Experiment set22IT056 for Pseudomonas fluorescens SBW25-INTG

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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 57 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
Transport of Zinc 3
Campylobacter Iron Metabolism 2
Ribosome biogenesis bacterial 2
Bacterial RNA-metabolizing Zn-dependent hydrolases 1
Beta-Glucoside Metabolism 1
Choline and Betaine Uptake and Betaine Biosynthesis 1
Conserved gene cluster associated with Met-tRNA formyltransferase 1
Copper homeostasis 1
Fatty Acid Biosynthesis FASII 1
Lysine Biosynthesis DAP Pathway 1
Methionine Salvage 1
Nudix proteins (nucleoside triphosphate hydrolases) 1
Phenylalanine and Tyrosine Branches from Chorismate 1
Polyamine Metabolism 1
Protein degradation 1
Queuosine-Archaeosine Biosynthesis 1
RNA processing and degradation, bacterial 1
Ubiquinone Biosynthesis 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
4-hydroxybenzoate biosynthesis II (bacteria) 1 1 1
neolinustatin bioactivation 3 2 2
L-phenylalanine biosynthesis III (cytosolic, plants) 2 2 1
indole-3-acetate biosynthesis III (bacteria) 2 2 1
acrylonitrile degradation I 2 2 1
indole-3-acetate biosynthesis IV (bacteria) 2 2 1
linustatin bioactivation 4 2 2
pseudouridine degradation 2 1 1
linamarin degradation 2 1 1
L-tyrosine degradation II 2 1 1
atromentin biosynthesis 2 1 1
lotaustralin degradation 2 1 1
spermine and spermidine degradation I 5 2 2
L-arginine degradation I (arginase pathway) 3 3 1
glycine cleavage 3 3 1
L-tyrosine biosynthesis I 3 3 1
L-proline biosynthesis III (from L-ornithine) 3 3 1
L-ornithine biosynthesis II 3 3 1
glycine biosynthesis II 3 3 1
L-phenylalanine biosynthesis I 3 3 1
cellulose degradation II (fungi) 3 2 1
superpathway of acrylonitrile degradation 3 2 1
L-arginine degradation X (arginine monooxygenase pathway) 3 2 1
L-phenylalanine degradation II (anaerobic) 3 2 1
5'-deoxyadenosine degradation I 3 1 1
5-(methoxycarbonylmethoxy)uridine biosynthesis 3 1 1
fatty acid biosynthesis initiation (type I) 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
biotin-carboxyl carrier protein assembly 4 4 1
queuosine biosynthesis I (de novo) 4 4 1
L-arginine degradation VI (arginase 2 pathway) 4 4 1
L-phenylalanine biosynthesis II 4 3 1
L-tyrosine biosynthesis III 4 3 1
putrescine degradation III 4 3 1
L-tyrosine biosynthesis II 4 2 1
L-phenylalanine degradation III 4 2 1
L-tyrosine degradation III 4 2 1
creatinine degradation I 4 2 1
5'-deoxyadenosine degradation II 4 1 1
polybrominated phenols biosynthesis 4 1 1
L-arginine degradation XIII (reductive Stickland reaction) 5 5 1
L-tyrosine degradation I 5 5 1
L-ornithine biosynthesis I 5 5 1
superpathway of L-phenylalanine and L-tyrosine biosynthesis 5 3 1
queuosine biosynthesis III (queuosine salvage) 5 3 1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III 5 2 1
superpathway of plastoquinol biosynthesis 5 2 1
creatinine degradation II 5 2 1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II 5 2 1
coumarin biosynthesis (via 2-coumarate) 5 2 1
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-tyrosine degradation V (reductive Stickland reaction) 5 1 1
α-tomatine degradation 6 1 1
L-Nδ-acetylornithine biosynthesis 7 6 1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation I 7 2 1
spongiadioxin C biosynthesis 7 2 1
L-citrulline biosynthesis 8 8 1
glycine betaine degradation I 8 6 1
bacterial bioluminescence 8 4 1
polybrominated dihydroxylated diphenyl ethers biosynthesis 8 2 1
superpathway of aromatic amino acid biosynthesis 18 18 2
L-lysine biosynthesis I 9 9 1
L-arginine biosynthesis I (via L-ornithine) 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
ubiquinol-8 biosynthesis (late decarboxylation) 9 4 1
jadomycin biosynthesis 9 3 1
p-HBAD biosynthesis 9 1 1
L-arginine biosynthesis II (acetyl cycle) 10 10 1
superpathway of L-tyrosine biosynthesis 10 10 1
superpathway of L-phenylalanine biosynthesis 10 10 1
L-histidine biosynthesis 10 10 1
rosmarinic acid biosynthesis I 10 1 1
L-methionine salvage cycle III 11 5 1
L-methionine salvage cycle II (plants) 11 3 1
(S)-reticuline biosynthesis I 11 1 1
tropane alkaloids biosynthesis 11 1 1
superpathway of L-citrulline metabolism 12 10 1
superpathway of ubiquinol-8 biosynthesis (early decarboxylation) 12 10 1
indole-3-acetate biosynthesis II 12 5 1
L-methionine salvage cycle I (bacteria and plants) 12 4 1
3-hydroxypropanoate cycle 13 6 1
glyoxylate assimilation 13 4 1
tetrahydromethanopterin biosynthesis 14 3 1
firefly bioluminescence 14 2 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
3-hydroxypropanoate/4-hydroxybutanate cycle 18 8 1
superpathway of the 3-hydroxypropanoate cycle 18 6 1
superpathway of chorismate metabolism 59 42 3
superpathway of polybrominated aromatic compound biosynthesis 20 2 1
phenolphthiocerol biosynthesis 23 1 1
aspartate superpathway 25 22 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 4 1
superpathway of histidine, purine, and pyrimidine biosynthesis 46 44 1
superpathway of mycolate biosynthesis 239 21 1