Experiment set11IT079 for Klebsiella michiganensis M5al

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2-Deoxy-D-ribonic acid lithium salt 10 mM carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 2-Deoxy-D-ribonic acid lithium salt (10 mM), pH=7
Culturing: Koxy_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 5/2/18
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: Koxy_deoxyribosePlus_plate D4

Specific Phenotypes

For 5 genes in this experiment

For carbon source 2-Deoxy-D-ribonic acid lithium salt in Klebsiella michiganensis M5al

For carbon source 2-Deoxy-D-ribonic acid lithium salt across organisms

SEED Subsystems

Subsystem #Specific
Acetyl-CoA fermentation to Butyrate 1
Allantoin Utilization 1
D-galactarate, D-glucarate and D-glycerate catabolism 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Glycine and Serine Utilization 1
Nitrate and nitrite ammonification 1
Photorespiration (oxidative C2 cycle) 1
Serine-glyoxylate cycle 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
acetoacetate degradation (to acetyl CoA) 2 2 1
(R)-lactate fermentation to propanoate II (acrylate pathway) 4 2 2
1,2-propanediol biosynthesis from lactate (engineered) 6 4 2
L-alanine degradation VI (reductive Stickland reaction) 6 4 2
superpathway of L-alanine fermentation (Stickland reaction) 9 7 2
pyruvate fermentation to acetone 5 3 1
gallate degradation III (anaerobic) 11 5 2
propanoate fermentation to 2-methylbutanoate 6 4 1
acetyl-CoA fermentation to butanoate 7 5 1
4-aminobutanoate degradation V 7 3 1
L-glutamate degradation XI (reductive Stickland reaction) 7 3 1
succinate fermentation to butanoate 7 1 1
photorespiration I 9 5 1
photorespiration III 9 5 1
L-glutamate degradation V (via hydroxyglutarate) 10 6 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 7 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 9 1