Experiment set5IT066 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 5.5 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 15 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
ABC transporter oligopeptide (TC 3.A.1.5.1)	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine and Serine Utilization	1
Ketoisovalerate oxidoreductase	1
Potassium homeostasis	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Sex pheromones in Enterococcus faecalis and other Firmicutes	1
Universal GTPases	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Purine metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Glycerophospholipid metabolism
• Pyruvate metabolism
• Propanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Drug metabolism - other enzymes
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
acetate conversion to acetyl-CoA	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
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
L-glutamate biosynthesis I	2	2	1
glycerol-3-phosphate shuttle	2	2	1
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
ethanol degradation IV	3	3	1
ammonia assimilation cycle III	3	3	1
glycine degradation	3	3	1
superpathway of acetate utilization and formation	3	3	1
ethanol degradation II	3	3	1
L-methionine biosynthesis II	6	5	2
L-isoleucine biosynthesis V	3	2	1
ethanol degradation III	3	2	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
CDP-diacylglycerol biosynthesis I	4	4	1
CDP-diacylglycerol biosynthesis II	4	4	1
guanosine ribonucleotides de novo biosynthesis	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
L-mimosine degradation	8	4	2
chitin deacetylation	4	2	1
glutathione-mediated detoxification I	8	3	2
CDP-diacylglycerol biosynthesis III	5	4	1
phosphatidate biosynthesis (yeast)	5	3	1
glucosylglycerol biosynthesis	5	2	1
2-methylcitrate cycle I	5	1	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis I	6	5	1
phosphatidylglycerol biosynthesis II	6	5	1
L-isoleucine biosynthesis IV	6	4	1
β-alanine biosynthesis II	6	4	1
superpathway of bitter acids biosynthesis	18	3	3
adlupulone and adhumulone biosynthesis	6	1	1
2-methylcitrate cycle II	6	1	1
lupulone and humulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	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
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
1,3-propanediol biosynthesis (engineered)	9	4	1
cis-geranyl-CoA degradation	9	1	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
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