Experiment set3IT061 for Agrobacterium fabrum C58

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L-Valine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Succinate_noNitrogen + L-Valine (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 5 genes in this experiment

For nitrogen source L-Valine in Agrobacterium fabrum C58

For nitrogen source L-Valine across organisms

SEED Subsystems

Subsystem #Specific
Alanine biosynthesis 1
Biotin biosynthesis 1
Branched-Chain Amino Acid Biosynthesis 1
Fatty Acid Biosynthesis FASII 1
Isoleucine degradation 1
Leucine Biosynthesis 1
Leucine Degradation and HMG-CoA Metabolism 1
Pyruvate Alanine Serine Interconversions 1
Valine degradation 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
L-alanine biosynthesis I 2 2 1
L-isoleucine degradation II 3 2 1
L-isoleucine biosynthesis V 3 2 1
L-valine degradation II 3 2 1
L-leucine degradation III 3 2 1
L-valine degradation III (oxidative Stickland reaction) 3 1 1
L-isoleucine degradation III (oxidative Stickland reaction) 3 1 1
L-leucine degradation V (oxidative Stickland reaction) 3 1 1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast) 12 12 3
superpathway of L-alanine biosynthesis 4 4 1
L-valine biosynthesis 4 4 1
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
anteiso-branched-chain fatty acid biosynthesis 34 30 7
odd iso-branched-chain fatty acid biosynthesis 34 30 7
even iso-branched-chain fatty acid biosynthesis 34 30 7
fatty acid elongation -- saturated 5 5 1
8-amino-7-oxononanoate biosynthesis IV 5 5 1
superpathway of unsaturated fatty acids biosynthesis (E. coli) 20 18 4
cis-vaccenate biosynthesis 5 4 1
L-leucine degradation IV (reductive Stickland reaction) 5 1 1
superpathway of fatty acid biosynthesis II (plant) 43 38 8
8-amino-7-oxononanoate biosynthesis I 11 9 2
superpathway of branched chain amino acid biosynthesis 17 17 3
(5Z)-dodecenoate biosynthesis I 6 6 1
L-leucine biosynthesis 6 6 1
(5Z)-dodecenoate biosynthesis II 6 5 1
stearate biosynthesis II (bacteria and plants) 6 5 1
L-leucine degradation I 6 5 1
L-isoleucine degradation I 6 4 1
stearate biosynthesis IV 6 4 1
L-isoleucine biosynthesis IV 6 3 1
petroselinate biosynthesis 6 2 1
streptorubin B biosynthesis 34 20 5
L-isoleucine biosynthesis I (from threonine) 7 7 1
L-isoleucine biosynthesis III 7 4 1
biotin biosynthesis I 15 13 2
superpathway of fatty acid biosynthesis I (E. coli) 16 15 2
L-isoleucine biosynthesis II 8 5 1
L-valine degradation I 8 5 1
2-allylmalonyl-CoA biosynthesis 8 2 1
superpathway of L-isoleucine biosynthesis I 13 13 1
superpathway of L-threonine metabolism 18 11 1
mycolate biosynthesis 205 21 5
superpathway of mycolate biosynthesis 239 22 5