Experiment set10S264 for Phocaeicola vulgatus CL09T03C04

Ammonium chloride nitrogen source; Varel_Bryant_medium_Glucose_DTT_NaS_noNitrogen

Group: nitrogen source
Media: Varel_Bryant_medium_Glucose_DTT_NaS_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, 134 uM L-Methionine, 15 uM Iron (II) sulfate heptahydrate, 3 mM Dithiothreitol, 23.8 mM Sodium bicarbonate, 20 mM D-Glucose, 3 mM Sodium sulfide nonahydrate, 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 3 genes in this experiment

For nitrogen source Ammonium chloride in Phocaeicola vulgatus CL09T03C04

For nitrogen source Ammonium chloride across organisms

SEED Subsystems

Subsystem	#Specific
Entner-Doudoroff Pathway	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Serine-glyoxylate cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
gallate biosynthesis	3	2	1
quinate degradation II	3	1	1
quinate degradation I	3	1	1
chorismate biosynthesis from 3-dehydroquinate	5	5	1
chorismate biosynthesis I	7	7	1
Entner-Doudoroff pathway I	9	8	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	6	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
glycolysis IV	10	9	1
Rubisco shunt	10	8	1
glycolysis V (Pyrococcus)	10	6	1
glycolysis III (from glucose)	11	11	1
glycolysis II (from fructose 6-phosphate)	11	10	1
glycolysis VI (from fructose)	11	8	1
homolactic fermentation	12	11	1
gluconeogenesis III	12	10	1
chorismate biosynthesis II (archaea)	12	8	1
superpathway of L-tryptophan biosynthesis	13	13	1
gluconeogenesis I	13	11	1
glycolysis I (from glucose 6-phosphate)	13	11	1
formaldehyde assimilation I (serine pathway)	13	7	1
Bifidobacterium shunt	15	12	1
glycerol degradation to butanol	16	8	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of aromatic amino acid biosynthesis	18	18	1
heterolactic fermentation	18	14	1
superpathway of hexitol degradation (bacteria)	18	12	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	8	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of anaerobic sucrose degradation	19	14	1
superpathway of N-acetylneuraminate degradation	22	17	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	16	1
ethene biosynthesis V (engineered)	25	15	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	19	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	13	1
1-butanol autotrophic biosynthesis (engineered)	27	14	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	3	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	3	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	18	1
superpathway of chorismate metabolism	59	38	1