Experiment set1IT021 for Rhizobium sp. OAE497

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5-Keto-D-Gluconic Acid potassium salt carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 5-Keto-D-Gluconic Acid potassium salt (20 mM)
Culturing: Rhizobium_OAE497_ML5, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Dennis/Robin on 4/4/22
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 16 genes in this experiment

For carbon source 5-Keto-D-Gluconic Acid potassium salt in Rhizobium sp. OAE497

For carbon source 5-Keto-D-Gluconic Acid potassium salt across organisms

SEED Subsystems

Subsystem #Specific
D-ribose utilization 4
Deoxyribose and Deoxynucleoside Catabolism 4
Pyrimidine utilization 4
Hydantoin metabolism 2
Biotin biosynthesis 1
CO2 uptake, carboxysome 1
Carboxysome 1
L-2-amino-thiazoline-4-carboxylic acid-Lcysteine conversion 1
Pentose phosphate pathway 1
Purine conversions 1
Pyruvate Alanine Serine Interconversions 1
Queuosine-Archaeosine Biosynthesis 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
thymine degradation 3 3 3
uracil degradation I (reductive) 3 3 3
L-glutamate biosynthesis I 2 2 2
L-glutamine degradation I 1 1 1
L-glutamine degradation II 1 1 1
L-glutamate biosynthesis IV 1 1 1
L-alanine degradation IV 1 1 1
ammonia assimilation cycle III 3 3 2
superpathway of pyrimidine ribonucleosides degradation 5 5 3
β-alanine degradation II 2 2 1
guanine and guanosine salvage II 2 2 1
ammonia assimilation cycle I 2 2 1
adenine and adenosine salvage II 2 2 1
L-glutamate and L-glutamine biosynthesis 7 4 3
pentose phosphate pathway (oxidative branch) I 3 3 1
superpathway of guanosine nucleotides degradation (plants) 6 5 2
superpathway of ammonia assimilation (plants) 3 2 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 4 1
L-asparagine biosynthesis III (tRNA-dependent) 4 4 1
guanosine nucleotides degradation II 4 4 1
biotin biosynthesis from 8-amino-7-oxononanoate I 4 4 1
adenosine nucleotides degradation I 8 7 2
purine nucleotides degradation I (plants) 12 10 3
guanosine nucleotides degradation I 4 3 1
superpathway of purines degradation in plants 18 13 3
β-alanine biosynthesis II 6 4 1
pentose phosphate pathway 8 8 1
L-citrulline biosynthesis 8 7 1
superpathway of coenzyme A biosynthesis II (plants) 10 8 1
superpathway of L-citrulline metabolism 12 9 1
biotin biosynthesis I 15 13 1
superpathway of glucose and xylose degradation 17 16 1