Experiment set10S253 for Phocaeicola vulgatus CL09T03C04

Compare to:

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 19 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 2
ATP-dependent RNA helicases, bacterial 1
Coenzyme B12 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:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
long-chain fatty acid activation 1 1 1
linoleate biosynthesis II (animals) 2 1 1
γ-linolenate biosynthesis II (animals) 2 1 1
L-homocysteine biosynthesis 2 1 1
superpathway of L-cysteine biosynthesis (fungi) 6 2 2
3-methyl-branched fatty acid α-oxidation 6 2 2
oleate biosynthesis I (plants) 3 1 1
alkane biosynthesis II 3 1 1
L-methionine biosynthesis III 4 2 1
phytol degradation 4 2 1
homocysteine and cysteine interconversion 4 1 1
long chain fatty acid ester synthesis (engineered) 4 1 1
phosphatidylcholine acyl editing 4 1 1
wax esters biosynthesis II 4 1 1
sporopollenin precursors biosynthesis 18 4 4
L-methionine biosynthesis I 5 3 1
superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) 10 4 2
sphingosine and sphingosine-1-phosphate metabolism 10 2 2
octane oxidation 5 1 1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III 5 1 1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II 5 1 1
stearate biosynthesis II (bacteria and plants) 6 5 1
stearate biosynthesis IV 6 4 1
L-methionine biosynthesis II 6 3 1
fatty acid salvage 6 2 1
stearate biosynthesis I (animals) 6 1 1
6-gingerol analog biosynthesis (engineered) 6 1 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
capsaicin biosynthesis 7 1 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
ceramide degradation by α-oxidation 7 1 1
superpathway of L-homoserine and L-methionine biosynthesis 8 6 1
ceramide and sphingolipid recycling and degradation (yeast) 16 2 2
superpathway of S-adenosyl-L-methionine biosynthesis 9 7 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 7 1
suberin monomers biosynthesis 20 2 2
superpathway of fatty acid biosynthesis II (plant) 43 37 4
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 8 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 12 1
palmitate biosynthesis II (type II fatty acid synthase) 31 29 2
cutin biosynthesis 16 1 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 12 1
aspartate superpathway 25 19 1
superpathway of fatty acids biosynthesis (E. coli) 53 47 2
palmitate biosynthesis III 29 21 1
oleate β-oxidation 35 4 1