Experiment set2S451 for Rhodopseudomonas palustris CGA009

PM with Sodium succinate dibasic hexahydrate and Sodium Formate aerobic in dark

Group: carbon source dark aerobic
Media: PM + Sodium succinate dibasic hexahydrate (10 mM) + Sodium Formate (20 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 106 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
Flagellum	20
Flagellar motility	6
Terminal cytochrome C oxidases	5
Formate hydrogenase	4
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	3
Biogenesis of cytochrome c oxidases	3
Flagellum in Campylobacter	2
Glutathione: Non-redox reactions	2
Molybdenum cofactor biosynthesis	2
Multidrug Resistance Efflux Pumps	2
Oxidative stress	2
Thioredoxin-disulfide reductase	2
Ton and Tol transport systems	2
Transport of Iron	2
Ubiquinone Biosynthesis	2
Alanine biosynthesis	1
Benzoate transport and degradation cluster	1
Biotin biosynthesis	1
Calvin-Benson cycle	1
Campylobacter Iron Metabolism	1
Carotenoids	1
Cobalt-zinc-cadmium resistance	1
Colanic acid biosynthesis	1
DNA-binding regulatory proteins, strays	1
ECF class transporters	1
Experimental tye	1
Glutaredoxins	1
Glutathione: Redox cycle	1
Glycine reductase, sarcosine reductase and betaine reductase	1
Glycolysis and Gluconeogenesis	1
Heme and Siroheme Biosynthesis	1
Hemin transport system	1
Hfl operon	1
Iron acquisition in Vibrio	1
Mannose Metabolism	1
Methylglyoxal Metabolism	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Phosphate metabolism	1
Salicylate and gentisate catabolism	1
Salicylate ester degradation	1
Transport of Molybdenum	1
Transport of Zinc	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:

• Purine metabolism
• Ubiquinone and menaquinone biosynthesis
• Biosynthesis of terpenoids and steroids
• Pyrimidine metabolism
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Methane metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Bile acid biosynthesis
• Oxidative phosphorylation
• Glycine, serine and threonine metabolism
• Methionine metabolism
• Histidine metabolism
• Phenylalanine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Benzoxazinone biosynthesis
• Cyanoamino acid metabolism
• Other glycan degradation
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• Toluene and xylene degradation
• 1,4-Dichlorobenzene degradation
• Fluorene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Styrene degradation
• Carbon fixation in photosynthetic organisms
• Thiamine metabolism
• Riboflavin metabolism
• Folate biosynthesis
• Terpenoid biosynthesis
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Brassinosteroid biosynthesis
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Isoflavonoid biosynthesis
• Alkaloid biosynthesis I
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
methylsalicylate degradation	2	2	2
bis(guanylyl molybdenum cofactor) biosynthesis	2	2	2
bis(guanylyl tungstenpterin) cofactor biosynthesis	1	1	1
L-cysteine degradation IV	1	1	1
guanylyl molybdenum cofactor biosynthesis	1	1	1
salicylate degradation I	1	1	1
L-alanine biosynthesis III	1	1	1
formate oxidation to CO2	1	1	1
polyphosphate metabolism	2	2	1
sedoheptulose bisphosphate bypass	2	1	1
thioredoxin pathway	2	1	1
cytidylyl molybdenum cofactor sulfurylation	2	1	1
arsenite to oxygen electron transfer	2	1	1
methylglyoxal degradation VIII	3	3	1
methylglyoxal degradation I	3	2	1
chitin degradation II (Vibrio)	6	2	2
bis(guanylyl molybdopterin) cofactor sulfurylation	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
thiazole component of thiamine diphosphate biosynthesis II	7	4	2
chlorosalicylate degradation	7	2	2
gallate degradation I	4	4	1
superpathway of L-alanine biosynthesis	4	4	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
heme b biosynthesis I (aerobic)	4	3	1
heme b biosynthesis V (aerobic)	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
oxalate degradation VI	4	1	1
tRNA-uridine 2-thiolation (mammalian mitochondria)	4	1	1
tRNA-uridine 2-thiolation (yeast mitochondria)	4	1	1
gallate degradation II	5	4	1
sucrose degradation V (sucrose α-glucosidase)	5	2	1
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	2	1
[2Fe-2S] iron-sulfur cluster biosynthesis	10	2	2
oxalate degradation III	5	1	1
superpathway of thiamine diphosphate biosynthesis II	11	8	2
ppGpp metabolism	6	6	1
methylgallate degradation	6	6	1
pentose phosphate pathway (non-oxidative branch) II	6	5	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	4	1
molybdopterin biosynthesis	6	2	1
thiazole component of thiamine diphosphate biosynthesis I	6	2	1
Fe(II) oxidation	6	2	1
Calvin-Benson-Bassham cycle	13	12	2
superpathway of salicylate degradation	7	5	1
chitin degradation III (Serratia)	7	2	1
protocatechuate degradation I (meta-cleavage pathway)	8	8	1
superpathway of heme b biosynthesis from glycine	8	7	1
superpathway of methylglyoxal degradation	8	3	1
tRNA-uridine 2-thiolation (cytoplasmic)	8	1	1
oxygenic photosynthesis	17	13	2
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
sucrose biosynthesis I (from photosynthesis)	9	7	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	7	1
1,3-propanediol biosynthesis (engineered)	9	4	1
superpathway of vanillin and vanillate degradation	10	8	1
glycolysis IV	10	8	1
superpathway of heme b biosynthesis from glutamate	10	7	1
glycolysis V (Pyrococcus)	10	6	1
superpathway of thiamine diphosphate biosynthesis I	10	6	1
peptidoglycan recycling II	10	2	1
glycolysis II (from fructose 6-phosphate)	11	9	1
glycolysis III (from glucose)	11	9	1
glycolysis VI (from fructose)	11	7	1
tRNA-uridine 2-thiolation and selenation (bacteria)	11	2	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
homolactic fermentation	12	9	1
gluconeogenesis III	12	8	1
syringate degradation	12	8	1
superpathway of C1 compounds oxidation to CO2	12	3	1
naphthalene degradation to acetyl-CoA	12	2	1
ethene biosynthesis V (engineered)	25	20	2
gluconeogenesis I	13	12	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	20	2
glycolysis I (from glucose 6-phosphate)	13	10	1
1-butanol autotrophic biosynthesis (engineered)	27	21	2
peptidoglycan recycling I	14	7	1
purine nucleobases degradation I (anaerobic)	15	6	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	12	1
superpathway of hexitol degradation (bacteria)	18	11	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	7	1
superpathway of anaerobic sucrose degradation	19	14	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	12	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	1
superpathway of N-acetylneuraminate degradation	22	12	1
purine nucleobases degradation II (anaerobic)	24	15	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	9	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	19	1