Experiment set5IT072 for Sphingomonas koreensis DSMZ 15582

L-Proline nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + L-Proline (5 mM)
Culturing: korea_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.8 generations
By: Mark on 1/26/2015
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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 33 genes in this experiment

For nitrogen source L-Proline in Sphingomonas koreensis DSMZ 15582

For nitrogen source L-Proline across organisms

SEED Subsystems

Subsystem	#Specific
Potassium homeostasis	2
ABC transporter oligopeptide (TC 3.A.1.5.1)	1
Arginine and Ornithine Degradation	1
Beta-lactamase	1
Carotenoids	1
Glutaredoxins	1
Glutathione: Redox cycle	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine and Serine Utilization	1
Heat shock dnaK gene cluster extended	1
Peptidoglycan Biosynthesis	1
Proline, 4-hydroxyproline uptake and utilization	1
Pyruvate Alanine Serine Interconversions	1
RNA processing and degradation, bacterial	1
Respiratory dehydrogenases 1	1
Sex pheromones in Enterococcus faecalis and other Firmicutes	1
Tn552	1
Universal GTPases	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Purine metabolism
• Cysteine metabolism
• Penicillin and cephalosporin biosynthesis
• beta-Lactam resistance
• Histidine metabolism
• Phenylalanine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Cyanoamino acid metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Toluene and xylene degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Benzoate degradation via CoA ligation
• Styrene degradation
• Methane metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Isoflavonoid biosynthesis
• Alkaloid biosynthesis I
• Drug metabolism - other enzymes
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
zeaxanthin biosynthesis	2	2	2
L-glutamine degradation I	1	1	1
L-cysteine degradation II	3	2	2
D-serine degradation	3	2	2
L-tryptophan degradation II (via pyruvate)	3	2	2
glycerol-3-phosphate shuttle	2	2	1
L-glutamate biosynthesis I	2	2	1
echinenone and zeaxanthin biosynthesis (Synechocystis)	4	2	2
glycine betaine degradation III	7	4	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	4	3
ammonia assimilation cycle III	3	3	1
glycine degradation	3	3	1
L-methionine biosynthesis II	6	5	2
L-proline degradation I	3	2	1
L-arginine degradation I (arginase pathway)	3	2	1
CDP-diacylglycerol biosynthesis II	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
guanosine ribonucleotides de novo biosynthesis	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
CDP-diacylglycerol biosynthesis I	4	4	1
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	3	2
ethene biosynthesis II (microbes)	4	1	1
tRNA processing	10	10	2
CDP-diacylglycerol biosynthesis III	5	4	1
phosphatidate biosynthesis (yeast)	5	3	1
glucosylglycerol biosynthesis	5	2	1
astaxanthin biosynthesis (bacteria, fungi, algae)	10	2	2
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis II	6	5	1
phosphatidylglycerol biosynthesis I	6	5	1
L-glutamate and L-glutamine biosynthesis	7	4	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	1
L-citrulline biosynthesis	8	6	1
purine nucleobases degradation II (anaerobic)	24	11	3
1,3-propanediol biosynthesis (engineered)	9	4	1
superpathway of carotenoid biosynthesis in plants	22	5	2
superpathway of phospholipid biosynthesis III (E. coli)	12	9	1
superpathway of L-citrulline metabolism	12	8	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
superpathway of purine nucleotide salvage	14	11	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
superpathway of purine nucleotides de novo biosynthesis II	26	24	1
superpathway of phospholipid biosynthesis II (plants)	28	9	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	43	1