Experiment set2IT085 for Rahnella sp. WP5

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NLDM_metabolites carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 0.5X NLDM_metabolites
Culturing: RahnellaWP5_ML7, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Robert Tournay on December 7, 2021
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)

NLDM_metabolites 0.5x includes: 437.5 uM Sucrose, 437.5 uM D-Glucose, 437.5 uM D-Trehalose dihydrate, 437.5 uM m-Inositol, 437.5 uM D-Xylose, 437.5 uM D-Mannitol, 437.5 uM N-Acetyl-D-Glucosamine, 262.5 uM Sodium L-Lactate, 262.5 uM D,L-Malic Acid, 262.5 uM Citric Acid, 262.5 uM Sodium succinate dibasic hexahydrate, 262.5 uM Sodium pyruvate, 262.5 uM a-Ketoglutaric acid disodium salt hydrate, 262.5 uM L-Citrulline, 87.5 uM L-Alanine, 87.5 uM L-Arginine, 87.5 uM L-Asparagine, 87.5 uM L-Aspartic Acid, 87.5 uM L-Cysteine, 87.5 uM L-Glutamic acid, 87.5 uM L-Glutamine, 87.5 uM Glycine, 87.5 uM L-Histidine, 87.5 uM L-Isoleucine, 87.5 uM L-Leucine, 87.5 uM L-Lysine, 87.5 uM L-Methionine, 87.5 uM L-Phenylalanine, 87.5 uM L-Proline, 87.5 uM L-Serine, 87.5 uM L-Threonine, 87.5 uM L-Tryptophan, 87.5 uM L-tyrosine, 87.5 uM L-Valine, 8.75 uM 5-methyluridine, 8.75 uM Adenine hydrochloride hydrate, 8.75 uM Adenosine, 8.75 uM Cytidine, 8.75 uM Cytosine, 8.75 uM Guanine, 8.75 uM Guanosine, 8.75 uM Hypoxanthine, 8.75 uM Inosine, 8.75 uM Thymine, 8.75 uM Uracil, 8.75 uM Uridine, 8.75 uM Xanthine, 8.75 uM Xanthosine, 8.75 uM Gamma-Aminobutyric Acid Hydrochloride, 8.75 uM Ectoine, 8.75 uM Betaine, 8.75 uM N-Acetyl-glutamic acid, 8.75 uM Nicotinamide, 8.75 uM L-Ornithine, 8.75 uM Shikimic Acid, 8.75 uM spermidine, 8.75 uM Taurine, 8.75 uM Trigonelline HCl, 8.75 uM Carnitine Hydrochloride, 8.75 uM Choline chloride, 8.75 uM n-Acetyl-glutamine, 8.75 uM n-Acetyl-lysine, 8.75 uM n-Acetyl-muramic acid, 8.75 uM sn-glycero-3-phosphocholine (final concentrations)

Specific Phenotypes

For 5 genes in this experiment

For carbon source NLDM_metabolites in Rahnella sp. WP5

For carbon source NLDM_metabolites across organisms

SEED Subsystems

Subsystem #Specific
Heat shock dnaK gene cluster extended 1
Serine-glyoxylate cycle 1
Succinate dehydrogenase 1
TCA Cycle 1
Transport of Manganese 1
Universal GTPases 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
succinate to cytochrome bd oxidase electron transfer 2 2 1
succinate to cytochrome bo oxidase electron transfer 2 1 1
aerobic respiration III (alternative oxidase pathway) 3 3 1
aerobic respiration II (cytochrome c) (yeast) 4 2 1
aerobic respiration I (cytochrome c) 4 2 1
TCA cycle III (animals) 10 8 1