Experiment set2S430 for Rhodopseudomonas palustris CGA009

Sodium Benzoate carbon source, sodium fluoride stress

Group: stress
Media: PM + Sodium Benzoate (5.7 mM) + sodium fluoride (50 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 16 genes in this experiment

For stress Sodium Benzoate in Rhodopseudomonas palustris CGA009

For stress Sodium Benzoate across organisms

SEED Subsystems

Subsystem	#Specific
Carotenoids	1
Chlorophyll Biosynthesis	1
Fatty Acid Biosynthesis FASII	1
Fermentations: Mixed acid	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Sulfur oxidation	1
mycolic acid synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Benzoate degradation via CoA ligation
• Retinol metabolism
• Biosynthesis of unsaturated fatty acids
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• C21-Steroid hormone metabolism
• Glutamate metabolism
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Benzoate degradation via hydroxylation
• Bisphenol A degradation
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Linoleic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• Naphthalene and anthracene degradation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Nicotinate and nicotinamide metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Metabolism of xenobiotics by cytochrome P450
• Insect hormone biosynthesis
• Drug metabolism - cytochrome P450
• Biosynthesis of type II polyketide products
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation I	1	1	1
L-glutamine degradation II	1	1	1
acetaldehyde biosynthesis I	1	1	1
ammonia assimilation cycle III	3	3	2
ethanol degradation I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation II	3	3	1
3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light independent)	9	8	3
3,8-divinyl-chlorophyllide a biosynthesis I (aerobic, light-dependent)	9	7	3
L-isoleucine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-valine degradation II	3	2	1
pyruvate fermentation to ethanol I	3	1	1
L-methionine degradation III	3	1	1
pyruvate fermentation to ethanol III	3	1	1
L-glutamate and L-glutamine biosynthesis	7	5	2
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	12	3
gondoate biosynthesis (anaerobic)	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
phytol degradation	4	3	1
L-phenylalanine degradation III	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
L-tyrosine degradation III	4	2	1
salidroside biosynthesis	4	2	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
palmitate biosynthesis III	29	28	7
tetradecanoate biosynthesis (mitochondria)	25	23	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	8	2
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
benzoyl-CoA degradation III (anaerobic)	9	7	2
spirilloxanthin and 2,2'-diketo-spirilloxanthin biosynthesis	9	2	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	49	11
fatty acid elongation -- saturated	5	5	1
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	18	4
8-amino-7-oxononanoate biosynthesis IV	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
ethanolamine utilization	5	4	1
cis-vaccenate biosynthesis	5	4	1
(S)-propane-1,2-diol degradation	5	3	1
acetylene degradation (anaerobic)	5	3	1
phenylethanol biosynthesis	5	2	1
flexixanthin biosynthesis	5	1	1
superpathway of fatty acid biosynthesis II (plant)	43	38	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
anteiso-branched-chain fatty acid biosynthesis	34	30	6
odd iso-branched-chain fatty acid biosynthesis	34	30	6
even iso-branched-chain fatty acid biosynthesis	34	30	6
(5Z)-dodecenoate biosynthesis I	6	6	1
(5Z)-dodecenoate biosynthesis II	6	5	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
petroselinate biosynthesis	6	2	1
noradrenaline and adrenaline degradation	13	8	2
streptorubin B biosynthesis	34	20	5
3-methylbutanol biosynthesis (engineered)	7	6	1
serotonin degradation	7	4	1
benzoyl-CoA degradation II (anaerobic)	7	2	1
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	16	2
L-citrulline biosynthesis	8	7	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
2-allylmalonyl-CoA biosynthesis	8	2	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	4	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of bacteriochlorophyll a biosynthesis	26	17	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	11	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	7	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
heterolactic fermentation	18	11	1
toluene degradation VI (anaerobic)	18	5	1
superpathway of anaerobic sucrose degradation	19	14	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	12	1
superpathway of N-acetylneuraminate degradation	22	12	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	8	1
mycolate biosynthesis	205	26	5
superpathway of mycolate biosynthesis	239	27	5