Experiment set11IT079 for Pseudomonas putida KT2440

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pH 5

Group: pH
Media: MOPS minimal media_noCarbon + D-Glucose (55.5 mM), pH=5
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
By: Thomas Eng on 09/16/2018
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 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 11 genes in this experiment

For pH D-Glucose in Pseudomonas putida KT2440

For pH D-Glucose across organisms

SEED Subsystems

Subsystem #Specific
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Thiamin 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
glyphosate degradation II 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
L-glutamate degradation II 2 2 1
malate/L-aspartate shuttle pathway 2 2 1
L-tyrosine degradation II 2 1 1
atromentin biosynthesis 2 1 1
L-tryptophan degradation IV (via indole-3-lactate) 2 1 1
L-phenylalanine biosynthesis I 3 3 1
L-tyrosine biosynthesis I 3 3 1
L-phenylalanine degradation II (anaerobic) 3 2 1
L-asparagine degradation III (mammalian) 3 2 1
(R)-cysteate degradation 3 1 1
sulfolactate degradation III 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
indole-3-acetate biosynthesis VI (bacteria) 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 5 1
trans-4-hydroxy-L-proline degradation I 5 3 1
superpathway of plastoquinol biosynthesis 5 2 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 2 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
L-tryptophan degradation XIII (reductive Stickland reaction) 5 1 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 7 2
superpathway of L-threonine biosynthesis 6 6 1
TCA cycle VIII (Chlamydia) 6 5 1
superpathway of sulfolactate degradation 6 2 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
thiazole component of thiamine diphosphate biosynthesis II 7 4 1
butanol and isobutanol biosynthesis (engineered) 8 3 1
superpathway of aromatic amino acid biosynthesis 18 18 2
superpathway of L-methionine biosynthesis (transsulfuration) 9 7 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 6 1
superpathway of L-tyrosine biosynthesis 10 10 1
superpathway of L-phenylalanine biosynthesis 10 10 1
rosmarinic acid biosynthesis I 10 2 1
superpathway of thiamine diphosphate biosynthesis II 11 8 1
(S)-reticuline biosynthesis I 11 3 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 12 1
indole-3-acetate biosynthesis II 12 5 1
superpathway of L-isoleucine biosynthesis I 13 13 1
superpathway of rosmarinic acid biosynthesis 14 2 1
superpathway of anaerobic energy metabolism (invertebrates) 17 10 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
aspartate superpathway 25 22 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 4 1
superpathway of chorismate metabolism 59 42 2
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 21 1