Experiment set10S446 for Pantoea sp. MT58

Ying_AminoAcid20 rep B; time point 2

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 8 genes in this experiment

For carbon source Ying_AminoAcid20 in Pantoea sp. MT58

For carbon source Ying_AminoAcid20 across organisms

SEED Subsystems

Subsystem	#Specific
Glycine and Serine Utilization	2
Allantoin Utilization	1
Arginine and Ornithine Degradation	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Histidine Degradation	1
Photorespiration (oxidative C2 cycle)	1
Proline, 4-hydroxyproline uptake and utilization	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Respiratory dehydrogenases 1	1
Serine-glyoxylate cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Histidine metabolism
• Cyanoamino acid metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Nitrogen metabolism

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
D-serine degradation	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
L-cysteine degradation II	3	2	2
proline to cytochrome bo oxidase electron transfer	2	1	1
2-O-α-mannosyl-D-glycerate degradation	2	1	1
glycine betaine degradation III	7	4	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	4	3
glycine degradation	3	3	1
L-methionine biosynthesis II	6	5	2
L-asparagine degradation III (mammalian)	3	2	1
L-proline degradation I	3	2	1
L-arginine degradation I (arginase pathway)	3	1	1
D-glucarate degradation I	4	4	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	4	1
D-galactarate degradation I	4	4	1
glycolate and glyoxylate degradation I	4	3	1
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	3	2
ethene biosynthesis II (microbes)	4	1	1
superpathway of D-glucarate and D-galactarate degradation	5	5	1
L-histidine degradation II	5	5	1
N-(1-deoxy-D-fructos-1-yl)-L-asparagine degradation	5	2	1
superpathway of glycol metabolism and degradation	7	6	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
purine nucleobases degradation II (anaerobic)	24	16	3
2-deoxy-D-ribose degradation II	8	3	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
photorespiration I	9	5	1
photorespiration III	9	5	1
glycolysis V (Pyrococcus)	10	7	1
photorespiration II	10	6	1
glycolysis II (from fructose 6-phosphate)	11	11	1
glycolysis I (from glucose 6-phosphate)	13	13	1
gluconeogenesis I	13	12	1
formaldehyde assimilation I (serine pathway)	13	8	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	16	1
superpathway of hexitol degradation (bacteria)	18	16	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	8	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	17	1
superpathway of anaerobic sucrose degradation	19	17	1
superpathway of N-acetylneuraminate degradation	22	18	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1