Experiment set1IT038 for Rhizobium sp. OAE497

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Sodium Formate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Sodium Formate (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 6 genes in this experiment

For carbon source Sodium Formate in Rhizobium sp. OAE497

For carbon source Sodium Formate across organisms

SEED Subsystems

Subsystem #Specific
4-Hydroxyphenylacetic acid catabolic pathway 1
Aromatic amino acid degradation 1
CO2 uptake, carboxysome 1
Carboxysome 1
Fermentations: Mixed acid 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 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
acetaldehyde biosynthesis I 1 1 1
ethanol degradation I 2 1 1
pyruvate fermentation to ethanol II 2 1 1
ethanol degradation II 3 3 1
L-isoleucine degradation II 3 2 1
L-leucine degradation III 3 2 1
L-valine degradation II 3 2 1
pyruvate fermentation to ethanol I 3 1 1
L-methionine degradation III 3 1 1
pyruvate fermentation to ethanol III 3 1 1
phytol degradation 4 3 1
L-phenylalanine degradation III 4 2 1
L-tyrosine degradation III 4 2 1
salidroside biosynthesis 4 2 1
cytidine-5'-diphosphate-glycerol biosynthesis 4 1 1
D-galacturonate degradation I 5 4 1
pyruvate fermentation to isobutanol (engineered) 5 4 1
D-xylose degradation VI 5 3 1
phenylethanol biosynthesis 5 2 1
(S)-propane-1,2-diol degradation 5 1 1
ethanolamine utilization 5 1 1
acetylene degradation (anaerobic) 5 1 1
L-arabinose degradation V 6 3 1
D-arabinose degradation IV 6 3 1
noradrenaline and adrenaline degradation 13 8 2
3-methylbutanol biosynthesis (engineered) 7 6 1
L-rhamnose degradation III 7 4 1
serotonin degradation 7 4 1
L-fucose degradation III 8 5 1
4-hydroxyphenylacetate degradation 8 4 1
butanol and isobutanol biosynthesis (engineered) 8 3 1
superpathway of fermentation (Chlamydomonas reinhardtii) 9 2 1
superpathway of hexuronide and hexuronate degradation 10 8 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 4 1
L-tryptophan degradation V (side chain pathway) 13 1 1
monolignol biosynthesis 15 1 1
mixed acid fermentation 16 8 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 4 1
heterolactic fermentation 18 12 1
superpathway of anaerobic sucrose degradation 19 13 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 9 1
superpathway of N-acetylneuraminate degradation 22 12 1
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 16 1