Experiment set10S257 for Phocaeicola vulgatus CL09T03C04

L-Glutamine 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-Glutamine (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 37 genes in this experiment

For nitrogen source L-Glutamine in Phocaeicola vulgatus CL09T03C04

For nitrogen source L-Glutamine across organisms

SEED Subsystems

Subsystem	#Specific
LOS core oligosaccharide biosynthesis	2
Folate Biosynthesis	1
KDO2-Lipid A biosynthesis	1
Lactose utilization	1
Methionine Biosynthesis	1
N-linked Glycosylation in Bacteria	1
Oxidative stress	1
Phosphate metabolism	1
Protein chaperones	1
Teichoic and lipoteichoic acids biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fructose and mannose metabolism
• Fatty acid metabolism
• Methionine metabolism
• Cysteine metabolism
• gamma-Hexachlorocyclohexane degradation
• Selenoamino acid metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Folate biosynthesis
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Nitrogen metabolism
• Sulfur metabolism
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis
• Biosynthesis of plant hormones

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
diethylphosphate degradation	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
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
wax esters biosynthesis II	4	1	1
phosphatidylcholine acyl editing	4	1	1
sporopollenin precursors biosynthesis	18	4	4
sphingosine and sphingosine-1-phosphate metabolism	10	2	2
octane oxidation	5	1	1
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
Arg/N-end rule pathway (eukaryotic)	14	6	2
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
ceramide degradation by α-oxidation	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	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
poly(glycerol phosphate) wall teichoic acid biosynthesis	11	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