Experiment set3IT072 for Agrobacterium fabrum C58

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L-Phenylalanine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Succinate_noNitrogen + L-Phenylalanine (5 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 L-Phenylalanine in Agrobacterium fabrum C58

For nitrogen source L-Phenylalanine across organisms

SEED Subsystems

Subsystem #Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 2
Cobalt-zinc-cadmium resistance 1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Threonine and Homoserine 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-aspartate degradation I 1 1 1
L-aspartate biosynthesis 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
malate/L-aspartate shuttle pathway 2 2 1
L-glutamate degradation II 2 2 1
atromentin biosynthesis 2 1 1
L-tyrosine degradation II 2 1 1
L-tryptophan degradation IV (via indole-3-lactate) 2 1 1
L-tyrosine biosynthesis I 3 3 1
L-phenylalanine biosynthesis I 3 3 1
L-asparagine degradation III (mammalian) 3 2 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
sulfolactate degradation III 3 1 1
indole-3-acetate biosynthesis VI (bacteria) 3 1 1
L-phenylalanine degradation II (anaerobic) 3 1 1
(R)-cysteate degradation 3 1 1
superpathway of L-aspartate and L-asparagine biosynthesis 4 3 1
L-tyrosine degradation III 4 2 1
L-phenylalanine degradation III 4 2 1
L-tryptophan degradation VIII (to tryptophol) 4 1 1
L-tyrosine degradation I 5 3 1
trans-4-hydroxy-L-proline degradation I 5 3 1
superpathway of plastoquinol biosynthesis 5 2 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-tryptophan degradation XIII (reductive Stickland reaction) 5 1 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 7 2
TCA cycle VIII (Chlamydia) 6 6 1
superpathway of L-threonine biosynthesis 6 6 1
superpathway of sulfolactate degradation 6 1 1
coenzyme M biosynthesis II 6 1 1
anaerobic energy metabolism (invertebrates, cytosol) 7 5 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 8 2
superpathway of aromatic amino acid biosynthesis 18 18 2
superpathway of L-methionine biosynthesis (transsulfuration) 9 8 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 2 1
superpathway of L-tyrosine biosynthesis 10 10 1
superpathway of L-phenylalanine biosynthesis 10 10 1
rosmarinic acid biosynthesis I 10 2 1
(S)-reticuline biosynthesis I 11 1 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 12 1
indole-3-acetate biosynthesis II 12 3 1
superpathway of L-isoleucine biosynthesis I 13 13 1
superpathway of rosmarinic acid biosynthesis 14 3 1
superpathway of anaerobic energy metabolism (invertebrates) 17 13 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 17 1
aspartate superpathway 25 24 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 1 1
superpathway of chorismate metabolism 59 38 2
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 18 1