Experiment set25S548 for Pseudomonas fluorescens FW300-N2E2

Compare to:

Ying_Nucleobase14 rep C; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_Nucleobase14
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_Nucleobase14 1x includes: 183 uM 5-methyluridine, 183 uM Adenine, 183 uM Adenosine, 183 uM Cytidine, 183 uM Cytosine, 183 uM Guanine, 183 uM Guanosine, 183 uM Hypoxanthine, 183 uM Inosine, 183 uM Thymine, 183 uM Uracil, 183 uM Uridine, 183 uM Xanthine, 183 uM Xanthosine

Specific Phenotypes

For 17 genes in this experiment

For carbon source Ying_Nucleobase14 in Pseudomonas fluorescens FW300-N2E2

For carbon source Ying_Nucleobase14 across organisms

SEED Subsystems

Subsystem #Specific
Purine Utilization 4
Allantoin Utilization 2
D-ribose utilization 2
DNA-binding regulatory proteins, strays 1
DNA repair, bacterial 1
Glycogen metabolism 1
Maltose and Maltodextrin Utilization 1
Photorespiration (oxidative C2 cycle) 1
Pyruvate Alanine Serine Interconversions 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
β-alanine degradation II 2 2 1
adenosine nucleotides degradation II 5 5 2
glycogen degradation I 8 6 3
glycogen degradation II 6 5 2
allantoin degradation to glyoxylate I 3 2 1
guanosine nucleotides degradation III 4 4 1
inosine 5'-phosphate degradation 4 4 1
glycolate and glyoxylate degradation I 4 4 1
guanosine nucleotides degradation II 4 4 1
adenosine nucleotides degradation I 8 7 2
starch degradation V 4 3 1
guanosine nucleotides degradation I 4 3 1
superpathway of allantoin degradation in plants 8 4 2
starch degradation III 4 2 1
allantoin degradation to glyoxylate II 5 1 1
allantoin degradation to glyoxylate III 5 1 1
purine nucleotides degradation II (aerobic) 11 11 2
purine nucleotides degradation I (plants) 12 10 2
superpathway of guanosine nucleotides degradation (plants) 6 5 1
β-alanine biosynthesis II 6 5 1
superpathway of allantoin degradation in yeast 6 5 1
superpathway of purines degradation in plants 18 14 3
purine nucleobases degradation II (anaerobic) 24 16 4
superpathway of glycol metabolism and degradation 7 7 1
ureide biosynthesis 7 6 1
caffeine degradation III (bacteria, via demethylation) 7 1 1
sucrose biosynthesis II 8 6 1
theophylline degradation 9 1 1
superpathway of coenzyme A biosynthesis II (plants) 10 9 1
caffeine degradation IV (bacteria, via demethylation and oxidation) 10 1 1