Experiment set2IT064 for Agrobacterium fabrum C58

Xylitol carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Xylitol (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 24 genes in this experiment

For carbon source Xylitol in Agrobacterium fabrum C58

For carbon source Xylitol across organisms

SEED Subsystems

Subsystem	#Specific
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	5
D-ribose utilization	3
Fructose utilization	3
Xylose utilization	2
Ammonia assimilation	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
D-Sorbitol(D-Glucitol) and L-Sorbose Utilization	1
Entner-Doudoroff Pathway	1
Mannitol Utilization	1
Terminal cytochrome C oxidases	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Glycine, serine and threonine metabolism
• Pentose phosphate pathway
• C21-Steroid hormone metabolism
• Oxidative phosphorylation
• Benzoate degradation via hydroxylation
• Bisphenol A degradation
• Aminophosphonate metabolism
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Linoleic acid metabolism
• Tetrachloroethene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Retinol metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• 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
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
D-xylose degradation I	2	2	1
xylitol degradation I	2	2	1
ribitol degradation I	2	2	1
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
choline degradation I	2	2	1
D-arabinitol degradation I	2	1	1
arsenite to oxygen electron transfer	2	1	1
sorbitol biosynthesis II	3	3	1
choline-O-sulfate degradation	3	3	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
aerobic respiration I (cytochrome c)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
L-ascorbate biosynthesis VI (plants, myo-inositol pathway)	4	1	1
glucose and glucose-1-phosphate degradation	5	4	1
mannitol cycle	5	4	1
glucose degradation (oxidative)	5	2	1
L-ascorbate degradation V	5	1	1
L-ascorbate biosynthesis IV (animals, D-glucuronate pathway)	6	3	1
Fe(II) oxidation	6	2	1
L-ascorbate biosynthesis VIII (engineered pathway)	7	3	1
L-ascorbate degradation II (bacterial, aerobic)	7	2	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	7	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of pentose and pentitol degradation	42	16	2