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 4 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 2
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-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
ammonia assimilation cycle I 2 2 1
NADH to cytochrome bo oxidase electron transfer I 2 1 1
NADH to cytochrome bd oxidase electron transfer I 2 1 1
ammonia assimilation cycle II 2 1 1
L-glutamate and L-glutamine biosynthesis 7 5 3
aerobic respiration III (alternative oxidase pathway) 3 2 1
L-aspartate degradation III (anaerobic) 3 2 1
L-aspartate degradation II (aerobic) 3 2 1
superpathway of ammonia assimilation (plants) 3 2 1
aerobic respiration I (cytochrome c) 4 2 1
L-asparagine biosynthesis III (tRNA-dependent) 4 1 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 1 1
NAD(P)/NADPH interconversion 6 2 1
Fe(II) oxidation 6 1 1
L-citrulline biosynthesis 8 7 1
L-arginine biosynthesis II (acetyl cycle) 10 9 1
superpathway of L-citrulline metabolism 12 9 1