Experiment set16IT042 for Pseudomonas fluorescens SBW25-INTG

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 49 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	7
HMG CoA Synthesis	4
Isoleucine degradation	4
Valine degradation	4
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	3
Terminal cytochrome C oxidases	3
Lysine degradation	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 cytochrome c oxidases	1
Biotin biosynthesis	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Entner-Doudoroff Pathway	1
Folate Biosynthesis	1
Glutathione: Redox cycle	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methylcitrate cycle	1
Methylglyoxal Metabolism	1
Propionate-CoA to Succinate Module	1
Protein degradation	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Queuosine-Archaeosine Biosynthesis	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine degradation
• Urea cycle and metabolism of amino groups
• Lysine degradation
• Arginine and proline metabolism
• Tryptophan metabolism
• Propanoate metabolism
• Butanoate metabolism
• Fatty acid metabolism
• beta-Alanine metabolism
• Benzoate degradation via CoA ligation
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Synthesis and degradation of ketone bodies
• Oxidative phosphorylation
• Glutamate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Histidine metabolism
• Phenylalanine metabolism
• Cyanoamino acid metabolism
• Glutathione metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Styrene degradation
• Folate biosynthesis
• Limonene and pinene degradation
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
cis-cyclopropane fatty acid (CFA) biosynthesis	1	1	1
L-glutamine degradation I	1	1	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	2
L-leucine degradation I	6	5	4
indole-3-acetate biosynthesis III (bacteria)	2	2	1
acrylonitrile degradation I	2	2	1
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
choline degradation I	2	2	1
4-aminobenzoate biosynthesis I	2	2	1
phenylethylamine degradation I	2	2	1
4-aminobutanoate degradation II	2	2	1
4-aminobutanoate degradation III	2	2	1
indole-3-acetate biosynthesis IV (bacteria)	2	2	1
4-aminobutanoate degradation I	2	2	1
L-glutamate biosynthesis I	2	2	1
putrescine degradation V	2	2	1
β-alanine biosynthesis IV	2	1	1
phenylethylamine degradation II	2	1	1
phenylethanol degradation	2	1	1
putrescine degradation I	2	1	1
sterculate biosynthesis	2	1	1
mevalonate degradation	2	1	1
β-alanine biosynthesis I	2	1	1
arsenite to oxygen electron transfer	2	1	1
ethylene glycol degradation	2	1	1
superpathway of 4-aminobutanoate degradation	3	3	1
putrescine biosynthesis II	3	3	1
ammonia assimilation cycle III	3	3	1
ethanol degradation II	3	3	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
choline-O-sulfate degradation	3	3	1
ethanol degradation IV	3	3	1
hypotaurine degradation	3	2	1
superpathway of acrylonitrile degradation	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
ethanol degradation III	3	2	1
putrescine degradation IV	3	2	1
glutathione-peroxide redox reactions	3	2	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
glycine betaine biosynthesis III (plants)	3	2	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
histamine degradation	3	1	1
dimethylsulfoniopropanoate biosynthesis I (Wollastonia)	3	1	1
styrene degradation	3	1	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
putrescine degradation III	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
GABA shunt II	4	3	1
phytol degradation	4	3	1
choline degradation IV	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
GABA shunt I	4	2	1
D-arabinose degradation II	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
dimethylsulfoniopropanoate biosynthesis II (Spartina)	4	1	1
L-lysine degradation IV	5	5	1
2-methylcitrate cycle I	5	5	1
octane oxidation	5	4	1
mitochondrial NADPH production (yeast)	5	4	1
ketogenesis	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
ferrichrome A biosynthesis	5	2	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	2
2-methylcitrate cycle II	6	5	1
L-lysine degradation X	6	5	1
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
L-glutamate and L-glutamine 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
L-citrulline biosynthesis	8	8	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
superpathway of polyamine biosynthesis II	8	6	1
aromatic biogenic amine degradation (bacteria)	8	4	1
superpathway of ornithine degradation	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
cis-geranyl-CoA degradation	9	4	1
chloramphenicol biosynthesis	9	1	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
peptidoglycan recycling II	10	8	1
superpathway of phenylethylamine degradation	11	6	1
superpathway of candicidin biosynthesis	11	4	1
superpathway of L-citrulline metabolism	12	10	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
indole-3-acetate biosynthesis II	12	5	1
peptidoglycan recycling I	14	11	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
superpathway of chorismate metabolism	59	42	1
mycolate biosynthesis	205	20	3
superpathway of mycolate biosynthesis	239	21	3