Experiment set2IT071 for Agrobacterium fabrum C58

D-(-)-lyxose carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + D-(-)-lyxose (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 10 genes in this experiment

For carbon source D-(-)-lyxose in Agrobacterium fabrum C58

For carbon source D-(-)-lyxose across organisms

SEED Subsystems

Subsystem	#Specific
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	3
Xylose utilization	2
D-Sorbitol(D-Glucitol) and L-Sorbose Utilization	1
Entner-Doudoroff Pathway	1
Homogentisate pathway of aromatic compound degradation	1
Mannitol Utilization	1
Sialic Acid Metabolism	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:

• Fructose and mannose metabolism
• Pentose and glucuronate interconversions
• Ascorbate and aldarate metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Pentose phosphate pathway
• C21-Steroid hormone metabolism
• Oxidative phosphorylation
• Glycine, serine and threonine metabolism
• Bisphenol A degradation
• Polyketide sugar unit biosynthesis
• Linoleic acid metabolism
• Tetrachloroethene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Retinol metabolism
• 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
D-xylose degradation I	2	2	2
xylitol 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
arsenite to oxygen electron transfer (via azurin)	3	1	1
N-acetylneuraminate and N-acetylmannosamine degradation II	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
superpathway of glucose and xylose degradation	17	16	2
Entner-Doudoroff pathway III (semi-phosphorylative)	9	7	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
superpathway of pentose and pentitol degradation	42	16	2