Experiment set10S244 for Phocaeicola vulgatus CL09T03C04

L-Asparagine nitrogen source; Varel_Bryant_medium_Glucose_DTT_noNitrogen

Group: nitrogen source
Media: Varel_Bryant_medium_Glucose_DTT_noNitrogen + L-Asparagine (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 6 genes in this experiment

For nitrogen source L-Asparagine in Phocaeicola vulgatus CL09T03C04

For nitrogen source L-Asparagine across organisms

SEED Subsystems

Subsystem	#Specific
Conserved gene cluster possibly involved in RNA metabolism	1
Cysteine Biosynthesis	1
Methionine Biosynthesis	1
Serine-glyoxylate cycle	1
TCA Cycle	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Citrate cycle (TCA cycle)
• Cysteine metabolism
• Glyoxylate and dicarboxylate metabolism
• Sulfur metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-cysteine biosynthesis I	2	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
seleno-amino acid biosynthesis (plants)	5	2	1
glyoxylate cycle	6	4	1
D-cycloserine biosynthesis	6	1	1
L-cysteine biosynthesis VI (reverse transsulfuration)	7	4	1
partial TCA cycle (obligate autotrophs)	8	5	1
nitrogen remobilization from senescing leaves	8	5	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	7	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
TCA cycle VI (Helicobacter)	9	6	1
TCA cycle VII (acetate-producers)	9	6	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	6	1
TCA cycle II (plants and fungi)	9	6	1
TCA cycle III (animals)	10	7	1
TCA cycle I (prokaryotic)	10	7	1
superpathway of glyoxylate bypass and TCA	12	7	1
superpathway of glyoxylate cycle and fatty acid degradation	14	6	1
mixed acid fermentation	16	12	1
methylaspartate cycle	19	10	1
superpathway of seleno-compound metabolism	19	5	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	16	1
ethene biosynthesis V (engineered)	25	15	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	19	1