Experiment setAIT075 for Pseudomonas fluorescens FW300-N2E2

Glycine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Glycine (20 mM)
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=500 rpm
Growth: about 4.6 generations
By: Mark on 1/21/2016
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 17 genes in this experiment

For nitrogen source Glycine in Pseudomonas fluorescens FW300-N2E2

For nitrogen source Glycine across organisms

SEED Subsystems

Subsystem	#Specific
Glycine and Serine Utilization	4
Glycine cleavage system	3
Photorespiration (oxidative C2 cycle)	3
Ammonia assimilation	1
Homogentisate pathway of aromatic compound degradation	1
L-rhamnose utilization	1
Lactate utilization	1
Pyruvate Alanine Serine Interconversions	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
• Puromycin biosynthesis
• Cysteine metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Trinitrotoluene degradation
• One carbon pool by folate
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
glycine betaine degradation III	7	7	5
glycine biosynthesis II	3	3	2
L-cysteine degradation II	3	3	2
D-serine degradation	3	3	2
glycine cleavage	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	6	3
glycine degradation	3	3	1
L-methionine biosynthesis II	6	5	2
queuosine biosynthesis I (de novo)	4	4	1
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	3	2
queuosine biosynthesis III (queuosine salvage)	5	3	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
purine nucleobases degradation II (anaerobic)	24	16	3