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 9 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 |
|---|
| long-chain fatty acid activation | 1 | 1 | 1 |
| sedoheptulose bisphosphate bypass | 2 | 2 | 1 |
| L-cysteine biosynthesis I | 2 | 2 | 1 |
| glutathione degradation (DUG pathway) | 2 | 1 | 1 |
| γ-linolenate biosynthesis II (animals) | 2 | 1 | 1 |
| linoleate biosynthesis II (animals) | 2 | 1 | 1 |
| 3-methyl-branched fatty acid α-oxidation | 6 | 2 | 2 |
| oleate biosynthesis I (plants) | 3 | 1 | 1 |
| alkane biosynthesis II | 3 | 1 | 1 |
| D-galactosamine and N-acetyl-D-galactosamine degradation | 4 | 2 | 1 |
| phytol degradation | 4 | 2 | 1 |
| muropeptide degradation | 4 | 2 | 1 |
| phosphatidylcholine acyl editing | 4 | 1 | 1 |
| wax esters biosynthesis II | 4 | 1 | 1 |
| long chain fatty acid ester synthesis (engineered) | 4 | 1 | 1 |
| sporopollenin precursors biosynthesis | 18 | 4 | 4 |
| (S)-propane-1,2-diol degradation | 5 | 3 | 1 |
| N-acetyl-D-galactosamine degradation | 5 | 2 | 1 |
| galactitol degradation | 5 | 2 | 1 |
| seleno-amino acid biosynthesis (plants) | 5 | 2 | 1 |
| sphingosine and sphingosine-1-phosphate metabolism | 10 | 2 | 2 |
| lactose degradation I | 5 | 1 | 1 |
| octane oxidation | 5 | 1 | 1 |
| L-threonine degradation I | 6 | 5 | 1 |
| stearate biosynthesis II (bacteria and plants) | 6 | 5 | 1 |
| stearate biosynthesis IV | 6 | 4 | 1 |
| fatty acid salvage | 6 | 2 | 1 |
| γ-glutamyl cycle | 6 | 1 | 1 |
| stearate biosynthesis I (animals) | 6 | 1 | 1 |
| 6-gingerol analog biosynthesis (engineered) | 6 | 1 | 1 |
| pyruvate fermentation to butanoate | 7 | 3 | 1 |
| icosapentaenoate biosynthesis III (8-desaturase, mammals) | 7 | 1 | 1 |
| icosapentaenoate biosynthesis II (6-desaturase, mammals) | 7 | 1 | 1 |
| ceramide degradation by α-oxidation | 7 | 1 | 1 |
| arachidonate biosynthesis III (6-desaturase, mammals) | 7 | 1 | 1 |
| capsaicin biosynthesis | 7 | 1 | 1 |
| 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 |
| superpathway of Clostridium acetobutylicum acidogenic fermentation | 9 | 5 | 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 |
| L-glutamate degradation VII (to butanoate) | 12 | 4 | 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 |
| superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation | 17 | 6 | 1 |
| superpathway of L-threonine metabolism | 18 | 13 | 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 |