Experiment set57IT040 for Escherichia coli BW25113

Compare to:

Ying_AminoAcid20 rep A; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_AminoAcid20
Culturing: Keio_ML9a, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying on 19-Oct-22
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 16 genes in this experiment

For carbon source Ying_AminoAcid20 in Escherichia coli BW25113

For carbon source Ying_AminoAcid20 across organisms

SEED Subsystems

Subsystem #Specific
Polyamine Metabolism 2
Pyruvate Alanine Serine Interconversions 2
Alanine biosynthesis 1
Aromatic amino acid degradation 1
DNA-binding regulatory proteins, strays 1
Glycine and Serine Utilization 1
Mannitol Utilization 1
Proteolysis in bacteria, ATP-dependent 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Staphylococcal phi-Mu50B-like prophages 1
TCA Cycle 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-tryptophan degradation II (via pyruvate) 3 3 3
spermidine biosynthesis I 2 2 2
L-alanine biosynthesis III 1 1 1
alanine racemization 1 1 1
L-cysteine degradation IV 1 1 1
aminopropylcadaverine biosynthesis 3 3 2
D-serine degradation 3 3 2
L-proline degradation I 3 3 2
L-serine degradation 3 3 2
L-cysteine degradation II 3 2 2
L-alanine degradation I 2 2 1
spermine biosynthesis 2 1 1
cytidylyl molybdenum cofactor sulfurylation 2 1 1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis 5 2 2
superpathway of polyamine biosynthesis I 8 7 3
L-methionine biosynthesis II 6 5 2
bis(guanylyl molybdopterin) cofactor sulfurylation 3 1 1
L-arginine degradation I (arginase pathway) 3 1 1
thiazole component of thiamine diphosphate biosynthesis II 7 5 2
glycine betaine degradation III 7 4 2
superpathway of L-alanine biosynthesis 4 4 1
superpathway of polyamine biosynthesis II 8 4 2
L-mimosine degradation 8 4 2
glycine betaine degradation I 8 4 2
spermidine biosynthesis III 4 2 1
glutathione-mediated detoxification I 8 3 2
tRNA-uridine 2-thiolation (mammalian mitochondria) 4 1 1
tRNA-uridine 2-thiolation (yeast mitochondria) 4 1 1
ethene biosynthesis II (microbes) 4 1 1
[2Fe-2S] iron-sulfur cluster biosynthesis 10 4 2
tRNA-uridine 2-thiolation (thermophilic bacteria) 5 1 1
superpathway of thiamine diphosphate biosynthesis II 11 9 2
L-methionine salvage cycle III 11 5 2
superpathway of arginine and polyamine biosynthesis 17 16 3
molybdopterin biosynthesis 6 6 1
thiazole component of thiamine diphosphate biosynthesis I 6 6 1
TCA cycle VIII (Chlamydia) 6 5 1
L-methionine salvage cycle I (bacteria and plants) 12 5 2
hydrogen sulfide biosynthesis II (mammalian) 6 1 1
(5R)-carbapenem carboxylate biosynthesis 6 1 1
incomplete reductive TCA cycle 7 5 1
pyruvate fermentation to propanoate I 7 5 1
anaerobic energy metabolism (invertebrates, cytosol) 7 5 1
L-Nδ-acetylornithine biosynthesis 7 4 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 2
partial TCA cycle (obligate autotrophs) 8 7 1
L-citrulline biosynthesis 8 6 1
tRNA-uridine 2-thiolation (cytoplasmic) 8 1 1
superpathway of anaerobic energy metabolism (invertebrates) 17 12 2
TCA cycle IV (2-oxoglutarate decarboxylase) 9 7 1
TCA cycle VI (Helicobacter) 9 7 1
TCA cycle V (2-oxoglutarate synthase) 9 7 1
TCA cycle II (plants and fungi) 9 7 1
TCA cycle VII (acetate-producers) 9 6 1
ansatrienin biosynthesis 9 1 1
superpathway of thiamine diphosphate biosynthesis I 10 10 1
TCA cycle I (prokaryotic) 10 9 1
TCA cycle III (animals) 10 8 1
anaerobic energy metabolism (invertebrates, mitochondrial) 10 7 1
reductive TCA cycle I 11 8 1
tRNA-uridine 2-thiolation and selenation (bacteria) 11 7 1
L-glutamate degradation VIII (to propanoate) 11 5 1
superpathway of glyoxylate bypass and TCA 12 11 1
purine nucleobases degradation II (anaerobic) 24 17 2
superpathway of L-citrulline metabolism 12 8 1
reductive TCA cycle II 12 8 1
(S)-lactate fermentation to propanoate, acetate and hydrogen 13 10 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 1
cyclosporin A biosynthesis 15 2 1
mixed acid fermentation 16 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
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 22 1