Experiment set5IT054 for Klebsiella michiganensis M5al

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D,L-Malic Acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D,L-Malic Acid (20 mM), pH=7
Culturing: Koxy_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 27-Mar-17
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 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)
Growth plate: 1766 A5

Specific Phenotypes

For 23 genes in this experiment

For carbon source D,L-Malic Acid in Klebsiella michiganensis M5al

For carbon source D,L-Malic Acid across organisms

SEED Subsystems

Subsystem #Specific
D-ribose utilization 2
Ammonia assimilation 1
Beta-Glucoside Metabolism 1
Calvin-Benson cycle 1
Cysteine Biosynthesis 1
D-gluconate and ketogluconates metabolism 1
Deoxyribose and Deoxynucleoside Catabolism 1
Glycine and Serine Utilization 1
Malonate decarboxylase 1
Orphan regulatory proteins 1
Phosphate metabolism 1
Pyruvate Alanine Serine Interconversions 1
Pyruvate metabolism I: anaplerotic reactions, PEP 1
Sialic Acid Metabolism 1
Sucrose utilization 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
D-serine degradation 3 3 3
L-tryptophan degradation II (via pyruvate) 3 3 2
L-cysteine degradation II 3 3 2
L-serine degradation 3 3 2
ribose phosphorylation 2 2 1
NAD phosphorylation and transhydrogenation 2 2 1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis 5 2 2
fatty acid biosynthesis initiation (type II) 3 3 1
malonate degradation I (biotin-independent) 3 3 1
molybdenum cofactor biosynthesis 3 3 1
NAD phosphorylation and dephosphorylation 3 3 1
2-deoxy-D-ribose degradation I 3 3 1
L-methionine biosynthesis II 6 5 2
glycine betaine degradation III 7 4 2
fatty acid biosynthesis initiation (mitochondria) 4 3 1
L-mimosine degradation 8 4 2
glycine betaine degradation I 8 4 2
glutathione-mediated detoxification I 8 3 2
fatty acid biosynthesis initiation (plant mitochondria) 4 1 1
superpathway of fatty acid biosynthesis initiation 5 5 1
NAD(P)/NADPH interconversion 6 4 1
pederin biosynthesis 14 2 2
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 2
bryostatin biosynthesis 19 2 2
Rubisco shunt 10 9 1
mycobactin biosynthesis 11 3 1
purine nucleobases degradation II (anaerobic) 24 17 2
Calvin-Benson-Bassham cycle 13 10 1
superpathway of fatty acid biosynthesis I (E. coli) 16 16 1
oxygenic photosynthesis 17 11 1
ethene biosynthesis V (engineered) 25 18 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 19 1
mupirocin biosynthesis 26 2 1
1-butanol autotrophic biosynthesis (engineered) 27 19 1
corallopyronin A biosynthesis 30 2 1
superpathway of fatty acid biosynthesis II (plant) 43 38 1
superpathway of fatty acids biosynthesis (E. coli) 53 51 1