Experiment set2S421 for Rhodopseudomonas palustris CGA009

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Sodium 4-Hydroxybenzoate carbon source

Group: carbon source
Media: PM + Sodium 4-Hydroxybenzoate (5.7 mM) + Sodium bicarbonate (10 mM) + Light intensity (30 µmol photons/m2/s from a 60-W incandescent light bulb)
Culturing: RPal_CGA009_ML8, tube, Anaerobic, at 30 (C)
By: Rpal_Fixen on 9/6/24
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 25 genes in this experiment

For carbon source Sodium 4-Hydroxybenzoate in Rhodopseudomonas palustris CGA009

For carbon source Sodium 4-Hydroxybenzoate across organisms

SEED Subsystems

Subsystem #Specific
Benzoate transport and degradation cluster 1
Cobalt-zinc-cadmium resistance 1
Flagellar motility 1
Flagellum 1
HMG CoA Synthesis 1
Leucine Degradation and HMG-CoA Metabolism 1
Nitric oxide synthase 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
long-chain fatty acid activation 1 1 1
benzoate degradation II (aerobic and anaerobic) 1 1 1
γ-linolenate biosynthesis II (animals) 2 1 1
linoleate biosynthesis II (animals) 2 1 1
gallate degradation II 5 4 2
methylgallate degradation 6 6 2
3-methyl-branched fatty acid α-oxidation 6 3 2
chitin degradation II (Vibrio) 6 2 2
oleate biosynthesis I (plants) 3 1 1
alkane biosynthesis II 3 1 1
protocatechuate degradation I (meta-cleavage pathway) 8 8 2
gallate degradation I 4 4 1
phytol degradation 4 3 1
long chain fatty acid ester synthesis (engineered) 4 1 1
phosphatidylcholine acyl editing 4 1 1
wax esters biosynthesis II 4 1 1
sporopollenin precursors biosynthesis 18 4 4
superpathway of vanillin and vanillate degradation 10 8 2
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
octane oxidation 5 2 1
protein O-mannosylation II (mammals, core M1 and core M2) 5 1 1
protein O-mannosylation III (mammals, core M3) 5 1 1
fatty acid salvage 6 6 1
stearate biosynthesis II (bacteria and plants) 6 5 1
syringate degradation 12 8 2
stearate biosynthesis IV 6 4 1
6-gingerol analog biosynthesis (engineered) 6 3 1
stearate biosynthesis I (animals) 6 1 1
ceramide degradation by α-oxidation 7 2 1
chitin degradation III (Serratia) 7 2 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
capsaicin biosynthesis 7 1 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
2-deoxy-D-ribose degradation II 8 2 1
protein O-mannosylation I (yeast) 8 1 1
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 4 1
peptidoglycan recycling II 10 2 1
suberin monomers biosynthesis 20 3 2
superpathway of fatty acid biosynthesis II (plant) 43 38 4
protein N-glycosylation (Haloferax volcanii) 11 1 1
peptidoglycan recycling I 14 7 1
palmitate biosynthesis II (type II fatty acid synthase) 31 29 2
cutin biosynthesis 16 1 1
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 7 1
protein N-glycosylation initial phase (eukaryotic) 19 1 1
superpathway of fatty acids biosynthesis (E. coli) 53 49 2
anaerobic aromatic compound degradation (Thauera aromatica) 27 8 1
palmitate biosynthesis III 29 28 1
oleate β-oxidation 35 28 1