Experiment set25S543 for Pseudomonas fluorescens FW300-N2E2

Compare to:

Ying_OrganicAcid7 rep A; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_OrganicAcid7
Culturing: pseudo6_N2E2_ML5b, 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_OrganicAcid7 1x includes: 366 uM Sodium L-Lactate, 366 uM D,L-Malic Acid, 366 uM Citric Acid, 366 uM Succinic Acid, 366 uM Sodium pyruvate, 366 uM a-Ketoglutaric acid disodium salt hydrate, 366 uM L-Citrulline

Specific Phenotypes

For 13 genes in this experiment

For carbon source Ying_OrganicAcid7 in Pseudomonas fluorescens FW300-N2E2

For carbon source Ying_OrganicAcid7 across organisms

SEED Subsystems

Subsystem #Specific
Aromatic amino acid degradation 1
Biogenesis of cytochrome c oxidases 1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 1
Homogentisate pathway of aromatic compound degradation 1
Lysine Biosynthesis DAP Pathway 1
Plastoquinone Biosynthesis 1
Pyruvate metabolism I: anaplerotic reactions, PEP 1
Tocopherol Biosynthesis 1
Tryptophan synthesis 1
YjeE 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-glutamine biosynthesis I 1 1 1
L-glutamine degradation I 1 1 1
ammonia assimilation cycle III 3 3 2
ammonia assimilation cycle I 2 2 1
ammonia assimilation cycle II 2 2 1
L-glutamate biosynthesis I 2 2 1
superpathway of ammonia assimilation (plants) 3 3 1
L-aspartate degradation II (aerobic) 3 2 1
L-aspartate degradation III (anaerobic) 3 2 1
plastoquinol-9 biosynthesis I 3 1 1
L-glutamate and L-glutamine biosynthesis 7 6 2
glutaminyl-tRNAgln biosynthesis via transamidation 4 4 1
putrescine degradation II 4 4 1
L-asparagine biosynthesis III (tRNA-dependent) 4 4 1
heme a biosynthesis 4 2 1
acridone alkaloid biosynthesis 4 1 1
L-tyrosine degradation I 5 5 1
superpathway of plastoquinol biosynthesis 5 2 1
4-hydroxy-2(1H)-quinolone biosynthesis 5 2 1
L-tryptophan biosynthesis 6 6 1
vitamin E biosynthesis (tocopherols) 7 1 1
superpathway of ornithine degradation 8 7 1
L-citrulline biosynthesis 8 6 1
L-lysine biosynthesis I 9 9 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 5 1
L-arginine biosynthesis II (acetyl cycle) 10 10 1
peptidoglycan recycling II 10 8 1
superpathway of quinolone and alkylquinolone biosynthesis 10 2 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 9 1
superpathway of L-citrulline metabolism 12 8 1
superpathway of L-tryptophan biosynthesis 13 13 1
superpathway of L-arginine and L-ornithine degradation 13 11 1
superpathway of aromatic amino acid biosynthesis 18 18 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
aspartate superpathway 25 22 1
superpathway of chorismate metabolism 59 43 1