Experiment set3IT064 for Agrobacterium fabrum C58

L-Leucine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Succinate_noNitrogen + L-Leucine (10 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 9 genes in this experiment

For nitrogen source L-Leucine in Agrobacterium fabrum C58

For nitrogen source L-Leucine across organisms

SEED Subsystems

Subsystem	#Specific
Orphan regulatory proteins	2
Pyruvate Alanine Serine Interconversions	2
Respiratory dehydrogenases 1	2
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	1
Alanine biosynthesis	1
Ammonia assimilation	1
Branched-Chain Amino Acid Biosynthesis	1
Carboxysome	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutamine synthetases	1
Isoleucine degradation	1
Leucine Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Lipid A modifications	1
NAD and NADP cofactor biosynthesis global	1
Peptidoglycan Biosynthesis	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Nitrogen metabolism
• Oxidative phosphorylation
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Arginine and proline metabolism
• Phenylalanine metabolism
• Pantothenate and CoA biosynthesis
• Sulfur metabolism
• 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-glutamine biosynthesis I	1	1	1
L-alanine biosynthesis I	2	2	1
NADH to cytochrome bo oxidase electron transfer I	2	2	1
ammonia assimilation cycle I	2	2	1
L-alanine degradation I	2	2	1
NADH to cytochrome bd oxidase electron transfer I	2	2	1
ammonia assimilation cycle II	2	1	1
ammonia assimilation cycle III	3	3	1
aerobic respiration III (alternative oxidase pathway)	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine degradation II	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
L-valine degradation II	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
L-valine biosynthesis	4	4	1
superpathway of L-alanine biosynthesis	4	4	1
aerobic respiration I (cytochrome c)	4	3	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
NAD(P)/NADPH interconversion	6	3	1
L-isoleucine biosynthesis IV	6	3	1
Fe(II) oxidation	6	2	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-glutamate and L-glutamine biosynthesis	7	4	1
L-isoleucine biosynthesis III	7	4	1
L-valine degradation I	8	5	1
L-isoleucine biosynthesis II	8	5	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	11	1
odd iso-branched-chain fatty acid biosynthesis	34	30	1
even iso-branched-chain fatty acid biosynthesis	34	30	1
anteiso-branched-chain fatty acid biosynthesis	34	30	1