Experiment set2H25 for Pseudomonas stutzeri RCH2

L-Isoleucine nitrogen source

Group: nitrogen source
Media: RCH2_defined_noNitrogen + L-Isoleucine (5 mM), pH=7.2
Culturing: psRCH2_ML7, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Kelly on 6/20/2013
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 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: 552 C1,C2

Specific Phenotypes

For 7 genes in this experiment

For nitrogen source L-Isoleucine in Pseudomonas stutzeri RCH2

For nitrogen source L-Isoleucine across organisms

SEED Subsystems

Subsystem	#Specific
Isoleucine degradation	2
Valine degradation	2
Alanine biosynthesis	1
Branched-Chain Amino Acid Biosynthesis	1
DNA repair, bacterial	1
Leucine Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	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:

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

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-alanine biosynthesis I	2	2	1
L-isoleucine biosynthesis V	3	3	1
L-leucine degradation V (oxidative Stickland reaction)	3	2	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	2	1
L-valine degradation III (oxidative Stickland reaction)	3	2	1
L-valine degradation II	3	2	1
L-isoleucine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-valine biosynthesis	4	4	1
superpathway of L-alanine biosynthesis	4	4	1
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
superpathway of branched chain amino acid biosynthesis	17	17	3
L-leucine biosynthesis	6	6	1
L-isoleucine degradation I	6	5	1
L-leucine degradation I	6	5	1
L-isoleucine biosynthesis IV	6	5	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
L-valine degradation I	8	6	1
L-isoleucine biosynthesis II	8	4	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	13	1
even iso-branched-chain fatty acid biosynthesis	34	24	1
odd iso-branched-chain fatty acid biosynthesis	34	24	1
anteiso-branched-chain fatty acid biosynthesis	34	24	1