Experiment set1IT081 for Acidovorax sp. GW101-3H11

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D-Ribose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Ribose (20 mM), pH=7
Culturing: acidovorax_3H11_ML3a, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/3/2015
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)

Specific Phenotypes

For 6 genes in this experiment

For carbon source D-Ribose in Acidovorax sp. GW101-3H11

For carbon source D-Ribose across organisms

SEED Subsystems

Subsystem #Specific
D-ribose utilization 2
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 2
Entner-Doudoroff Pathway 1
Fructose utilization 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Lipid A modifications 1
Mannitol Utilization 1
Methylglyoxal Metabolism 1
Orphan regulatory proteins 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Sucrose utilization 1
Sucrose utilization Shewanella 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-arabinitol degradation I 2 2 1
putrescine degradation I 2 1 1
ethylene glycol degradation 2 1 1
putrescine degradation V 2 1 1
ethanol degradation II 3 3 1
D-sorbitol degradation I 3 3 1
ethanol degradation IV 3 3 1
putrescine degradation IV 3 2 1
ethanol degradation III 3 2 1
hypotaurine degradation 3 2 1
sucrose degradation I (sucrose phosphotransferase) 3 1 1
histamine degradation 3 1 1
sucrose degradation IV (sucrose phosphorylase) 4 3 1
sucrose degradation III (sucrose invertase) 4 3 1
phytol degradation 4 3 1
fatty acid α-oxidation I (plants) 4 2 1
sucrose degradation VII (sucrose 3-dehydrogenase) 4 1 1
putrescine degradation III 4 1 1
L-tryptophan degradation X (mammalian, via tryptamine) 4 1 1
D-arabinose degradation II 4 1 1
propane degradation I 4 1 1
sucrose degradation II (sucrose synthase) 5 4 1
octane oxidation 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
mannitol cycle 5 2 1
mitochondrial NADPH production (yeast) 5 2 1
propane degradation II 5 2 1
dopamine degradation 5 1 1
3-methyl-branched fatty acid α-oxidation 6 3 1
alkane oxidation 6 1 1
noradrenaline and adrenaline degradation 13 4 2
superpathway of glycol metabolism and degradation 7 5 1
serotonin degradation 7 3 1
ceramide degradation by α-oxidation 7 2 1
limonene degradation IV (anaerobic) 7 1 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 4 1
superpathway of ornithine degradation 8 3 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
aromatic biogenic amine degradation (bacteria) 8 1 1
Entner-Doudoroff pathway II (non-phosphorylative) 9 4 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 4 1
superpathway of L-arginine and L-ornithine degradation 13 6 1
heterolactic fermentation 18 12 1
superpathway of anaerobic sucrose degradation 19 17 1
superpathway of pentose and pentitol degradation 42 14 2