Experiment set22IT055 for Pseudomonas fluorescens SBW25-INTG

Sodium acetate 30 mM carbon source

Group: carbon source
Media: MME_noNitrogen_noCarbon + Sodium acetate (30 mM) + Ammonium chloride (10 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on 8-Mar-22
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium 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 22 genes in this experiment

For carbon source Sodium acetate in Pseudomonas fluorescens SBW25-INTG

For carbon source Sodium acetate across organisms

SEED Subsystems

Subsystem	#Specific
Iron acquisition in Vibrio	3
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	3
Transport of Iron	3
Campylobacter Iron Metabolism	2
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Lysine Biosynthesis DAP Pathway	1
Phenylalanine and Tyrosine Branches from Chorismate	1
Polyamine Metabolism	1
RNA processing and degradation, bacterial	1
Ribosome biogenesis bacterial	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Lysine biosynthesis
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Alkaloid biosynthesis II
• Urea cycle and metabolism of amino groups
• Histidine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• 1- and 2-Methylnaphthalene degradation
• Alkaloid biosynthesis I
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Fatty acid biosynthesis
• Methionine metabolism
• Geraniol degradation
• Lysine degradation
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
spermine and spermidine degradation I	5	2	2
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-arginine degradation I (arginase pathway)	3	3	1
L-proline biosynthesis III (from L-ornithine)	3	3	1
L-ornithine biosynthesis II	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-arginine degradation VI (arginase 2 pathway)	4	4	1
putrescine degradation III	4	3	1
L-phenylalanine biosynthesis II	4	3	1
L-tyrosine biosynthesis III	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
L-tyrosine biosynthesis II	4	2	1
L-ornithine biosynthesis I	5	5	1
L-tyrosine degradation I	5	5	1
L-arginine degradation XIII (reductive Stickland reaction)	5	5	1
superpathway of L-phenylalanine and L-tyrosine biosynthesis	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-Nδ-acetylornithine biosynthesis	7	6	1
L-citrulline biosynthesis	8	8	1
superpathway of aromatic amino acid biosynthesis	18	18	2
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
L-histidine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	1	1
(S)-reticuline biosynthesis I	11	1	1
tropane alkaloids biosynthesis	11	1	1
superpathway of L-citrulline metabolism	12	10	1
superpathway of rosmarinic acid biosynthesis	14	1	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	4	1
superpathway of arginine and polyamine biosynthesis	17	15	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of chorismate metabolism	59	42	2
superpathway of histidine, purine, and pyrimidine biosynthesis	46	44	1