Experiment set5H11 for Phaeobacter inhibens DSM 17395

D-Xylose carbon source

Group: carbon source
Media: DinoMM_noCarbon_HighNutrient + D-Xylose (20 mM), pH=7
Culturing: Phaeo_ML1, tube, Aerobic, at 25 (C), shaken=200 rpm
Growth: about 5.3 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 9 genes in this experiment

For carbon source D-Xylose in Phaeobacter inhibens DSM 17395

For carbon source D-Xylose across organisms

SEED Subsystems

Subsystem	#Specific
Xylose utilization	3
Isobutyryl-CoA to Propionyl-CoA Module	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Pyrimidine utilization	1
Redox-dependent regulation of nucleus processes	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Valine degradation	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Valine, leucine and isoleucine degradation
• Inositol phosphate metabolism
• Propanoate metabolism
• Nicotinate and nicotinamide metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-xylose degradation I	2	2	2
β-alanine degradation I	2	1	1
β-alanine degradation II	2	1	1
D-arabinitol degradation I	2	1	1
xylitol degradation I	2	1	1
NAD salvage pathway V (PNC V cycle)	5	4	1
propanoyl-CoA degradation II	5	3	1
myo-inositol degradation I	7	7	1
NAD salvage pathway I (PNC VI cycle)	7	6	1
2,4-dinitrotoluene degradation	7	1	1
L-valine degradation I	8	5	1
superpathway of glucose and xylose degradation	17	14	2
phenylacetate degradation I (aerobic)	9	6	1
myo-, chiro- and scyllo-inositol degradation	10	7	1
superpathway of phenylethylamine degradation	11	6	1
NAD salvage (plants)	11	6	1
superpathway of NAD biosynthesis in eukaryotes	14	8	1
superpathway of pentose and pentitol degradation	42	11	2