Experiment set1IT046 for Pseudomonas sp. RS175

Sodium propionate carbon 20 mM

Group: carbon source
Media: MME_noCarbon + Sodium propionate (20 mM), pH=7
Culturing: Pseudomonas_RS175_ML2, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on 1-Jul-22
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 16 genes in this experiment

For carbon source Sodium propionate in Pseudomonas sp. RS175

For carbon source Sodium propionate across organisms

SEED Subsystems

Subsystem	#Specific
Potassium homeostasis	2
Arginine Biosynthesis extended	1
Arginine and Ornithine Degradation	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Copper homeostasis	1
Flavodoxin	1
Folate Biosynthesis	1
Glutathione-regulated potassium-efflux system and associated functions	1
Glycine reductase, sarcosine reductase and betaine reductase	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	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:

• Arginine and proline metabolism
• Urea cycle and metabolism of amino groups
• Lysine biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Ubiquinone and menaquinone biosynthesis
• Pyrimidine metabolism
• Geraniol degradation
• Tryptophan metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Folate biosynthesis
• Limonene and pinene degradation
• Biosynthesis of phenylpropanoids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-hydroxybenzoate biosynthesis II (bacteria)	1	1	1
4-aminobenzoate biosynthesis I	2	2	1
4-aminobenzoate biosynthesis II	2	2	1
thioredoxin pathway	2	1	1
L-ornithine biosynthesis I	5	5	2
L-proline biosynthesis III (from L-ornithine)	3	3	1
L-ornithine biosynthesis II	3	3	1
L-arginine degradation I (arginase pathway)	3	2	1
L-arginine degradation VI (arginase 2 pathway)	4	3	1
polybrominated phenols biosynthesis	4	1	1
L-arginine biosynthesis I (via L-ornithine)	9	9	2
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	2
L-arginine biosynthesis II (acetyl cycle)	10	10	2
L-arginine degradation II (AST pathway)	5	5	1
L-arginine degradation XIII (reductive Stickland reaction)	5	5	1
L-Nδ-acetylornithine biosynthesis	7	5	1
spongiadioxin C biosynthesis	7	2	1
L-citrulline biosynthesis	8	7	1
polybrominated dihydroxylated diphenyl ethers biosynthesis	8	2	1
superpathway of arginine and polyamine biosynthesis	17	14	2
L-lysine biosynthesis I	9	9	1
ubiquinol-8 biosynthesis (late decarboxylation)	9	5	1
p-HBAD biosynthesis	9	1	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
superpathway of candicidin biosynthesis	11	4	1
superpathway of ubiquinol-8 biosynthesis (early decarboxylation)	12	11	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
superpathway of L-citrulline metabolism	12	9	1
tetrahydromethanopterin biosynthesis	14	3	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
superpathway of polybrominated aromatic compound biosynthesis	20	2	1
phenolphthiocerol biosynthesis	23	1	1
aspartate superpathway	25	22	1
superpathway of chorismate metabolism	59	43	2