Experiment set2S454 for Rhodopseudomonas palustris CGA009

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PM with Sodium succinate dibasic hexahydrate aerobic in dark

Group: carbon source dark aerobic
Media: PM + Sodium succinate dibasic hexahydrate (10 mM)
Culturing: RPal_CGA009_ML8, tube, Aerobic, 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 9 genes in this experiment

For carbon source dark aerobic Sodium succinate dibasic hexahydrate in Rhodopseudomonas palustris CGA009

For carbon source dark aerobic Sodium succinate dibasic hexahydrate across organisms

SEED Subsystems

Subsystem #Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 3
Benzoate transport and degradation cluster 1
Biogenesis of cytochrome c oxidases 1
Experimental tye 1
Glycine reductase, sarcosine reductase and betaine reductase 1
Heme and Siroheme Biosynthesis 1
Oxidative stress 1
Salicylate and gentisate catabolism 1
Salicylate ester degradation 1
Thioredoxin-disulfide reductase 1
Wyeosine-MimG Biosynthesis 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
methylsalicylate degradation 2 2 2
salicylate degradation I 1 1 1
superoxide radicals degradation 2 2 1
thioredoxin pathway 2 1 1
chlorosalicylate degradation 7 2 2
reactive oxygen species degradation 4 4 1
heme b biosynthesis I (aerobic) 4 3 1
heme b biosynthesis V (aerobic) 4 3 1
superpathway of heme b biosynthesis from uroporphyrinogen-III 6 4 1
superpathway of salicylate degradation 7 5 1
ethene biosynthesis III (microbes) 7 5 1
superpathway of heme b biosynthesis from glycine 8 7 1
3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light independent) 9 8 1
3,8-divinyl-chlorophyllide a biosynthesis I (aerobic, light-dependent) 9 7 1
superpathway of heme b biosynthesis from glutamate 10 7 1
naphthalene degradation to acetyl-CoA 12 2 1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate 42 9 1