Experiment set2IT012 for Agrobacterium fabrum C58

D-Arabinose carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + D-Arabinose (10 mM)
Culturing: Agro_ML11, 24-well transparent microplate; Multitron, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 10/20/20
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 13 genes in this experiment

For carbon source D-Arabinose in Agrobacterium fabrum C58

For carbon source D-Arabinose across organisms

SEED Subsystems

Subsystem	#Specific
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	3
4-Hydroxyphenylacetic acid catabolic pathway	1
Aromatic amino acid degradation	1
Bacterial Chemotaxis	1
D-ribose utilization	1
Fermentations: Mixed acid	1
Gentisare degradation	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
L-fucose utilization temp	1
Mannitol Utilization	1
Salicylate and gentisate catabolism	1
Xylose utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ascorbate and aldarate metabolism
• Tyrosine metabolism
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Glycine, serine and threonine metabolism
• Retinol metabolism
• Pentose and glucuronate interconversions
• Fatty acid metabolism
• C21-Steroid hormone metabolism
• Bisphenol A degradation
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Glycerolipid metabolism
• Linoleic acid metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• Benzoate degradation via CoA ligation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Caprolactam degradation
• Alkaloid biosynthesis I
• Metabolism of xenobiotics by cytochrome P450
• Insect hormone biosynthesis
• Drug metabolism - cytochrome P450
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide products
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
xylitol degradation I	2	2	1
D-xylose degradation I	2	2	1
D-arabinitol degradation I	2	1	1
ethanol degradation I	2	1	1
erythritol biosynthesis II	2	1	1
erythritol biosynthesis I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
D-galactarate degradation II	3	3	1
ethanol degradation II	3	3	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
pyruvate fermentation to ethanol I	3	1	1
pyruvate fermentation to ethanol III	3	1	1
L-methionine degradation III	3	1	1
phytol degradation	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
D-xylose degradation to ethylene glycol (engineered)	4	2	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
D-galactarate degradation I	4	2	1
salidroside biosynthesis	4	1	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
mannitol cycle	5	4	1
superpathway of D-glucarate and D-galactarate degradation	5	3	1
D-xylose degradation VI	5	3	1
ethanolamine utilization	5	1	1
phenylethanol biosynthesis	5	1	1
(S)-propane-1,2-diol degradation	5	1	1
acetylene degradation (anaerobic)	5	1	1
D-arabinose degradation IV	6	4	1
L-arabinose degradation V	6	2	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	2
noradrenaline and adrenaline degradation	13	4	2
3-methylbutanol biosynthesis (engineered)	7	6	1
L-rhamnose degradation III	7	4	1
serotonin degradation	7	3	1
L-fucose degradation III	8	5	1
4-hydroxyphenylacetate degradation	8	4	1
pyruvate fermentation to butanol I	8	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	5	2
superpathway of fermentation (Chlamydomonas reinhardtii)	9	3	1
detoxification of reactive carbonyls in chloroplasts	10	2	1
traumatin and (Z)-3-hexen-1-yl acetate biosynthesis	12	3	1
L-tryptophan degradation V (side chain pathway)	13	1	1
monolignol biosynthesis	15	3	1
glycerol degradation to butanol	16	11	1
mixed acid fermentation	16	9	1
superpathway of glucose and xylose degradation	17	16	1
heterolactic fermentation	18	12	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 lipoxygenase	22	4	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	22	1
superpathway of pentose and pentitol degradation	42	16	1