Experiment set2S448 for Rhodopseudomonas palustris CGA009

Compare to:

PM with Sodium Formate and Sodium bicarbonate anaerobic with light

Group: carbon source
Media: PM + Sodium Formate (20 mM) + Sodium bicarbonate (20 mM) + Light intensity (12 µmol photons/m2/s from a 60-W incandescent light bulb)
Culturing: RPal_CGA009_ML8, tube, Anaerobic, at 30 (C)
By: Rpal_McKinlay on 9/7/24
Media components: 12.5 mM Disodium phosphate, 12.5 mM Potassium phosphate monobasic, 1 g/L Ammonium Sulfate, 0.1 mM Sodium thiosulfate pentahydrate, 0.002 g/L 4-Aminobenzoic acid, UW concentrated base (0.02 g/L Nitrilotriacetic acid, 0.0289 g/L Magnesium sulfate, 0.00667 g/L Calcium chloride dihydrate, 1.85e-05 g/L ammonium molybdate tetrahydrate, 0.000698 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L EDTA, 0.001095 g/L Zinc sulfate heptahydrate, 0.000154 g/L Manganese (II) sulfate monohydrate, 3.92e-05 g/L Copper (II) sulfate pentahydrate, 2.5e-05 g/L Cobalt(II) nitrate hexahydrate, 1.77e-05 g/L sodium tetraborate decahydrate)

Specific Phenotypes

For 22 genes in this experiment

For carbon source Sodium Formate in Rhodopseudomonas palustris CGA009

For carbon source Sodium Formate across organisms

SEED Subsystems

Subsystem #Specific
Formate hydrogenase 5
Oxidative stress 2
Ammonia assimilation 1
Auxin degradation 1
Bacterial Cell Division 1
Carotenoids 1
DNA-binding regulatory proteins, strays 1
Molybdenum cofactor biosynthesis 1
Photorespiration (oxidative C2 cycle) 1
RNA processing and degradation, bacterial 1
Thioredoxin-disulfide reductase 1
ZZ gjo need homes 1
cAMP signaling 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
bis(guanylyl molybdenum cofactor) biosynthesis 2 2 2
L-glutamate biosynthesis I 2 2 2
guanylyl molybdenum cofactor biosynthesis 1 1 1
L-glutamine degradation I 1 1 1
betanidin degradation 1 1 1
formate oxidation to CO2 1 1 1
L-glutamine degradation II 1 1 1
bis(guanylyl tungstenpterin) cofactor biosynthesis 1 1 1
ammonia assimilation cycle III 3 3 2
isoniazid activation 2 2 1
superoxide radicals degradation 2 2 1
methanol oxidation to formaldehyde IV 2 1 1
baicalein degradation (hydrogen peroxide detoxification) 2 1 1
ethanol degradation IV 3 3 1
L-glutamate and L-glutamine biosynthesis 7 5 2
L-asparagine biosynthesis III (tRNA-dependent) 4 4 1
reactive oxygen species degradation 4 4 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 1
luteolin triglucuronide degradation 4 1 1
oxalate degradation VI 4 1 1
xanthommatin biosynthesis 4 1 1
tRNA processing 10 10 2
oxalate degradation III 5 1 1
L-citrulline biosynthesis 8 7 1
sesamin biosynthesis 8 1 1
justicidin B biosynthesis 10 1 1
matairesinol biosynthesis 10 1 1
superpathway of L-citrulline metabolism 12 9 1
superpathway of C1 compounds oxidation to CO2 12 3 1
purine nucleobases degradation I (anaerobic) 15 6 1
purine nucleobases degradation II (anaerobic) 24 15 1