Experiment set10IT050 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 19 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
Glycine and Serine Utilization	2
Peptidoglycan Biosynthesis	2
Entner-Doudoroff Pathway	1
Folate Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	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
Synechocystis experimental	1
Triacylglycerol metabolism	1
Type IV pilus	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Peptidoglycan biosynthesis
• Glycine, serine and threonine metabolism
• Urea cycle and metabolism of amino groups
• Lysine degradation
• Arginine and proline metabolism
• Tryptophan metabolism
• Glycerolipid metabolism
• Limonene and pinene degradation
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Histidine metabolism
• beta-Alanine metabolism
• Cyanoamino acid metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Biotin metabolism
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
glycine biosynthesis I	1	1	1
glycine betaine degradation I	8	6	6
glycine degradation	3	3	2
D-serine degradation	3	3	2
L-cysteine degradation II	3	2	2
L-tryptophan degradation II (via pyruvate)	3	2	2
glycine betaine degradation III	7	4	4
putrescine degradation V	2	2	1
ethylene glycol degradation	2	1	1
putrescine 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 II	3	3	1
ethanol degradation IV	3	3	1
L-methionine biosynthesis II	6	5	2
hypotaurine degradation	3	2	1
ethanol degradation III	3	2	1
putrescine degradation IV	3	2	1
histamine degradation	3	1	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
phytol degradation	4	3	1
L-mimosine degradation	8	4	2
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
creatinine degradation I	4	2	1
glutathione-mediated detoxification I	8	3	2
peptidoglycan maturation (meso-diaminopimelate containing)	12	3	3
D-arabinose degradation II	4	1	1
putrescine degradation III	4	1	1
glycine betaine degradation II (mammalian)	4	1	1
folate polyglutamylation	5	4	1
mitochondrial NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
creatinine degradation II	5	2	1
dopamine degradation	5	1	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	3
peptidoglycan biosynthesis II (staphylococci)	17	12	3
purine nucleobases degradation II (anaerobic)	24	14	4
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
superpathway of glycol metabolism and degradation	7	4	1
serotonin degradation	7	3	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
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
aromatic biogenic amine degradation (bacteria)	8	1	1
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
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
photorespiration II	10	6	1
folate transformations II (plants)	11	8	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	11	1
folate transformations I	13	8	1
superpathway of L-arginine and L-ornithine degradation	13	8	1
formaldehyde assimilation I (serine pathway)	13	5	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
superpathway of pentose and pentitol degradation	42	16	1