Experiment set3IT075 for Agrobacterium fabrum C58

L-Threonine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Succinate_noNitrogen + L-Threonine (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 6 genes in this experiment

For nitrogen source L-Threonine in Agrobacterium fabrum C58

For nitrogen source L-Threonine across organisms

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	2
Alanine biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutamine synthetases	1
Glycine and Serine Utilization	1
Methionine Biosynthesis	1
One-carbon metabolism by tetrahydropterines	1
Peptidoglycan Biosynthesis	1
Pyruvate Alanine Serine Interconversions	1
Serine-glyoxylate cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Glutamate metabolism
• Cysteine metabolism
• Arginine and proline metabolism
• One carbon pool by folate
• Methane metabolism
• Thiamine metabolism
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
glycine biosynthesis IV	1	1	1
L-cysteine degradation IV	1	1	1
L-glutamine biosynthesis I	1	1	1
L-alanine biosynthesis III	1	1	1
D-serine degradation	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
L-cysteine degradation II	3	2	2
ammonia assimilation cycle I	2	2	1
cytidylyl molybdenum cofactor sulfurylation	2	1	1
L-threonine degradation IV	2	1	1
ammonia assimilation cycle II	2	1	1
glycine betaine degradation III	7	4	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	6	3
glycine degradation	3	3	1
ammonia assimilation cycle III	3	3	1
L-methionine biosynthesis II	6	5	2
L-aspartate degradation III (anaerobic)	3	2	1
superpathway of ammonia assimilation (plants)	3	2	1
L-aspartate degradation II (aerobic)	3	2	1
bis(guanylyl molybdopterin) cofactor sulfurylation	3	1	1
thiazole component of thiamine diphosphate biosynthesis II	7	4	2
superpathway of L-alanine biosynthesis	4	4	1
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	3	2
tRNA-uridine 2-thiolation (mammalian mitochondria)	4	1	1
tRNA-uridine 2-thiolation (yeast mitochondria)	4	1	1
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	2	1
[2Fe-2S] iron-sulfur cluster biosynthesis	10	2	2
superpathway of thiamine diphosphate biosynthesis II	11	7	2
molybdopterin biosynthesis	6	2	1
thiazole component of thiamine diphosphate biosynthesis I	6	2	1
L-glutamate and L-glutamine biosynthesis	7	4	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
purine nucleobases degradation II (anaerobic)	24	14	3
tRNA-uridine 2-thiolation (cytoplasmic)	8	1	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of thiamine diphosphate biosynthesis I	10	5	1
tRNA-uridine 2-thiolation and selenation (bacteria)	11	2	1
folate transformations I	13	8	1
superpathway of L-threonine metabolism	18	11	1