Experiment set10S265 for Phocaeicola vulgatus CL09T03C04

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Ammonium chloride nitrogen source; Varel_Bryant_medium_Glucose_noMET_DTT_NaS_B12_noNitrogen

Group: nitrogen source
Media: Varel_Bryant_medium_Glucose_noMET_DTT_NaS_B12_noNitrogen + Ammonium chloride (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 5 genes in this experiment

For nitrogen source Ammonium chloride in Phocaeicola vulgatus CL09T03C04

For nitrogen source Ammonium chloride across organisms

SEED Subsystems

Subsystem #Specific
Branched-Chain Amino Acid Biosynthesis 1
Threonine degradation 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
L-methionine degradation II 3 2 2
L-threonine degradation I 6 6 3
L-threonine degradation V 2 2 1
γ-linolenate biosynthesis II (animals) 2 1 1
linoleate biosynthesis II (animals) 2 1 1
L-isoleucine biosynthesis I (from threonine) 7 7 3
3-methyl-branched fatty acid α-oxidation 6 2 2
oleate biosynthesis I (plants) 3 1 1
alkane biosynthesis II 3 1 1
phytol degradation 4 2 1
long chain fatty acid ester synthesis (engineered) 4 1 1
phosphatidylcholine acyl editing 4 1 1
wax esters biosynthesis II 4 1 1
superpathway of L-isoleucine biosynthesis I 13 12 3
sporopollenin precursors biosynthesis 18 4 4
hypoglycin biosynthesis 14 3 3
sphingosine and sphingosine-1-phosphate metabolism 10 2 2
octane oxidation 5 1 1
superpathway of branched chain amino acid biosynthesis 17 17 3
superpathway of L-threonine metabolism 18 15 3
stearate biosynthesis II (bacteria and plants) 6 5 1
stearate biosynthesis IV 6 4 1
fatty acid salvage 6 2 1
stearate biosynthesis I (animals) 6 1 1
6-gingerol analog biosynthesis (engineered) 6 1 1
ceramide degradation by α-oxidation 7 1 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
capsaicin biosynthesis 7 1 1
ceramide and sphingolipid recycling and degradation (yeast) 16 2 2
suberin monomers biosynthesis 20 2 2
superpathway of fatty acid biosynthesis II (plant) 43 37 4
cyclosporin A biosynthesis 15 2 1
palmitate biosynthesis II (type II fatty acid synthase) 31 29 2
cutin biosynthesis 16 1 1
superpathway of fatty acids biosynthesis (E. coli) 53 47 2
palmitate biosynthesis III 29 21 1
oleate β-oxidation 35 4 1