Experiment set16IT044 for Pseudomonas fluorescens SBW25-INTG

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4-Hydroxybenzoic Acid (C) and Ammonium chloride (N); with MOPS

Group: no stress control
Media: MME_noNitrogen_noCarbon + 4-Hydroxybenzoic Acid (5 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 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 51 genes in this experiment

For no stress control 4-Hydroxybenzoic Acid in Pseudomonas fluorescens SBW25-INTG

For no stress control 4-Hydroxybenzoic Acid across organisms

SEED Subsystems

Subsystem #Specific
Leucine Degradation and HMG-CoA Metabolism 6
ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 4
Isoleucine degradation 4
Valine degradation 4
HMG CoA Synthesis 3
Terminal cytochrome C oxidases 3
Biogenesis of cytochrome c oxidases 2
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria 2
Serine-glyoxylate cycle 2
Ammonia assimilation 1
Benzoate transport and degradation cluster 1
Biogenesis of c-type cytochromes 1
Biotin biosynthesis 1
Entner-Doudoroff Pathway 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Heat shock dnaK gene cluster extended 1
Lysine degradation 1
Methylcitrate cycle 1
Methylglyoxal Metabolism 1
Periplasmic disulfide interchange 1
Propionate-CoA to Succinate Module 1
Protein degradation 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Queuosine-Archaeosine 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
cis-cyclopropane fatty acid (CFA) biosynthesis 1 1 1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA 3 3 2
phenylethylamine degradation I 2 2 1
putrescine degradation V 2 2 1
4-aminobutanoate degradation I 2 2 1
polyphosphate metabolism 2 2 1
4-aminobutanoate degradation II 2 2 1
4-aminobutanoate degradation III 2 2 1
L-leucine degradation I 6 5 3
ethylene glycol degradation 2 1 1
phenylethanol degradation 2 1 1
phenylethylamine degradation II 2 1 1
sterculate biosynthesis 2 1 1
arsenite to oxygen electron transfer 2 1 1
putrescine degradation I 2 1 1
ethanol degradation IV 3 3 1
superpathway of 4-aminobutanoate degradation 3 3 1
ethanol degradation II 3 3 1
NAD salvage pathway III (to nicotinamide riboside) 3 2 1
L-phenylalanine degradation II (anaerobic) 3 2 1
hypotaurine degradation 3 2 1
ethanol degradation III 3 2 1
putrescine degradation IV 3 2 1
styrene degradation 3 1 1
arsenite to oxygen electron transfer (via azurin) 3 1 1
histamine degradation 3 1 1
UTP and CTP dephosphorylation I 7 5 2
purine nucleotides degradation II (aerobic) 11 11 3
guanosine nucleotides degradation III 4 4 1
inosine 5'-phosphate degradation 4 4 1
guanosine nucleotides degradation II 4 4 1
adenosine nucleotides degradation I 8 7 2
purine nucleotides degradation I (plants) 12 10 3
putrescine degradation III 4 3 1
aerobic respiration I (cytochrome c) 4 3 1
guanosine nucleotides degradation I 4 3 1
GABA shunt II 4 3 1
phytol degradation 4 3 1
aerobic respiration II (cytochrome c) (yeast) 4 3 1
L-tryptophan degradation X (mammalian, via tryptamine) 4 2 1
GABA shunt I 4 2 1
fatty acid α-oxidation I (plants) 4 2 1
D-arabinose degradation II 4 2 1
2-methylcitrate cycle I 5 5 1
L-lysine degradation IV 5 5 1
adenosine nucleotides degradation II 5 5 1
octane oxidation 5 4 1
mitochondrial NADPH production (yeast) 5 4 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
ferrichrome A biosynthesis 5 2 1
dopamine degradation 5 2 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 7 2
L-lysine degradation X 6 5 1
2-methylcitrate cycle II 6 5 1
superpathway of guanosine nucleotides degradation (plants) 6 5 1
superpathway of purines degradation in plants 18 14 3
Fe(II) oxidation 6 3 1
3-methyl-branched fatty acid α-oxidation 6 3 1
L-lysine degradation III 6 2 1
alkane oxidation 6 1 1
superpathway of L-arginine and L-ornithine degradation 13 9 2
noradrenaline and adrenaline degradation 13 8 2
ureide biosynthesis 7 6 1
superpathway of glycol metabolism and degradation 7 5 1
L-lysine degradation I 7 4 1
serotonin degradation 7 4 1
4-aminobutanoate degradation V 7 3 1
ceramide degradation by α-oxidation 7 2 1
limonene degradation IV (anaerobic) 7 1 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 7 1
superpathway of ornithine degradation 8 4 1
aromatic biogenic amine degradation (bacteria) 8 4 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
Entner-Doudoroff pathway II (non-phosphorylative) 9 6 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 5 1
tunicamycin biosynthesis 9 2 1
superpathway of phenylethylamine degradation 11 6 1
NAD salvage (plants) 11 5 1
nicotine degradation I (pyridine pathway) 17 5 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 4 1
superpathway of pentose and pentitol degradation 42 16 1
superpathway of L-lysine degradation 43 17 1
mycolate biosynthesis 205 20 3
superpathway of mycolate biosynthesis 239 21 3