Experiment set3IT079 for Agrobacterium fabrum C58

2,6-diaminopimelic acid nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Succinate_noNitrogen + 2,6-diaminopimelic acid (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 2,6-diaminopimelic acid in Agrobacterium fabrum C58

For nitrogen source 2,6-diaminopimelic acid across organisms

SEED Subsystems

Subsystem	#Specific
Acetoin, butanediol metabolism	1
Branched-Chain Amino Acid Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methylglyoxal Metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Butanoate metabolism
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• C5-Branched dibasic acid metabolism
• Pantothenate and CoA biosynthesis
• Limonene and pinene degradation
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-lactaldehyde degradation (aerobic)	2	2	1
pyruvate fermentation to (R)-acetoin II	2	1	1
pyruvate fermentation to (R)-acetoin I	3	3	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
ethanol degradation III	3	2	1
pyruvate fermentation to (S)-acetoin	3	2	1
methylglyoxal degradation IV	3	2	1
methylglyoxal degradation V	3	2	1
hypotaurine degradation	3	2	1
histamine degradation	3	1	1
L-valine biosynthesis	4	4	1
phytol degradation	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
putrescine degradation III	4	1	1
superpathway of (R,R)-butanediol biosynthesis	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
mitochondrial NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
lactate biosynthesis (archaea)	5	2	1
dopamine degradation	5	1	1
L-isoleucine biosynthesis IV	6	3	1
3-methyl-branched fatty acid α-oxidation	6	3	1
superpathway of 2,3-butanediol biosynthesis	6	2	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
L-isoleucine biosynthesis II	8	5	1
superpathway of methylglyoxal degradation	8	5	1
L-rhamnose degradation II	8	5	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
aromatic biogenic amine degradation (bacteria)	8	1	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of fucose and rhamnose degradation	12	7	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	11	1