Experiment set2IT024 for Agrobacterium fabrum C58

L-Fucose carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-Fucose (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 17 genes in this experiment

For carbon source L-Fucose in Agrobacterium fabrum C58

For carbon source L-Fucose across organisms

SEED Subsystems

Subsystem	#Specific
D-ribose utilization	3
L-fucose utilization temp	3
4-Hydroxyphenylacetic acid catabolic pathway	1
Aromatic amino acid degradation	1
Cysteine Biosynthesis	1
D-Galacturonate and D-Glucuronate Utilization	1
L-rhamnose utilization	1
Lactate utilization	1
Respiratory dehydrogenases 1	1
Threonine degradation	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
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• C21-Steroid hormone metabolism
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Bisphenol A degradation
• Selenoamino acid metabolism
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Linoleic acid metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Tetrachloroethene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Retinol metabolism
• Sulfur metabolism
• 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
L-cysteine biosynthesis I	2	2	1
L-lactaldehyde degradation (aerobic)	2	2	1
D-xylose degradation VI	5	3	2
L-fucose degradation III	8	5	3
D-arabinose degradation IV	6	4	2
methylglyoxal degradation IV	3	2	1
methylglyoxal degradation V	3	2	1
seleno-amino acid biosynthesis (plants)	5	3	1
D-galacturonate degradation I	5	3	1
D-galacturonate degradation IV	5	2	1
L-fucose degradation II	5	2	1
L-arabinose degradation V	6	2	1
L-rhamnose degradation III	7	4	1
superpathway of methylglyoxal degradation	8	5	1
4-hydroxyphenylacetate degradation	8	4	1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	2	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
superpathway of hexuronide and hexuronate degradation	10	6	1
superpathway of fucose and rhamnose degradation	12	7	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	22	2
superpathway of seleno-compound metabolism	19	8	1