Experiment set2IT004 for Pseudomonas fluorescens FW300-N2E2

L-Arabinose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Arabinose (20 mM), pH=7
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/9/2015
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 8 genes in this experiment

For carbon source L-Arabinose in Pseudomonas fluorescens FW300-N2E2

For carbon source L-Arabinose across organisms

SEED Subsystems

Subsystem	#Specific
L-Arabinose utilization	5
D-Galacturonate and D-Glucuronate Utilization	1
Nitrate and nitrite ammonification	1
Proline, 4-hydroxyproline uptake and utilization	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
• Valine, leucine and isoleucine biosynthesis
• Pantothenate and CoA biosynthesis
• Caprolactam degradation
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-arabinose degradation III	6	5	3
pyruvate fermentation to acetate VIII	2	1	1
D-galactarate degradation II	3	3	1
D-glucarate degradation II	3	3	1
L-arabinose degradation V	6	4	2
L-lyxonate degradation	3	2	1
L-carnitine degradation II	3	1	1
L-valine biosynthesis	4	4	1
trans-4-hydroxy-L-proline degradation II	4	4	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	2
L-arabinose degradation IV	8	5	2
1,2-dichloroethane degradation	4	2	1
mitochondrial NADPH production (yeast)	5	4	1
cytosolic NADPH production (yeast)	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
D-glucuronate degradation II	5	4	1
D-galacturonate degradation II	5	3	1
D-xylose degradation III	5	2	1
D-xylose degradation V	5	2	1
L-isoleucine biosynthesis IV	6	4	1
D-arabinose degradation III	6	3	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
L-isoleucine biosynthesis II	8	4	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of pentose and pentitol degradation	42	15	4
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	13	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	16	1