Experiment set2IT064 for Pedobacter sp. GW460-11-11-14-LB5

D-Galacturonic Acid monohydrate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Galacturonic Acid monohydrate (20 mM), pH=7
Culturing: Pedo557_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.7 generations
By: Adam on 16-May-17
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)
Growth plate: 1742 C6

Specific Phenotypes

For 14 genes in this experiment

For carbon source D-Galacturonic Acid monohydrate in Pedobacter sp. GW460-11-11-14-LB5

For carbon source D-Galacturonic Acid monohydrate across organisms

SEED Subsystems

Subsystem	#Specific
D-Galacturonate and D-Glucuronate Utilization	4
Alginate metabolism	1
Calvin-Benson cycle	1
D-gluconate and ketogluconates metabolism	1
Entner-Doudoroff Pathway	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Propionate-CoA to Succinate Module	1
Serine-glyoxylate cycle	1
TCA Cycle	1
tRNA processing	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
• Pentose phosphate pathway
• Arginine and proline metabolism
• Glyoxylate and dicarboxylate metabolism
• Biosynthesis of phenylpropanoids
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Fructose and mannose metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-galacturonate degradation I	5	5	5
superpathway of hexuronide and hexuronate degradation	10	10	6
D-fructuronate degradation	4	4	2
Entner-Doudoroff shunt	2	1	1
superpathway of β-D-glucuronosides degradation	7	7	3
4-deoxy-L-threo-hex-4-enopyranuronate degradation	5	5	2
β-D-glucuronide and D-glucuronate degradation	3	3	1
glyoxylate cycle	6	4	2
D-glucosaminate degradation	3	1	1
3,6-anhydro-α-L-galactopyranose degradation	7	4	2
partial TCA cycle (obligate autotrophs)	8	7	2
nitrogen remobilization from senescing leaves	8	6	2
Entner-Doudoroff pathway III (semi-phosphorylative)	9	7	2
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle VI (Helicobacter)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle VII (acetate-producers)	9	6	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	6	2
TCA cycle I (prokaryotic)	10	9	2
TCA cycle III (animals)	10	8	2
trans-4-hydroxy-L-proline degradation I	5	4	1
pectin degradation II	5	3	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	18	6
reductive TCA cycle I	11	7	2
superpathway of glyoxylate bypass and TCA	12	9	2
reductive TCA cycle II	12	5	2
superpathway of glyoxylate cycle and fatty acid degradation	14	10	2
alginate degradation	7	3	1
mixed acid fermentation	16	12	2
ethene biosynthesis V (engineered)	25	16	3
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	3
Entner-Doudoroff pathway I	9	7	1
sucrose biosynthesis I (from photosynthesis)	9	6	1
methylaspartate cycle	19	11	2
glycolysis II (from fructose 6-phosphate)	11	10	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
gluconeogenesis III	12	9	1
gluconeogenesis I	13	12	1
glycolysis I (from glucose 6-phosphate)	13	11	1
Calvin-Benson-Bassham cycle	13	9	1
oxygenic photosynthesis	17	9	1
superpathway of hexitol degradation (bacteria)	18	12	1
superpathway of anaerobic sucrose degradation	19	14	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	13	1
superpathway of N-acetylneuraminate degradation	22	16	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	15	1
1-butanol autotrophic biosynthesis (engineered)	27	17	1