Experiment setAIT072 for Pseudomonas fluorescens FW300-N2E2

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L-Serine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + L-Serine (20 mM)
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=500 rpm
Growth: about 3.5 generations
By: Mark on 1/21/2016
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 33 genes in this experiment

For nitrogen source L-Serine in Pseudomonas fluorescens FW300-N2E2

For nitrogen source L-Serine across organisms

SEED Subsystems

Subsystem #Specific
Glycine and Serine Utilization 4
Glycine cleavage system 3
Photorespiration (oxidative C2 cycle) 3
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 2
Ammonia assimilation 1
Branched-Chain Amino Acid Biosynthesis 1
Choline and Betaine Uptake and Betaine Biosynthesis 1
Cysteine Biosynthesis 1
DNA-binding regulatory proteins, strays 1
Pyruvate Alanine Serine Interconversions 1
SigmaB stress responce regulation 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-serine degradation 3 3 3
L-aspartate degradation I 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
L-asparagine degradation I 1 1 1
L-aspartate biosynthesis 1 1 1
glycine betaine degradation III 7 7 5
L-methionine degradation II 3 3 2
D-serine degradation 3 3 2
L-cysteine degradation II 3 3 2
L-tryptophan degradation II (via pyruvate) 3 2 2
L-asparagine degradation III (mammalian) 3 2 2
L-glutamate degradation II 2 2 1
superpathway of L-aspartate and L-asparagine biosynthesis 4 3 2
L-threonine degradation I 6 4 3
malate/L-aspartate shuttle pathway 2 1 1
L-tryptophan degradation IV (via indole-3-lactate) 2 1 1
L-tyrosine degradation II 2 1 1
L-threonine degradation V 2 1 1
atromentin biosynthesis 2 1 1
L-isoleucine biosynthesis I (from threonine) 7 7 3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis 5 2 2
glycine betaine degradation I 8 6 3
glycine biosynthesis II 3 3 1
glycine cleavage 3 3 1
L-phenylalanine biosynthesis I 3 3 1
glycine degradation 3 3 1
L-tyrosine biosynthesis I 3 3 1
L-methionine biosynthesis II 6 5 2
L-phenylalanine degradation II (anaerobic) 3 2 1
indole-3-acetate biosynthesis VI (bacteria) 3 1 1
(R)-cysteate degradation 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
sulfolactate degradation III 3 1 1
superpathway of L-isoleucine biosynthesis I 13 13 4
poly-β-1,6-N-acetyl-D-glucosamine biosynthesis 4 3 1
L-mimosine degradation 8 4 2
L-phenylalanine degradation III 4 2 1
L-tyrosine degradation III 4 2 1
glutathione-mediated detoxification I 8 3 2
L-tryptophan degradation VIII (to tryptophol) 4 1 1
hypoglycin biosynthesis 14 4 3
L-tyrosine degradation I 5 5 1
trans-4-hydroxy-L-proline degradation I 5 3 1
superpathway of plastoquinol biosynthesis 5 2 1
N-(1-deoxy-D-fructos-1-yl)-L-asparagine degradation 5 2 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
L-tryptophan degradation XIII (reductive Stickland reaction) 5 1 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 6 2
superpathway of branched chain amino acid biosynthesis 17 17 3
superpathway of L-threonine biosynthesis 6 6 1
superpathway of L-threonine metabolism 18 13 3
TCA cycle VIII (Chlamydia) 6 4 1
superpathway of sulfolactate degradation 6 2 1
coenzyme M biosynthesis II 6 1 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 9 2
anaerobic energy metabolism (invertebrates, cytosol) 7 4 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 2
purine nucleobases degradation II (anaerobic) 24 16 3
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 5 1
superpathway of L-phenylalanine biosynthesis 10 10 1
superpathway of L-tyrosine biosynthesis 10 10 1
rosmarinic acid biosynthesis I 10 3 1
(S)-reticuline biosynthesis I 11 1 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 12 1
indole-3-acetate biosynthesis II 12 5 1
superpathway of rosmarinic acid biosynthesis 14 4 1
cyclosporin A biosynthesis 15 2 1
superpathway of anaerobic energy metabolism (invertebrates) 17 8 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 43 2
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 21 1