Experiment set16IT017 for Pseudomonas fluorescens SBW25-INTG

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p-Coumaric acid (C) and Ammonium chloride (N); with MOPS

Group: no stress control
Media: MME_noNitrogen_noCarbon + p-Coumaric acid (5 mM) + Ammonium chloride (10 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 8 (C), shaken=1200 rpm
By: Joshua Elmore on September 1, 2021
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 54 genes in this experiment

For no stress control p-Coumaric acid in Pseudomonas fluorescens SBW25-INTG

For no stress control p-Coumaric acid across organisms

SEED Subsystems

Subsystem #Specific
ABC transporter oligopeptide (TC 3.A.1.5.1) 5
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 2
Arginine and Ornithine Degradation 1
DNA repair, bacterial MutL-MutS system 1
Lipid A modifications 1
Lysine degradation 1
Pyruvate Alanine Serine Interconversions 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Ribosome biogenesis bacterial 1
Rrf2 family transcriptional regulators 1
Rubrerythrin 1
SigmaB stress responce regulation 1
tRNA processing 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
UDP-α-D-glucuronate biosynthesis (from UDP-glucose) 1 1 1
thiosulfate disproportionation IV (rhodanese) 1 1 1
β-alanine degradation II 2 2 1
pseudouridine degradation 2 1 1
UDP-α-D-xylose biosynthesis 2 1 1
L-cysteine degradation III 2 1 1
L-ornithine biosynthesis II 3 3 1
L-proline biosynthesis III (from L-ornithine) 3 3 1
L-arginine degradation I (arginase pathway) 3 3 1
urate conversion to allantoin I 3 2 1
polymyxin resistance 6 3 2
L-arginine degradation VI (arginase 2 pathway) 4 4 1
queuosine biosynthesis I (de novo) 4 4 1
L-arginine degradation II (AST pathway) 5 5 1
L-arginine degradation XIII (reductive Stickland reaction) 5 5 1
L-ornithine biosynthesis I 5 5 1
sulfide oxidation IV (mitochondria) 5 2 1
L-leucine degradation I 6 5 1
β-alanine biosynthesis II 6 5 1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis 6 4 1
ureide biosynthesis 7 6 1
L-Nδ-acetylornithine biosynthesis 7 6 1
L-citrulline biosynthesis 8 8 1
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
UDP-sugars interconversion 9 2 1
teichuronic acid biosynthesis (B. subtilis 168) 9 2 1
L-arginine biosynthesis II (acetyl cycle) 10 10 1
superpathway of coenzyme A biosynthesis II (plants) 10 9 1
peptidoglycan recycling II 10 8 1
methyl tert-butyl ether degradation 10 4 1
colanic acid building blocks biosynthesis 11 11 1
superpathway of L-citrulline metabolism 12 10 1
peptidoglycan recycling I 14 11 1
superpathway of arginine and polyamine biosynthesis 17 15 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
superpathway of purines degradation in plants 18 14 1
aspartate superpathway 25 22 1