L-Serine nitrogen source; Varel_Bryant_medium_Glucose_DTT_noNitrogen
Group:
nitrogen source
Media:
Varel_Bryant_medium_Glucose_DTT_noNitrogen +
L-Serine (10 mM)
Culturing: Btheta_ML6a, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya Tripathi on
3/20/24
Media components: 15 uM
Hemin, 134 uM
L-Methionine, 15 uM
Iron (II) sulfate heptahydrate, 3 mM
Dithiothreitol, 23.8 mM
Sodium bicarbonate, 20 mM
D-Glucose, Mineral 3B solution minus Nitrogen
(6.6 mM Potassium phosphate monobasic, 15.4 mM Sodium Chloride, 98 uM Magnesium chloride hexahydrate, 176.5 uM Calcium chloride dihydrate, 4.2 uM Cobalt chloride hexahydrate, 50.5 uM Manganese (II) chloride tetrahydrate, 1.75 mM Sodium sulfate)
Specific Phenotypes
For 7 genes in this experiment
For nitrogen source L-Serine in Bacteroides thetaiotaomicron VPI-5482
For nitrogen source L-Serine across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|
| L-serine degradation | 3 | 3 | 3 |
| long-chain fatty acid activation | 1 | 1 | 1 |
| L-tryptophan degradation II (via pyruvate) | 3 | 3 | 2 |
| L-cysteine degradation II | 3 | 2 | 2 |
| D-serine degradation | 3 | 2 | 2 |
| sedoheptulose bisphosphate bypass | 2 | 2 | 1 |
| L-cysteine biosynthesis I | 2 | 2 | 1 |
| linoleate biosynthesis II (animals) | 2 | 1 | 1 |
| γ-linolenate biosynthesis II (animals) | 2 | 1 | 1 |
| glycine betaine degradation III | 7 | 4 | 3 |
| felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis | 5 | 2 | 2 |
| glycine betaine degradation I | 8 | 4 | 3 |
| glycine degradation | 3 | 2 | 1 |
| L-methionine biosynthesis II | 6 | 3 | 2 |
| 3-methyl-branched fatty acid α-oxidation | 6 | 2 | 2 |
| oleate biosynthesis I (plants) | 3 | 1 | 1 |
| alkane biosynthesis II | 3 | 1 | 1 |
| L-mimosine degradation | 8 | 4 | 2 |
| D-galactosamine and N-acetyl-D-galactosamine degradation | 4 | 2 | 1 |
| phytol degradation | 4 | 2 | 1 |
| glutathione-mediated detoxification I | 8 | 2 | 2 |
| phosphatidylcholine acyl editing | 4 | 1 | 1 |
| long chain fatty acid ester synthesis (engineered) | 4 | 1 | 1 |
| wax esters biosynthesis II | 4 | 1 | 1 |
| sporopollenin precursors biosynthesis | 18 | 4 | 4 |
| N-acetyl-D-galactosamine degradation | 5 | 2 | 1 |
| seleno-amino acid biosynthesis (plants) | 5 | 2 | 1 |
| galactitol degradation | 5 | 2 | 1 |
| sphingosine and sphingosine-1-phosphate metabolism | 10 | 2 | 2 |
| octane oxidation | 5 | 1 | 1 |
| lactose degradation I | 5 | 1 | 1 |
| stearate biosynthesis II (bacteria and plants) | 6 | 5 | 1 |
| stearate biosynthesis IV | 6 | 4 | 1 |
| fatty acid salvage | 6 | 2 | 1 |
| stearate biosynthesis I (animals) | 6 | 1 | 1 |
| 6-gingerol analog biosynthesis (engineered) | 6 | 1 | 1 |
| icosapentaenoate biosynthesis II (6-desaturase, mammals) | 7 | 1 | 1 |
| capsaicin biosynthesis | 7 | 1 | 1 |
| ceramide degradation by α-oxidation | 7 | 1 | 1 |
| icosapentaenoate biosynthesis III (8-desaturase, mammals) | 7 | 1 | 1 |
| arachidonate biosynthesis III (6-desaturase, mammals) | 7 | 1 | 1 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis II | 15 | 12 | 2 |
| purine nucleobases degradation II (anaerobic) | 24 | 12 | 3 |
| ceramide and sphingolipid recycling and degradation (yeast) | 16 | 2 | 2 |
| superpathway of sulfate assimilation and cysteine biosynthesis | 9 | 7 | 1 |
| formaldehyde assimilation II (assimilatory RuMP Cycle) | 9 | 7 | 1 |
| superpathway of hexitol degradation (bacteria) | 18 | 12 | 2 |
| 1,3-propanediol biosynthesis (engineered) | 9 | 6 | 1 |
| glycolysis IV | 10 | 9 | 1 |
| suberin monomers biosynthesis | 20 | 2 | 2 |
| superpathway of fatty acid biosynthesis II (plant) | 43 | 37 | 4 |
| glycolysis III (from glucose) | 11 | 11 | 1 |
| glycolysis II (from fructose 6-phosphate) | 11 | 10 | 1 |
| homolactic fermentation | 12 | 11 | 1 |
| glycolysis I (from glucose 6-phosphate) | 13 | 11 | 1 |
| palmitate biosynthesis II (type II fatty acid synthase) | 31 | 29 | 2 |
| cutin biosynthesis | 16 | 1 | 1 |
| superpathway of glycolysis and the Entner-Doudoroff pathway | 17 | 14 | 1 |
| hexitol fermentation to lactate, formate, ethanol and acetate | 19 | 14 | 1 |
| superpathway of anaerobic sucrose degradation | 19 | 14 | 1 |
| superpathway of seleno-compound metabolism | 19 | 5 | 1 |
| superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle | 22 | 17 | 1 |
| superpathway of N-acetylneuraminate degradation | 22 | 16 | 1 |
| superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass | 26 | 18 | 1 |
| superpathway of fatty acids biosynthesis (E. coli) | 53 | 47 | 2 |
| palmitate biosynthesis III | 29 | 21 | 1 |
| oleate β-oxidation | 35 | 4 | 1 |