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 109 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	13
Flagellar motility	5
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
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
CO2 uptake, carboxysome	1
Calvin-Benson cycle	1
Campylobacter Iron Metabolism	1
Carboxysome	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
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
NAD and NADP cofactor biosynthesis global	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Phosphate metabolism	1
Transport of Molybdenum	1
Transport of Zinc	1
Wyeosine-MimG Biosynthesis	1
cAMP signaling in bacteria	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
• 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
• 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
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Pyruvate metabolism
• Toluene and xylene degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene 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
formate oxidation to CO2	1	1	1
bis(guanylyl tungstenpterin) cofactor biosynthesis	1	1	1
thiosulfate disproportionation IV (rhodanese)	1	1	1
L-alanine biosynthesis III	1	1	1
L-cysteine degradation IV	1	1	1
guanylyl molybdenum cofactor biosynthesis	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
L-cysteine degradation III	2	1	1
sedoheptulose bisphosphate bypass	2	1	1
cytidylyl molybdenum cofactor sulfurylation	2	1	1
4-hydroxy-4-methyl-L-glutamate biosynthesis	2	1	1
arsenite to oxygen electron transfer	2	1	1
thioredoxin pathway	2	1	1
superpathway of vanillin and vanillate degradation	10	8	4
methylglyoxal degradation VIII	3	3	1
syringate degradation	12	8	4
methylglyoxal degradation I	3	2	1
5,6-dimethylbenzimidazole biosynthesis I (aerobic)	3	2	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
bis(guanylyl molybdopterin) cofactor sulfurylation	3	1	1
thiazole component of thiamine diphosphate biosynthesis II	7	4	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 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
tRNA-uridine 2-thiolation (mammalian mitochondria)	4	1	1
tRNA-uridine 2-thiolation (yeast mitochondria)	4	1	1
oxalate degradation VI	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
fatty acid elongation -- saturated	5	5	1
L-ornithine biosynthesis I	5	5	1
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	18	4
8-amino-7-oxononanoate biosynthesis IV	5	4	1
cis-vaccenate biosynthesis	5	4	1
sulfide oxidation IV (mitochondria)	5	3	1
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	2	1
sucrose degradation V (sucrose α-glucosidase)	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
even iso-branched-chain fatty acid biosynthesis	34	30	6
odd iso-branched-chain fatty acid biosynthesis	34	30	6
anteiso-branched-chain fatty acid biosynthesis	34	30	6
(5Z)-dodecenoate biosynthesis I	6	6	1
ppGpp metabolism	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
Fe(II) oxidation	6	2	1
petroselinate biosynthesis	6	2	1
molybdopterin biosynthesis	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
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
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light independent)	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
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
superpathway of C1 compounds oxidation to CO2	12	3	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
hopanoid biosynthesis (bacteria)	14	12	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
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
adenosylcobalamin biosynthesis II (aerobic)	33	29	1
mycolate biosynthesis	205	26	5
superpathway of mycolate biosynthesis	239	27	5
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	19	1