Experiment set2IT065 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	4
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

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
• 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
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
xylitol degradation I	2	2	1
mannosylfructose biosynthesis	2	2	1
ribitol degradation I	2	2	1
D-xylose degradation I	2	2	1
choline degradation I	2	2	1
D-arabinitol degradation I	2	1	1
choline-O-sulfate degradation	3	3	1
sorbitol biosynthesis II	3	3	1
L-ascorbate biosynthesis VI (plants, myo-inositol pathway)	4	1	1
mannitol cycle	5	4	1
glucose and glucose-1-phosphate degradation	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
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