Experiment set16IT013 for Pseudomonas fluorescens SBW25-INTG

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Betaine (C)(N); with MOPS; with Sodium chloride

Group: stress
Media: MME_noNitrogen_noCarbon + Betaine (10 mM) + Betaine (10 mM) + Sodium Chloride (400 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 8 (C), shaken=1200 rpm
By: Joshua Elmore on September 1, 2021
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 38 genes in this experiment

For stress Betaine in Pseudomonas fluorescens SBW25-INTG

For stress Betaine across organisms

SEED Subsystems

Subsystem #Specific
Choline and Betaine Uptake and Betaine Biosynthesis 4
Phosphate metabolism 3
Formate hydrogenase 2
ATP-dependent RNA helicases, bacterial 1
Bacterial Cell Division 1
Bacterial Chemotaxis 1
Beta-lactamase 1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 1
DNA-replication 1
Flagellar motility 1
Folate Biosynthesis 1
Glycine and Serine Utilization 1
HMG CoA Synthesis 1
Lysine degradation 1
Methylcitrate cycle 1
Molybdenum cofactor biosynthesis 1
One-carbon metabolism by tetrahydropterines 1
Oxidative stress 1
Proline, 4-hydroxyproline uptake and utilization 1
Propionate-CoA to Succinate Module 1
Purine conversions 1
Pyruvate Alanine Serine Interconversions 1
Riboflavin, FMN and FAD metabolism 1
Threonine degradation 1
Transcription factors bacterial 1
Two-component regulatory systems in Campylobacter 1
Ubiquinone Biosynthesis 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
formate oxidation to CO2 1 1 1
L-glutamine degradation I 1 1 1
formaldehyde oxidation IV (thiol-independent) 1 1 1
L-cysteine degradation II 3 3 2
D-serine degradation 3 3 2
L-tryptophan degradation II (via pyruvate) 3 2 2
inosine 5'-phosphate degradation 4 4 2
L-glutamate biosynthesis I 2 2 1
polyphosphate metabolism 2 2 1
acrylonitrile degradation I 2 2 1
4-aminobenzoate biosynthesis I 2 2 1
indole-3-acetate biosynthesis IV (bacteria) 2 2 1
indole-3-acetate biosynthesis III (bacteria) 2 2 1
glycine betaine degradation III 7 7 3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis 5 2 2
adenosine nucleotides degradation I 8 7 3
glycine betaine degradation I 8 6 3
purine nucleotides degradation II (aerobic) 11 11 4
glycine degradation 3 3 1
ammonia assimilation cycle III 3 3 1
purine nucleotides degradation I (plants) 12 10 4
L-methionine biosynthesis II 6 5 2
L-arginine degradation X (arginine monooxygenase pathway) 3 2 1
NAD salvage pathway III (to nicotinamide riboside) 3 2 1
superpathway of acrylonitrile degradation 3 2 1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis 3 1 1
ureide biosynthesis 7 6 2
UTP and CTP dephosphorylation I 7 5 2
guanosine nucleotides degradation II 4 4 1
guanosine nucleotides degradation III 4 4 1
guanosine ribonucleotides de novo biosynthesis 4 4 1
L-asparagine biosynthesis III (tRNA-dependent) 4 4 1
formaldehyde oxidation VII (THF pathway) 4 4 1
guanosine nucleotides degradation I 4 3 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 1
L-mimosine degradation 8 4 2
glutathione-mediated detoxification I 8 3 2
putrescine degradation II 4 1 1
oxalate degradation VI 4 1 1
flavin biosynthesis I (bacteria and plants) 9 8 2
superpathway of purines degradation in plants 18 14 4
flavin biosynthesis III (fungi) 9 7 2
purine nucleobases degradation II (anaerobic) 24 16 5
adenosine nucleotides degradation II 5 5 1
2-methylcitrate cycle I 5 5 1
6-hydroxymethyl-dihydropterin diphosphate biosynthesis III (Chlamydia) 5 3 1
oxalate degradation III 5 1 1
superpathway of guanosine nucleotides de novo biosynthesis I 6 6 1
superpathway of guanosine nucleotides degradation (plants) 6 5 1
2-methylcitrate cycle II 6 5 1
methanol oxidation to carbon dioxide 6 3 1
NAD(P)/NADPH interconversion 6 3 1
superpathway of C1 compounds oxidation to CO2 12 5 2
L-glutamate and L-glutamine biosynthesis 7 6 1
toxoflavin biosynthesis 7 3 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 2
purine nucleobases degradation I (anaerobic) 15 6 2
L-citrulline biosynthesis 8 8 1
superpathway of guanosine nucleotides de novo biosynthesis II 8 7 1
superpathway of ornithine degradation 8 4 1
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis 8 1 1
tunicamycin biosynthesis 9 2 1
chloramphenicol biosynthesis 9 1 1
superpathway of tetrahydrofolate biosynthesis 10 8 1
flavin biosynthesis II (archaea) 10 5 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 7 1
NAD salvage (plants) 11 5 1
superpathway of candicidin biosynthesis 11 4 1
superpathway of L-citrulline metabolism 12 10 1
superpathway of tetrahydrofolate biosynthesis and salvage 12 10 1
indole-3-acetate biosynthesis II 12 5 1
superpathway of L-arginine and L-ornithine degradation 13 9 1
folate transformations I 13 9 1
superpathway of purine nucleotide salvage 14 13 1
superpathway of purine nucleotides de novo biosynthesis I 21 21 1
superpathway of purine nucleotides de novo biosynthesis II 26 24 1
superpathway of histidine, purine, and pyrimidine biosynthesis 46 44 1
superpathway of chorismate metabolism 59 42 1