Experiment set3IT065 for Burkholderia phytofirmans PsJN

L-Isoleucine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + L-Isoleucine (20 mM), pH=7
Culturing: BFirm_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 5.5 generations
By: Mark on 1/27/2016
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)
Growth plate: Plate 1 C3

Specific Phenotypes

For 6 genes in this experiment

For nitrogen source L-Isoleucine in Burkholderia phytofirmans PsJN

For nitrogen source L-Isoleucine across organisms

SEED Subsystems

Subsystem	#Specific
Branched-Chain Amino Acid Biosynthesis	2
Leucine Biosynthesis	2
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	1
Alanine biosynthesis	1
Isoleucine degradation	1
Leucine Degradation and HMG-CoA Metabolism	1
Pyruvate Alanine Serine Interconversions	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine biosynthesis
• Biosynthesis of alkaloids derived from histidine and purine
• Valine, leucine and isoleucine degradation
• Pyruvate metabolism
• Pantothenate and CoA biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-alanine biosynthesis I	2	2	1
L-leucine biosynthesis	6	6	2
L-valine degradation II	3	2	1
L-isoleucine degradation II	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
L-valine biosynthesis	4	4	1
superpathway of L-alanine biosynthesis	4	4	1
superpathway of branched chain amino acid biosynthesis	17	17	4
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
L-leucine degradation I	6	5	1
L-isoleucine degradation I	6	4	1
L-isoleucine biosynthesis IV	6	4	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
3-methylbutanol biosynthesis (engineered)	7	6	1
L-isoleucine biosynthesis III	7	4	1
L-isoleucine biosynthesis II	8	6	1
L-valine degradation I	8	5	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	16	1
anteiso-branched-chain fatty acid biosynthesis	34	30	1
odd iso-branched-chain fatty acid biosynthesis	34	30	1
even iso-branched-chain fatty acid biosynthesis	34	30	1