Experiment set3IT067 for Pseudomonas sp. RS175

Vanillic Acid carbon source 2.5 mM

Group: carbon source
Media: MME_noCarbon + Vanillic Acid (2.5 mM), pH=7
Culturing: Pseudomonas_RS175_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Joshua Elmore on 1-July-22
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium 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 30 genes in this experiment

For carbon source Vanillic Acid in Pseudomonas sp. RS175

For carbon source Vanillic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Bacterial Chemotaxis	3
ABC transporter oligopeptide (TC 3.A.1.5.1)	2
Phosphate metabolism	2
Terminal cytochrome C oxidases	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Entner-Doudoroff Pathway	1
Flagellar motility	1
Formate hydrogenase	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
High affinity phosphate transporter and control of PHO regulon	1
Histidine Degradation	1
Lipid A modifications	1
Methylglyoxal Metabolism	1
One-carbon metabolism by tetrahydropterines	1
Photorespiration (oxidative C2 cycle)	1
Proteasome bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Universal stress protein family	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Histidine metabolism
• Glyoxylate and dicarboxylate metabolism
• One carbon pool by folate
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Oxidative phosphorylation
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Methane metabolism
• Limonene and pinene degradation
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
formate oxidation to CO2	1	1	1
putrescine degradation I	2	2	1
putrescine degradation V	2	2	1
phenylethanol degradation	2	2	1
phenylethylamine degradation I	2	2	1
arsenite to oxygen electron transfer	2	1	1
ethylene glycol degradation	2	1	1
phenylethylamine degradation II	2	1	1
glycine cleavage	3	3	1
glycine degradation	3	3	1
glycine biosynthesis II	3	3	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
hypotaurine degradation	3	2	1
putrescine degradation IV	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
ethanol degradation III	3	2	1
histamine degradation	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
styrene degradation	3	1	1
L-histidine degradation I	4	4	1
formaldehyde oxidation VII (THF pathway)	4	4	1
aerobic respiration I (cytochrome c)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
phytol degradation	4	3	1
putrescine degradation III	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
D-arabinose degradation II	4	2	1
oxalate degradation VI	4	1	1
L-histidine degradation II	5	5	1
mitochondrial NADPH production (yeast)	5	4	1
octane oxidation	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
oxalate degradation III	5	1	1
L-histidine degradation III	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
Fe(II) oxidation	6	3	1
alkane oxidation	6	1	1
folate transformations I	13	9	2
noradrenaline and adrenaline degradation	13	8	2
superpathway of glycol metabolism and degradation	7	6	1
serotonin degradation	7	4	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
purine nucleobases degradation I (anaerobic)	15	6	2
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
L-histidine degradation VI	8	7	1
superpathway of ornithine degradation	8	6	1
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
folate transformations III (E. coli)	9	9	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
photorespiration III	9	5	1
photorespiration I	9	5	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
photorespiration II	10	6	1
folate transformations II (plants)	11	10	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
superpathway of phenylethylamine degradation	11	6	1
purine nucleobases degradation II (anaerobic)	24	16	2
superpathway of C1 compounds oxidation to CO2	12	5	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of pentose and pentitol degradation	42	14	1