Experiment set6IT034 for Phaeobacter inhibens DSM 17395

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L-Threonine carbon source

Group: carbon source
Media: DinoMM_noCarbon_HighNutrient + L-Threonine (20 mM), pH=7
Culturing: Phaeo_ML1, tube, Aerobic, at 25 (C), shaken=200 rpm
Growth: about 6.5 generations
By: Adam on marchapr14
Media components: 20 g/L Sea salts, 0.3 g/L Ammonium Sulfate, 0.1 g/L Potassium phosphate monobasic, 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 31 genes in this experiment

For carbon source L-Threonine in Phaeobacter inhibens DSM 17395

For carbon source L-Threonine across organisms

SEED Subsystems

Subsystem #Specific
Branched-Chain Amino Acid Biosynthesis 2
Formate hydrogenase 2
Glycine Biosynthesis 2
Pyruvate Alanine Serine Interconversions 2
tRNA processing 2
ABC transporter tungstate (TC 3.A.1.6.2) 1
Alanine biosynthesis 1
Aromatic amino acid interconversions with aryl acids 1
Glycine and Serine Utilization 1
Heat shock dnaK gene cluster extended 1
Molybdenum cofactor biosynthesis 1
Photorespiration (oxidative C2 cycle) 1
Pyruvate metabolism I: anaplerotic reactions, PEP 1
Serine-glyoxylate cycle 1
Soluble cytochromes and functionally related electron carriers 1
Threonine degradation 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-threonine degradation II 2 2 2
bis(guanylyl molybdenum cofactor) biosynthesis 2 2 2
bis(guanylyl tungstenpterin) cofactor biosynthesis 1 1 1
L-alanine degradation IV 1 1 1
guanylyl molybdenum cofactor biosynthesis 1 1 1
L-methionine degradation II 3 3 2
L-threonine degradation III (to methylglyoxal) 3 2 2
L-alanine biosynthesis I 2 2 1
L-threonine degradation I 6 5 3
aminopropanol phosphate biosynthesis II 4 2 2
pseudouridine degradation 2 1 1
L-threonine degradation V 2 1 1
L-isoleucine biosynthesis I (from threonine) 7 7 3
ethylmalonyl-CoA pathway 11 7 4
superpathway of L-threonine metabolism 18 15 6
C4 photosynthetic carbon assimilation cycle, NADP-ME type 7 4 2
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered) 14 7 4
superpathway of L-alanine biosynthesis 4 3 1
(2S)-ethylmalonyl-CoA biosynthesis 4 3 1
superpathway of L-isoleucine biosynthesis I 13 12 3
hypoglycin biosynthesis 14 4 3
methylaspartate cycle 19 15 4
tRNA processing 10 10 2
superpathway of branched chain amino acid biosynthesis 17 17 3
superpathway of the 3-hydroxypropanoate cycle 18 11 3
methylgallate degradation 6 2 1
glyoxylate assimilation 13 7 2
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 7 2
sulfur oxidation IV (intracellular sulfur) 7 2 1
protocatechuate degradation I (meta-cleavage pathway) 8 3 1
superpathway of vanillin and vanillate degradation 10 3 1
syringate degradation 12 3 1
superpathway of sulfide oxidation (phototrophic sulfur bacteria) 12 3 1
gluconeogenesis I 13 12 1
3-hydroxypropanoate cycle 13 9 1
formaldehyde assimilation I (serine pathway) 13 8 1
cyclosporin A biosynthesis 15 2 1