Experiment set2S450 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 116 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
Formate hydrogenase	5
Terminal cytochrome C oxidases	5
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	3
Biogenesis of cytochrome c oxidases	3
Ton and Tol transport systems	3
Flagellum in Campylobacter	2
Glutathione: Non-redox reactions	2
Molybdenum cofactor biosynthesis	2
Oxidative stress	2
Thioredoxin-disulfide reductase	2
Transport of Iron	2
Ubiquinone Biosynthesis	2
Alanine biosynthesis	1
Arginine Biosynthesis extended	1
Benzoate transport and degradation cluster	1
Biotin biosynthesis	1
Calvin-Benson cycle	1
Campylobacter Iron Metabolism	1
Carotenoids	1
Colanic acid biosynthesis	1
DNA-binding regulatory proteins, strays	1
ECF class transporters	1
Experimental tye	1
Fatty Acid Biosynthesis FASII	1
Glutaredoxins	1
Glutathione: Redox cycle	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	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
mycolic acid synthesis	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
• Benzoate degradation via hydroxylation
• 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 alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Bile acid biosynthesis
• Oxidative phosphorylation
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Methionine metabolism
• Cysteine metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Histidine metabolism
• Phenylalanine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Benzoxazinone biosynthesis
• Cyanoamino acid metabolism
• Other glycan degradation
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• 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
• C5-Branched dibasic acid metabolism
• 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 unsaturated fatty acids
• 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
bis(guanylyl molybdenum cofactor) biosynthesis	2	2	2
methylsalicylate degradation	2	2	2
L-alanine biosynthesis III	1	1	1
thiosulfate disproportionation IV (rhodanese)	1	1	1
L-cysteine degradation IV	1	1	1
bis(guanylyl tungstenpterin) cofactor biosynthesis	1	1	1
guanylyl molybdenum cofactor biosynthesis	1	1	1
formate oxidation to CO2	1	1	1
salicylate degradation I	1	1	1
gallate degradation I	4	4	3
methylgallate degradation	6	6	4
gallate degradation II	5	4	3
protocatechuate degradation I (meta-cleavage pathway)	8	8	4
polyphosphate metabolism	2	2	1
sedoheptulose bisphosphate bypass	2	1	1
L-cysteine degradation III	2	1	1
thioredoxin pathway	2	1	1
arsenite to oxygen electron transfer	2	1	1
cytidylyl molybdenum cofactor sulfurylation	2	1	1
4-hydroxy-4-methyl-L-glutamate biosynthesis	2	1	1
superpathway of vanillin and vanillate degradation	10	8	4
methylglyoxal degradation VIII	3	3	1
syringate degradation	12	8	4
5,6-dimethylbenzimidazole biosynthesis I (aerobic)	3	2	1
cardiolipin biosynthesis III	3	2	1
cardiolipin biosynthesis II	3	2	1
methylglyoxal degradation I	3	2	1
cardiolipin biosynthesis 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
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	12	3
gondoate biosynthesis (anaerobic)	4	4	1
superpathway of L-alanine biosynthesis	4	4	1
heme b biosynthesis I (aerobic)	4	3	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
oxalate degradation VI	4	1	1
tRNA-uridine 2-thiolation (mammalian mitochondria)	4	1	1
tRNA-uridine 2-thiolation (yeast mitochondria)	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
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	49	11
L-ornithine biosynthesis I	5	5	1
fatty acid elongation -- saturated	5	5	1
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	18	4
cis-vaccenate biosynthesis	5	4	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
sulfide oxidation IV (mitochondria)	5	3	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 fatty acid biosynthesis II (plant)	43	38	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
superpathway of thiamine diphosphate biosynthesis II	11	8	2
anteiso-branched-chain fatty acid biosynthesis	34	30	6
even iso-branched-chain fatty acid biosynthesis	34	30	6
odd iso-branched-chain fatty acid biosynthesis	34	30	6
ppGpp metabolism	6	6	1
phosphatidylglycerol biosynthesis I	6	6	1
(5Z)-dodecenoate biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis II	6	6	1
pentose phosphate pathway (non-oxidative branch) II	6	5	1
stearate biosynthesis II (bacteria and plants)	6	5	1
(5Z)-dodecenoate biosynthesis II	6	5	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	4	1
stearate biosynthesis IV	6	4	1
petroselinate biosynthesis	6	2	1
molybdopterin biosynthesis	6	2	1
Fe(II) oxidation	6	2	1
thiazole component of thiamine diphosphate biosynthesis I	6	2	1
Calvin-Benson-Bassham cycle	13	12	2
streptorubin B biosynthesis	34	20	5
superpathway of salicylate degradation	7	5	1
chitin degradation III (Serratia)	7	2	1
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	16	2
superpathway of heme b biosynthesis from glycine	8	7	1
superpathway of methylglyoxal degradation	8	3	1
2-allylmalonyl-CoA biosynthesis	8	2	1
tRNA-uridine 2-thiolation (cytoplasmic)	8	1	1
oxygenic photosynthesis	17	13	2
L-arginine biosynthesis I (via L-ornithine)	9	9	1
3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light independent)	9	8	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	7	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
3,8-divinyl-chlorophyllide a biosynthesis I (aerobic, light-dependent)	9	7	1
1,3-propanediol biosynthesis (engineered)	9	4	1
L-arginine biosynthesis II (acetyl cycle)	10	10	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
superpathway of phospholipid biosynthesis III (E. coli)	12	10	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
homolactic fermentation	12	9	1
gluconeogenesis III	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
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
1-butanol autotrophic biosynthesis (engineered)	27	21	2
hopanoid biosynthesis (bacteria)	14	12	1
peptidoglycan recycling I	14	7	1
purine nucleobases degradation I (anaerobic)	15	6	1
superpathway of arginine and polyamine biosynthesis	17	13	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	12	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	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 phospholipid biosynthesis II (plants)	28	12	1
adenosylcobalamin biosynthesis II (aerobic)	33	29	1
mycolate biosynthesis	205	26	5
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	9	1
superpathway of mycolate biosynthesis	239	27	5
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	19	1