Experiment set3IT063 for Agrobacterium fabrum C58

L-Isoleucine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Succinate_noNitrogen + L-Isoleucine (5 mM)
Culturing: Agro_ML11, 24-well transparent microplate; Multitron, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 11/20/20
Media components: 10 mM Sodium succinate dibasic hexahydrate, 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 3 genes in this experiment

For nitrogen source L-Isoleucine in Agrobacterium fabrum C58

For nitrogen source L-Isoleucine across organisms

SEED Subsystems

Subsystem	#Specific
Alanine biosynthesis	1
Branched-Chain Amino Acid Biosynthesis	1
Isoleucine degradation	1
Leucine Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Nitrate and nitrite ammonification	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 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-valine degradation II	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine degradation II	3	2	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
superpathway of L-alanine biosynthesis	4	4	1
L-valine 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-leucine degradation I	6	5	1
L-isoleucine degradation I	6	4	1
L-isoleucine biosynthesis IV	6	3	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
L-valine degradation I	8	5	1
L-isoleucine biosynthesis II	8	5	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	11	1
anteiso-branched-chain fatty acid biosynthesis	34	30	1
even iso-branched-chain fatty acid biosynthesis	34	30	1
odd iso-branched-chain fatty acid biosynthesis	34	30	1