Experiment set5IT063 for Pedobacter sp. GW460-11-11-14-LB5

methyl 3-keto-a-D-glucopyranoside carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + methyl 3-keto-a-D-glucopyranoside (5 mM)
Culturing: Pedo557_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Valentine on 10/5/22
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)

Specific Phenotypes

For 7 genes in this experiment

For carbon source methyl 3-keto-a-D-glucopyranoside in Pedobacter sp. GW460-11-11-14-LB5

For carbon source methyl 3-keto-a-D-glucopyranoside across organisms

SEED Subsystems

Subsystem	#Specific
Anaerobic respiratory reductases	1
DNA-binding regulatory proteins, strays	1
Oxidative stress	1
Propionate-CoA to Succinate Module	1
Queuosine-Archaeosine Biosynthesis	1
Serine-glyoxylate cycle	1
TCA Cycle	1
Thioredoxin-disulfide reductase	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Citrate cycle (TCA cycle)
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of phenylpropanoids
• 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
glyoxylate cycle	6	4	2
partial TCA cycle (obligate autotrophs)	8	7	2
nitrogen remobilization from senescing leaves	8	6	2
TCA cycle VI (Helicobacter)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	6	2
TCA cycle VII (acetate-producers)	9	6	2
TCA cycle I (prokaryotic)	10	9	2
TCA cycle III (animals)	10	8	2
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
mixed acid fermentation	16	12	2
methylaspartate cycle	19	11	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
ethene biosynthesis V (engineered)	25	16	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	2