Experiment set10S242 for Phocaeicola vulgatus CL09T03C04

Compare to:

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: Bvulgatus_CL09T03C04_ML5, 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 8 genes in this experiment

For nitrogen source L-Serine in Phocaeicola vulgatus CL09T03C04

For nitrogen source L-Serine across organisms

SEED Subsystems

Subsystem #Specific
Ammonia assimilation 3
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 2
Carboxysome 1
Glutamine synthetases 1
Peptidoglycan Biosynthesis 1
Respiratory dehydrogenases 1 1

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
ammonia assimilation cycle III 3 3 3
L-serine degradation 3 3 3
L-glutamate biosynthesis I 2 2 2
L-glutamine biosynthesis I 1 1 1
L-glutamine degradation II 1 1 1
L-glutamine degradation I 1 1 1
L-tryptophan degradation II (via pyruvate) 3 2 2
L-cysteine degradation II 3 2 2
D-serine degradation 3 2 2
ammonia assimilation cycle I 2 2 1
ammonia assimilation cycle II 2 1 1
NADH to cytochrome bd oxidase electron transfer I 2 1 1
NADH to cytochrome bo oxidase electron transfer I 2 1 1
L-glutamate and L-glutamine biosynthesis 7 5 3
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 3 1
aerobic respiration III (alternative oxidase pathway) 3 2 1
L-aspartate degradation II (aerobic) 3 2 1
superpathway of ammonia assimilation (plants) 3 2 1
L-aspartate degradation III (anaerobic) 3 2 1
L-methionine biosynthesis II 6 3 2
L-mimosine degradation 8 4 2
aerobic respiration I (cytochrome c) 4 2 1
glutathione-mediated detoxification I 8 2 2
glutaminyl-tRNAgln biosynthesis via transamidation 4 1 1
L-asparagine biosynthesis III (tRNA-dependent) 4 1 1
NAD(P)/NADPH interconversion 6 2 1
Fe(II) oxidation 6 1 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 12 2
L-citrulline biosynthesis 8 7 1
purine nucleobases degradation II (anaerobic) 24 13 3
L-arginine biosynthesis II (acetyl cycle) 10 9 1
superpathway of L-citrulline metabolism 12 9 1