Experiment set3IT045 for Agrobacterium fabrum C58

L-Ornithine nitrogen source

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

For nitrogen source L-Ornithine in Agrobacterium fabrum C58

For nitrogen source L-Ornithine across organisms

SEED Subsystems

Subsystem	#Specific
Urea decomposition	3
Ammonia assimilation	1
Arginine and Ornithine Degradation	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:

• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Purine metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• beta-Alanine metabolism
• Propanoate metabolism
• Atrazine degradation
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
urea degradation II	1	1	1
β-alanine degradation II	2	2	1
L-arginine degradation VII (arginase 3 pathway)	2	2	1
putrescine biosynthesis III	2	2	1
L-canavanine degradation I	2	1	1
L-arginine degradation I (arginase pathway)	3	2	1
superpathway of putrescine biosynthesis	4	4	1
L-arginine degradation VI (arginase 2 pathway)	4	3	1
urea cycle	5	4	1
β-alanine biosynthesis II	6	3	1
L-Nδ-acetylornithine biosynthesis	7	5	1
L-citrulline biosynthesis	8	7	1
superpathway of polyamine biosynthesis I	8	5	1
superpathway of polyamine biosynthesis II	8	3	1
superpathway of allantoin degradation in plants	8	2	1
superpathway of coenzyme A biosynthesis II (plants)	10	7	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	4	1
superpathway of arginine and polyamine biosynthesis	17	14	1