Experiment set3S383 for Phocaeicola dorei CL03T12C01

L-Asparagine nitrogen source; Varel_Bryant_medium_Glucose_lowCys_noNitrogen

Group: nitrogen source
Media: Varel_Bryant_medium_Glucose_lowCys_noNitrogen + L-Asparagine (10 mM)
Culturing: Bdorei_CL03T12C01_ML9, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya Tripathi on 20-Mar-24
Media components: 15 uM Hemin, 134 uM L-Methionine, 15 uM Iron (II) sulfate heptahydrate, 3 mM L-Cysteine, 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 23 genes in this experiment

For nitrogen source L-Asparagine in Phocaeicola dorei CL03T12C01

For nitrogen source L-Asparagine across organisms

SEED Subsystems

Subsystem	#Specific
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Bacterial Cell Division	1
Glycine and Serine Utilization	1
Heat shock dnaK gene cluster extended	1
High affinity phosphate transporter and control of PHO regulon	1
Peptidyl-prolyl cis-trans isomerase	1
Phosphate metabolism	1
Potassium homeostasis	1
Serine Biosynthesis	1
Sialic Acid Metabolism	1
UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Alanine and aspartate metabolism
• Nitrogen metabolism
• Ubiquinone and menaquinone biosynthesis
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Cyanoamino acid metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Peptidoglycan biosynthesis
• Naphthalene and anthracene degradation
• Biotin metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-asparagine degradation I	1	1	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	4	2
L-glutamate degradation II	2	2	1
L-serine biosynthesis I	3	3	1
L-aspartate degradation II (aerobic)	3	2	1
L-aspartate degradation III (anaerobic)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
UDP-N-acetyl-D-glucosamine biosynthesis I	5	3	1
N-(1-deoxy-D-fructos-1-yl)-L-asparagine degradation	5	2	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	3	1
UDP-N-acetyl-D-galactosamine biosynthesis III	6	2	1
L-canavanine degradation II	6	1	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	7	1
chitin biosynthesis	9	5	1
CMP-legionaminate biosynthesis I	10	2	1
O-antigen building blocks biosynthesis (E. coli)	11	9	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	4	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	11	1