Experiment set3IT013 for Agrobacterium fabrum C58

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Choline chloride nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Succinate_noNitrogen + Choline chloride (10 mM)
Culturing: Agro_ML11, 24-well transparent microplate; Multitron, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 11/20/20
Media components: 10 mM Sodium succinate dibasic hexahydrate, 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 17 genes in this experiment

For nitrogen source Choline chloride in Agrobacterium fabrum C58

For nitrogen source Choline chloride across organisms

SEED Subsystems

Subsystem #Specific
Choline and Betaine Uptake and Betaine Biosynthesis 7
Anaerobic respiratory reductases 1
Glycine and Serine Utilization 1
Histidine Degradation 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
L-serine degradation 3 3 3
glycine betaine biosynthesis I (Gram-negative bacteria) 2 2 2
choline degradation I 2 2 2
glycine betaine biosynthesis II (Gram-positive bacteria) 2 2 2
choline-O-sulfate degradation 3 3 2
D-serine degradation 3 3 2
L-tryptophan degradation II (via pyruvate) 3 2 2
L-cysteine degradation II 3 2 2
β-alanine biosynthesis I 2 1 1
β-alanine biosynthesis IV 2 1 1
benzoate degradation I (aerobic) 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 6 3
glycine degradation 3 3 1
L-methionine biosynthesis II 6 5 2
proline betaine degradation I 3 2 1
glycine betaine biosynthesis III (plants) 3 2 1
dimethylsulfoniopropanoate biosynthesis I (Wollastonia) 3 1 1
L-mimosine degradation 8 4 2
choline degradation IV 4 2 1
glutathione-mediated detoxification I 8 3 2
dimethylsulfoniopropanoate biosynthesis II (Spartina) 4 1 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 2
purine nucleobases degradation II (anaerobic) 24 14 3
meta cleavage pathway of aromatic compounds 10 4 1
toluene degradation IV (aerobic) (via catechol) 13 5 1
mandelate degradation to acetyl-CoA 18 8 1
superpathway of aerobic toluene degradation 30 12 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 15 1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate 42 11 1