Experiment set3IT079 for Sphingomonas koreensis DSMZ 15582

a-Cyclodextrin carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + a-Cyclodextrin (20 mM)
Culturing: korea_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
By: Jordan on 10/21/2014
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 16 genes in this experiment

For carbon source a-Cyclodextrin in Sphingomonas koreensis DSMZ 15582

For carbon source a-Cyclodextrin across organisms

SEED Subsystems

Subsystem	#Specific
Maltose and Maltodextrin Utilization	5
Glycine and Serine Utilization	4
Glycine cleavage system	4
Photorespiration (oxidative C2 cycle)	4
Ammonia assimilation	1
Arginine and Ornithine Degradation	1
Inositol catabolism	1
Polyhydroxybutyrate metabolism	1
Proline, 4-hydroxyproline uptake and utilization	1
Respiratory dehydrogenases 1	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Glutamate metabolism
• Starch and sucrose metabolism
• Glycerophospholipid metabolism
• 2,4-Dichlorobenzoate degradation
• 1- and 2-Methylnaphthalene degradation
• Butanoate metabolism
• One carbon pool by folate
• Retinol metabolism
• Nitrogen metabolism
• Alkaloid biosynthesis II

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycine cleavage	3	3	2
glycine biosynthesis II	3	3	2
L-arginine degradation I (arginase pathway)	3	2	1
L-proline degradation I	3	2	1
starch degradation I	3	1	1
ethene biosynthesis II (microbes)	4	1	1
glycogen degradation I	8	3	1