Experiment set1IT017 for Rhizobium sp. OAE497

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D-Ribose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Ribose (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 17 genes in this experiment

For carbon source D-Ribose in Rhizobium sp. OAE497

For carbon source D-Ribose across organisms

SEED Subsystems

Subsystem #Specific
Histidine Degradation 7
Molybdenum cofactor biosynthesis 2
Allantoin Utilization 1
Arginine and Ornithine Degradation 1
DNA-replication 1
DNA repair, bacterial 1
DNA repair, bacterial RecFOR pathway 1
Hydantoin metabolism 1
Xylose utilization 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
L-histidine degradation II 5 5 4
L-histidine degradation I 4 3 3
L-histidine degradation III 6 4 3
allantoin degradation to ureidoglycolate I (urea producing) 2 1 1
L-histidine degradation VI 8 7 3
allantoin degradation to glyoxylate I 3 1 1
allantoin degradation to ureidoglycolate II (ammonia producing) 4 1 1
tRNA-uridine 2-thiolation (thermophilic bacteria) 5 2 1
allantoin degradation to glyoxylate II 5 2 1
allantoin degradation to glyoxylate III 5 1 1
superpathway of allantoin degradation in yeast 6 3 1
superpathway of allantoin degradation in plants 8 3 1
allantoin degradation IV (anaerobic) 9 5 1
superpathway of purines degradation in plants 18 13 1