Experiment set5IT091 for Pseudomonas fluorescens FW300-N2C3

Gly-Glu nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Gly-Glu (5 mM), pH=7
Culturing: pseudo5_N2-C3_1_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/17/2014
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 20 genes in this experiment

For nitrogen source Gly-Glu in Pseudomonas fluorescens FW300-N2C3

For nitrogen source Gly-Glu across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	4
ABC transporter dipeptide (TC 3.A.1.5.2)	4
D-ribose utilization	3
Glycine and Serine Utilization	3
Bacterial Chemotaxis	2
Glycine cleavage system	2
Photorespiration (oxidative C2 cycle)	2
Deoxyribose and Deoxynucleoside Catabolism	1
HMG CoA Synthesis	1
Pyruvate Alanine Serine Interconversions	1
Type IV pilus	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
• Pentose phosphate pathway
• Ubiquinone and menaquinone biosynthesis
• Cysteine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Naphthalene and anthracene degradation
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
D-serine degradation	3	3	2
glycine cleavage	3	3	2
glycine biosynthesis II	3	3	2
L-cysteine degradation II	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
ribose phosphorylation	2	2	1
glycine betaine degradation III	7	7	3
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
2-deoxy-D-ribose degradation I	3	2	1
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	3	2
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
purine nucleobases degradation II (anaerobic)	24	16	3