Experiment set10S247 for Phocaeicola vulgatus CL09T03C04

Compare to:

L-Serine nitrogen source; Varel_Bryant_medium_Glucose_DTT_NaS_noNitrogen

Group: nitrogen source
Media: Varel_Bryant_medium_Glucose_DTT_NaS_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, 3 mM Sodium sulfide nonahydrate, 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 6 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
Conserved gene cluster possibly involved in RNA metabolism 1
Cysteine Biosynthesis 1
Glutamine synthetases 1
Methionine Biosynthesis 1
Peptidoglycan Biosynthesis 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
L-cysteine biosynthesis I 2 2 1
ammonia assimilation cycle II 2 1 1
L-glutamate and L-glutamine biosynthesis 7 5 3
superpathway of ammonia assimilation (plants) 3 2 1
L-aspartate degradation II (aerobic) 3 2 1
L-aspartate degradation III (anaerobic) 3 2 1
L-cysteine biosynthesis VII (from S-sulfo-L-cysteine) 4 2 1
N-3-oxalyl-L-2,3-diaminopropanoate biosynthesis 4 1 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 1 1
L-asparagine biosynthesis III (tRNA-dependent) 4 1 1
seleno-amino acid biosynthesis (plants) 5 2 1
D-cycloserine biosynthesis 6 1 1
L-cysteine biosynthesis VI (reverse transsulfuration) 7 4 1
L-citrulline biosynthesis 8 7 1
superpathway of sulfate assimilation and cysteine biosynthesis 9 7 1
L-arginine biosynthesis II (acetyl cycle) 10 9 1
superpathway of L-citrulline metabolism 12 9 1
superpathway of seleno-compound metabolism 19 5 1