Experiment set2IT063 for Agrobacterium fabrum C58

D-Glucuronic acid gamma lactone carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + D-Glucuronic acid gamma lactone (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 20 genes in this experiment

For carbon source D-Glucuronic acid gamma lactone in Agrobacterium fabrum C58

For carbon source D-Glucuronic acid gamma lactone across organisms

SEED Subsystems

Subsystem	#Specific
D-ribose utilization	5
D-Galacturonate and D-Glucuronate Utilization	2
Entner-Doudoroff Pathway	2
Proline, 4-hydroxyproline uptake and utilization	2
Branched-Chain Amino Acid Biosynthesis	1
D-gluconate and ketogluconates metabolism	1
Inositol catabolism	1
Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway	1
Lactose and Galactose Uptake and Utilization	1
N-linked Glycosylation in Bacteria	1
Rhamnose containing glycans	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Caprolactam degradation
• Valine, leucine and isoleucine biosynthesis
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Inositol phosphate metabolism
• Pantothenate and CoA biosynthesis
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-galactose biosynthesis	1	1	1
UDP-N-acetyl-D-galactosamine biosynthesis I	1	1	1
D-gluconate degradation	1	1	1
sorbitol biosynthesis II	3	3	2
D-galactose degradation II	2	2	1
D-glucuronate degradation III	2	2	1
UDP-α-D-galactofuranose biosynthesis	2	2	1
pyruvate fermentation to acetate VIII	2	1	1
D-galacturonate degradation III	2	1	1
D-galacturonate degradation II	5	5	2
D-glucuronate degradation II	5	5	2
D-galactarate degradation II	3	3	1
D-glucarate degradation II	3	3	1
L-idonate degradation	3	3	1
L-carnitine degradation II	3	2	1
D-galactose detoxification	3	1	1
L-lyxonate degradation	3	1	1
L-valine biosynthesis	4	4	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	2
1,2-dichloroethane degradation	4	3	1
trans-4-hydroxy-L-proline degradation II	4	2	1
L-ascorbate biosynthesis VI (plants, myo-inositol pathway)	4	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
glucose and glucose-1-phosphate degradation	5	4	1
cytosolic NADPH production (yeast)	5	4	1
D-galactose degradation I (Leloir pathway)	5	3	1
mitochondrial NADPH production (yeast)	5	3	1
D-xylose degradation V	5	2	1
D-xylose degradation III	5	2	1
cyclohexanol degradation	5	2	1
glucose degradation (oxidative)	5	2	1
L-ascorbate degradation V	5	1	1
myo-inositol degradation II	5	1	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	5	1
D-arabinose degradation III	6	3	1
L-ascorbate biosynthesis IV (animals, D-glucuronate pathway)	6	3	1
L-isoleucine biosynthesis IV	6	3	1
L-arabinose degradation III	6	2	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
myo-inositol degradation I	7	6	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
stachyose degradation	7	4	1
L-isoleucine biosynthesis III	7	4	1
nylon-6 oligomer degradation	7	4	1
L-ascorbate biosynthesis VIII (engineered pathway)	7	3	1
L-ascorbate degradation II (bacterial, aerobic)	7	2	1
L-isoleucine biosynthesis II	8	5	1
ketogluconate metabolism	8	4	1
superpathway of branched chain amino acid biosynthesis	17	17	2
Entner-Doudoroff pathway III (semi-phosphorylative)	9	7	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
UDP-sugars interconversion	9	4	1
teichuronic acid biosynthesis (B. subtilis 168)	9	2	1
myo-, chiro- and scyllo-inositol degradation	10	6	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	22	3
colanic acid building blocks biosynthesis	11	11	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	11	1
streptomycin biosynthesis	18	3	1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	18	2	1
superpathway of pentose and pentitol degradation	42	16	2
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	13	1