Experiment set2S452 for Rhodopseudomonas palustris CGA009

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 11 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
Terminal cytochrome C oxidases	2
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
Thioredoxin-disulfide reductase	1
Ubiquinone Biosynthesis	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:

• Ubiquinone and menaquinone biosynthesis
• Tryptophan metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Biosynthesis of terpenoids and steroids
• Oxidative phosphorylation
• Pyrimidine metabolism
• Methionine metabolism
• Histidine metabolism
• Phenylalanine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Cyanoamino acid metabolism
• Toluene and xylene degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Benzoate degradation via CoA ligation
• Styrene degradation
• Methane metabolism
• Riboflavin metabolism
• Terpenoid biosynthesis
• Limonene and pinene degradation
• Brassinosteroid biosynthesis
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Isoflavonoid biosynthesis
• Alkaloid biosynthesis I
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
superoxide radicals degradation	2	2	1
thioredoxin pathway	2	1	1
arsenite to oxygen electron transfer	2	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
reactive oxygen species degradation	4	4	1
heme b biosynthesis V (aerobic)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
heme b biosynthesis I (aerobic)	4	3	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	4	1
Fe(II) oxidation	6	2	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