Experiment set1IT079 for Pseudomonas sp. RS175

D-Glucosamine Hydrochloride carbon 10 mM

Group: carbon source
Media: MME_noCarbon + D-Glucosamine Hydrochloride (10 mM), pH=7
Culturing: Pseudomonas_RS175_ML2, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on 1-Jul-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 16 genes in this experiment

For carbon source D-Glucosamine Hydrochloride in Pseudomonas sp. RS175

For carbon source D-Glucosamine Hydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
D-gluconate and ketogluconates metabolism	1
Ethanolamine utilization	1
Fermentations: Lactate	1
Fermentations: Mixed acid	1
MLST	1
Phage capsid proteins	1
Propanediol utilization	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Threonine anaerobic catabolism gene cluster	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Taurine and hypotaurine metabolism
• Pyruvate metabolism
• Propanoate metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-serine degradation	3	3	3
L-serine degradation	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
L-cysteine degradation II	3	2	2
acetate and ATP formation from acetyl-CoA I	2	2	1
sulfoacetaldehyde degradation I	2	1	1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
pyruvate fermentation to acetate II	3	3	1
superpathway of acetate utilization and formation	3	3	1
L-methionine biosynthesis II	6	5	2
pyruvate fermentation to acetate VII	3	2	1
pyruvate fermentation to acetate I	3	2	1
pyruvate fermentation to acetate IV	3	2	1
glycine betaine degradation III	7	7	2
pyruvate fermentation to acetate and (S)-lactate I	4	4	1
glycine betaine degradation I	8	6	2
pyruvate fermentation to acetate and lactate II	4	3	1
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	3	2
sulfolactate degradation II	4	1	1
ethanolamine utilization	5	5	1
chorismate biosynthesis from 3-dehydroquinate	5	5	1
acetylene degradation (anaerobic)	5	4	1
(S)-propane-1,2-diol degradation	5	2	1
L-threonine degradation I	6	4	1
superpathway of sulfolactate degradation	6	3	1
methanogenesis from acetate	6	2	1
superpathway of taurine degradation	6	2	1
chorismate biosynthesis I	7	7	1
acetyl-CoA fermentation to butanoate	7	3	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
purine nucleobases degradation II (anaerobic)	24	16	3
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	3	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	1
superpathway of L-alanine fermentation (Stickland reaction)	9	4	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
L-lysine fermentation to acetate and butanoate	10	3	1
gallate degradation III (anaerobic)	11	3	1
chorismate biosynthesis II (archaea)	12	8	1
superpathway of L-tryptophan biosynthesis	13	13	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	1
mixed acid fermentation	16	12	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
superpathway of aromatic amino acid biosynthesis	18	18	1
heterolactic fermentation	18	16	1
superpathway of L-threonine metabolism	18	13	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of methanogenesis	21	2	1
superpathway of N-acetylneuraminate degradation	22	15	1
superpathway of L-lysine degradation	43	18	1
superpathway of chorismate metabolism	59	43	1