Experiment set1IT031 for Rhizobium sp. OAE497

Trisodium citrate dihydrate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Trisodium citrate dihydrate (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 8 genes in this experiment

For carbon source Trisodium citrate dihydrate in Rhizobium sp. OAE497

For carbon source Trisodium citrate dihydrate across organisms

SEED Subsystems

Subsystem	#Specific
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
L-Arabinose utilization	1
Methylglyoxal Metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Galactose metabolism
• Ascorbate and aldarate metabolism
• Pyruvate metabolism
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-galactose degradation II	2	2	2
L-lactaldehyde degradation (aerobic)	2	2	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
L-lyxonate degradation	3	2	1
methylglyoxal degradation V	3	2	1
methylglyoxal degradation IV	3	2	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
D-glucarate degradation II	3	1	1
histamine degradation	3	1	1
D-galactarate degradation II	3	1	1
phytol degradation	4	3	1
trans-4-hydroxy-L-proline degradation II	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
putrescine degradation III	4	2	1
lactate biosynthesis (archaea)	5	3	1
mitochondrial NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
D-xylose degradation III	5	2	1
octane oxidation	5	2	1
D-xylose degradation V	5	2	1
dopamine degradation	5	2	1
D-glucuronate degradation II	5	2	1
D-galacturonate degradation II	5	1	1
L-arabinose degradation III	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
D-arabinose degradation III	6	2	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
serotonin degradation	7	4	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
superpathway of methylglyoxal degradation	8	5	1
L-rhamnose degradation II	8	4	1
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of fucose and rhamnose degradation	12	9	1
superpathway of pentose and pentitol degradation	42	19	2
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	16	1