Experiment set10S253 for Phocaeicola vulgatus CL09T03C04

L-Serine nitrogen source; Varel_Bryant_medium_Glucose_noMET_DTT_NaS_B12_noNitrogen

Group: nitrogen source
Media: Varel_Bryant_medium_Glucose_noMET_DTT_NaS_B12_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, 15 uM Iron (II) sulfate heptahydrate, 3 mM Dithiothreitol, 23.8 mM Sodium bicarbonate, 20 mM D-Glucose, 3 mM Sodium sulfide nonahydrate, 0.1 ng/L Cyanocobalamin, 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 22 genes in this experiment

For nitrogen source L-Serine in Phocaeicola vulgatus CL09T03C04

For nitrogen source L-Serine across organisms

SEED Subsystems

Subsystem	#Specific
Methionine Biosynthesis	4
ATP-dependent RNA helicases, bacterial	1
Coenzyme B12 biosynthesis	1
Conserved gene cluster possibly involved in RNA metabolism	1
Cysteine Biosynthesis	1
Na(+) H(+) antiporter	1
Potassium homeostasis	1
Queuosine-Archaeosine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Cysteine metabolism
• Methionine metabolism
• Sulfur metabolism
• Selenoamino acid metabolism
• Biosynthesis of plant hormones
• Nitrogen metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-cysteine biosynthesis I	2	2	1
L-homocysteine biosynthesis	2	1	1
superpathway of L-cysteine biosynthesis (fungi)	6	2	2
L-cysteine biosynthesis VII (from S-sulfo-L-cysteine)	4	2	1
L-methionine biosynthesis III	4	2	1
N-3-oxalyl-L-2,3-diaminopropanoate biosynthesis	4	1	1
homocysteine and cysteine interconversion	4	1	1
L-methionine biosynthesis I	5	3	1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae)	10	4	2
seleno-amino acid biosynthesis (plants)	5	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	1	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	1	1
L-methionine biosynthesis II	6	3	1
D-cycloserine biosynthesis	6	1	1
L-cysteine biosynthesis VI (reverse transsulfuration)	7	4	1
superpathway of L-homoserine and L-methionine biosynthesis	8	6	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	7	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	7	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	8	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	12	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	12	1
superpathway of seleno-compound metabolism	19	5	1
aspartate superpathway	25	19	1