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis 24 7 1
ethene biosynthesis V (engineered) 25 18 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 19 1
1-butanol autotrophic biosynthesis (engineered) 27 19 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 3 1
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 19 1
superpathway of pentose and pentitol degradation 42 12 1