Experiment set3IT017 for Agrobacterium fabrum C58

Betaine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Succinate_noNitrogen + Betaine (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 11 genes in this experiment

For nitrogen source Betaine in Agrobacterium fabrum C58

For nitrogen source Betaine across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	4
Anaerobic respiratory reductases	1
Glutathione-dependent pathway of formaldehyde detoxification	1
Glycine and Serine Utilization	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:

• Glycine, serine and threonine metabolism
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Cysteine metabolism
• Tyrosine metabolism
• Benzoate degradation via hydroxylation
• Fluorobenzoate degradation
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• 3-Chloroacrylic acid degradation
• Methane metabolism
• Retinol metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
acetaldehyde biosynthesis I	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
glycine betaine degradation I	8	6	5
benzoate degradation I (aerobic)	2	1	1
ethanol degradation I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
glycine betaine degradation III	7	4	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine degradation	3	3	1
formaldehyde oxidation II (glutathione-dependent)	3	3	1
ethanol degradation II	3	3	1
L-methionine biosynthesis II	6	5	2
L-leucine degradation III	3	2	1
proline betaine degradation I	3	2	1
L-valine degradation II	3	2	1
L-isoleucine degradation II	3	2	1
pyruvate fermentation to ethanol III	3	1	1
pyruvate fermentation to ethanol I	3	1	1
L-methionine degradation III	3	1	1
phytol degradation	4	3	1
L-mimosine degradation	8	4	2
L-phenylalanine degradation III	4	2	1
creatinine degradation I	4	2	1
L-tyrosine degradation III	4	2	1
glutathione-mediated detoxification I	8	3	2
salidroside biosynthesis	4	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
protein S-nitrosylation and denitrosylation	5	3	1
creatinine degradation II	5	2	1
acetylene degradation (anaerobic)	5	1	1
(S)-propane-1,2-diol degradation	5	1	1
phenylethanol biosynthesis	5	1	1
ethanolamine utilization	5	1	1
noradrenaline and adrenaline degradation	13	4	2
3-methylbutanol biosynthesis (engineered)	7	6	1
serotonin degradation	7	3	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
purine nucleobases degradation II (anaerobic)	24	14	3
butanol and isobutanol biosynthesis (engineered)	8	3	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	3	1
meta cleavage pathway of aromatic compounds	10	4	1
superpathway of C1 compounds oxidation to CO2	12	5	1
toluene degradation IV (aerobic) (via catechol)	13	5	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	9	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	5	1
heterolactic fermentation	18	12	1
mandelate degradation to acetyl-CoA	18	8	1
superpathway of anaerobic sucrose degradation	19	13	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	10	1
superpathway of N-acetylneuraminate degradation	22	12	1
superpathway of aerobic toluene degradation	30	12	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	15	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	11	1