Experiment set3IT025 for Agrobacterium fabrum C58

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5-Aminovaleric acid nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Succinate_noNitrogen + 5-Aminovaleric acid (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 6 genes in this experiment

For nitrogen source 5-Aminovaleric acid in Agrobacterium fabrum C58

For nitrogen source 5-Aminovaleric acid across organisms

SEED Subsystems

Subsystem #Specific
Pyruvate Alanine Serine Interconversions 2
Fatty Acid Biosynthesis FASII 1
Respiratory dehydrogenases 1 1
mycolic acid synthesis 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
L-alanine degradation I 2 2 1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast) 12 12 3
gondoate biosynthesis (anaerobic) 4 4 1
palmitate biosynthesis III 29 28 7
tetradecanoate biosynthesis (mitochondria) 25 23 6
palmitate biosynthesis II (type II fatty acid synthase) 31 29 7
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate) 9 8 2
oleate biosynthesis IV (anaerobic) 14 13 3
superpathway of fatty acids biosynthesis (E. coli) 53 49 11
8-amino-7-oxononanoate biosynthesis IV 5 5 1
fatty acid elongation -- saturated 5 5 1
superpathway of unsaturated fatty acids biosynthesis (E. coli) 20 18 4
cis-vaccenate biosynthesis 5 4 1
superpathway of fatty acid biosynthesis II (plant) 43 38 8
8-amino-7-oxononanoate biosynthesis I 11 9 2
even iso-branched-chain fatty acid biosynthesis 34 30 6
anteiso-branched-chain fatty acid biosynthesis 34 30 6
odd iso-branched-chain fatty acid biosynthesis 34 30 6
(5Z)-dodecenoate biosynthesis I 6 6 1
stearate biosynthesis II (bacteria and plants) 6 5 1
(5Z)-dodecenoate biosynthesis II 6 5 1
stearate biosynthesis IV 6 4 1
β-alanine biosynthesis II 6 3 1
petroselinate biosynthesis 6 2 1
streptorubin B biosynthesis 34 20 5
biotin biosynthesis I 15 13 2
superpathway of fatty acid biosynthesis I (E. coli) 16 15 2
2-allylmalonyl-CoA biosynthesis 8 2 1
superpathway of coenzyme A biosynthesis II (plants) 10 7 1
mycolate biosynthesis 205 21 5
superpathway of mycolate biosynthesis 239 22 5