Experiment set2IT032 for Agrobacterium fabrum C58

L-Xylose carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-Xylose (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 18 genes in this experiment

For carbon source L-Xylose in Agrobacterium fabrum C58

For carbon source L-Xylose across organisms

SEED Subsystems

Subsystem	#Specific
Glycolate, glyoxylate interconversions	4
Photorespiration (oxidative C2 cycle)	3
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	2
4-Hydroxyphenylacetic acid catabolic pathway	1
Aromatic amino acid degradation	1
Biogenesis of cytochrome c oxidases	1
Chitin and N-acetylglucosamine utilization	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Entner-Doudoroff Pathway	1
Gentisare degradation	1
Salicylate and gentisate catabolism	1
Terminal cytochrome C oxidases	1
Threonine degradation	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
• Pentose and glucuronate interconversions
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• Glyoxylate and dicarboxylate metabolism
• Pentose phosphate pathway
• Fructose and mannose metabolism
• 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
• alpha-Linolenic 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
xylitol degradation I	2	2	2
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
glycolate and glyoxylate degradation II	2	2	1
choline degradation I	2	2	1
D-xylose degradation I	2	2	1
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
arsenite to oxygen electron transfer	2	1	1
D-arabinitol degradation I	2	1	1
sorbitol biosynthesis II	3	3	1
D-galactarate degradation II	3	3	1
choline-O-sulfate degradation	3	3	1
D-arabinose degradation IV	6	4	2
arsenite to oxygen electron transfer (via azurin)	3	1	1
gentisate degradation I	3	1	1
glycolate and glyoxylate degradation III	3	1	1
aerobic respiration I (cytochrome c)	4	3	1
glycolate and glyoxylate degradation I	4	2	1
D-galactarate degradation I	4	2	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
superpathway of D-glucarate and D-galactarate degradation	5	3	1
D-xylose degradation VI	5	3	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
D-arabinose degradation III	6	3	1
5-nitroanthranilate degradation	6	2	1
Fe(II) oxidation	6	2	1
L-arabinose degradation V	6	2	1
L-rhamnose degradation III	7	4	1
superpathway of glycol metabolism and degradation	7	4	1
L-ascorbate biosynthesis VIII (engineered pathway)	7	3	1
L-ascorbate degradation II (bacterial, aerobic)	7	2	1
L-fucose degradation III	8	5	1
4-hydroxyphenylacetate degradation	8	4	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	7	1
photorespiration I	9	6	1
photorespiration III	9	6	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
photorespiration II	10	6	1
3-phenylpropanoate degradation	10	4	1
superpathway of pentose and pentitol degradation	42	16	3
superpathway of glucose and xylose degradation	17	16	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	22	1