Experiment set1IT039 for Rhizobium sp. OAE497

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 5 genes in this experiment

For carbon source Sodium Formate in Rhizobium sp. OAE497

For carbon source Sodium Formate across organisms

SEED Subsystems

Subsystem	#Specific
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:

• Glycolysis / Gluconeogenesis
• Pentose and glucuronate interconversions
• Fatty acid metabolism
• Puromycin biosynthesis
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Trinitrotoluene degradation
• 3-Chloroacrylic acid degradation
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Metabolism of xenobiotics by cytochrome P450
• Insect hormone biosynthesis
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation I	2	1	1
ethanol degradation II	3	3	1
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine 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
salidroside biosynthesis	4	2	1
L-tyrosine degradation III	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
phenylethanol biosynthesis	5	2	1
acetylene degradation (anaerobic)	5	1	1
(S)-propane-1,2-diol degradation	5	1	1
ethanolamine utilization	5	1	1
noradrenaline and adrenaline degradation	13	8	2
3-methylbutanol biosynthesis (engineered)	7	6	1
serotonin degradation	7	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