Experiment set1IT070 for Agrobacterium fabrum C58

L-Alanine carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-Alanine (10 mM)
Culturing: Agro_ML11, 24-well transparent microplate; Multitron, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 8/25/20
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 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 12 genes in this experiment

For carbon source L-Alanine in Agrobacterium fabrum C58

For carbon source L-Alanine across organisms

SEED Subsystems

Subsystem	#Specific
Pyruvate Alanine Serine Interconversions	2
Alanine biosynthesis	1
Ammonia assimilation	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Homogentisate pathway of aromatic compound degradation	1
Respiratory dehydrogenases 1	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Alanine and aspartate metabolism
• Nitrogen metabolism
• Glycine, serine and threonine metabolism
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Aminophosphonate metabolism
• Cyanoamino acid metabolism
• D-Alanine metabolism
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-alanine degradation I	2	2	2
L-asparagine degradation I	1	1	1
alanine racemization	1	1	1
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
choline degradation I	2	2	1
choline-O-sulfate degradation	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
N-(1-deoxy-D-fructos-1-yl)-L-asparagine degradation	5	2	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
ansatrienin biosynthesis	9	1	1
cyclosporin A biosynthesis	15	2	1
superpathway of anaerobic energy metabolism (invertebrates)	17	13	1