Experiment set10IT051 for Agrobacterium fabrum C58

sarcosine carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + sarcosine (10 mM), pH=7
Culturing: Agro_ML11, 24-well plate, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 1/6/22
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 10 genes in this experiment

For carbon source sarcosine in Agrobacterium fabrum C58

For carbon source sarcosine across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	4
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Glycine and Serine Utilization	2
Entner-Doudoroff Pathway	1
Fermentations: Mixed acid	1
Folate Biosynthesis	1
Glycine Biosynthesis	1
Glycolate, glyoxylate interconversions	1
LMPTP YwlE cluster	1
Methylglyoxal Metabolism	1
Photorespiration (oxidative C2 cycle)	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Serine-glyoxylate cycle	1
Serine Biosynthesis	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
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Tryptophan metabolism
• 1- and 2-Methylnaphthalene degradation
• 3-Chloroacrylic acid degradation
• Limonene and pinene degradation
• Ascorbate and aldarate metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• beta-Alanine metabolism
• Cyanoamino acid metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Retinol metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
acetaldehyde biosynthesis I	1	1	1
glycine biosynthesis I	1	1	1
glycine betaine degradation I	8	6	6
glycine degradation	3	3	2
D-serine degradation	3	3	2
ethanol degradation II	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
L-cysteine degradation II	3	2	2
glycine betaine degradation III	7	4	4
putrescine degradation V	2	2	1
phytol degradation	4	3	2
putrescine degradation I	2	1	1
ethylene glycol degradation	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation I	2	1	1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
dTMP de novo biosynthesis (mitochondrial)	3	3	1
ethanol degradation IV	3	3	1
L-methionine biosynthesis II	6	5	2
hypotaurine degradation	3	2	1
putrescine degradation IV	3	2	1
ethanol degradation III	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
histamine degradation	3	1	1
pyruvate fermentation to ethanol I	3	1	1
L-methionine degradation III	3	1	1
pyruvate fermentation to ethanol III	3	1	1
noradrenaline and adrenaline degradation	13	4	4
serotonin degradation	7	3	2
superpathway of L-serine and glycine biosynthesis I	4	4	1
L-mimosine degradation	8	4	2
L-phenylalanine degradation III	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
L-tyrosine degradation III	4	2	1
creatinine degradation I	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
glutathione-mediated detoxification I	8	3	2
putrescine degradation III	4	1	1
glycine betaine degradation II (mammalian)	4	1	1
D-arabinose degradation II	4	1	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
salidroside biosynthesis	4	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
folate polyglutamylation	5	4	1
mitochondrial NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
creatinine degradation II	5	2	1
octane oxidation	5	2	1
phenylethanol biosynthesis	5	1	1
acetylene degradation (anaerobic)	5	1	1
ethanolamine utilization	5	1	1
(S)-propane-1,2-diol degradation	5	1	1
dopamine degradation	5	1	1
purine nucleobases degradation II (anaerobic)	24	14	4
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
3-methylbutanol biosynthesis (engineered)	7	6	1
superpathway of glycol metabolism and degradation	7	4	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
superpathway of ornithine degradation	8	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
aromatic biogenic amine degradation (bacteria)	8	1	1
folate transformations III (E. coli)	9	8	1
photorespiration I	9	6	1
photorespiration III	9	6	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	3	1
photorespiration II	10	6	1
folate transformations II (plants)	11	8	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	1
folate transformations I	13	8	1
superpathway of L-arginine and L-ornithine degradation	13	8	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
formaldehyde assimilation I (serine pathway)	13	5	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	9	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	5	1
heterolactic fermentation	18	12	1
superpathway of anaerobic sucrose degradation	19	13	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	10	1
superpathway of N-acetylneuraminate degradation	22	12	1
superpathway of pentose and pentitol degradation	42	16	1