Experiment set10S259 for Phocaeicola vulgatus CL09T03C04

Compare to:

Ammonium chloride nitrogen source; Varel_Bryant_medium_Glucose_lowCys_noNitrogen

Group: nitrogen source
Media: Varel_Bryant_medium_Glucose_lowCys_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 L-Cysteine, 23.8 mM Sodium bicarbonate, 20 mM D-Glucose, 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
Autoinducer 2 (AI-2) transport and processing (lsrACDBFGE operon) 1
D-ribose utilization 1
Deoxyribose and Deoxynucleoside Catabolism 1
Entner-Doudoroff Pathway 1
Glycolysis and Gluconeogenesis 1
Glycolysis and Gluconeogenesis, including Archaeal enzymes 1
Methionine Biosynthesis 1
Methionine Degradation 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:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
ribose phosphorylation 2 1 1
2-deoxy-D-ribose degradation I 3 2 1
gallate biosynthesis 3 2 1
quinate degradation II 3 1 1
quinate degradation I 3 1 1
S-adenosyl-L-methionine salvage I 4 3 1
chorismate biosynthesis from 3-dehydroquinate 5 5 1
autoinducer AI-2 biosynthesis I 5 4 1
autoinducer AI-2 biosynthesis II (Vibrio) 6 5 1
chorismate biosynthesis I 7 7 1
L-cysteine biosynthesis VI (reverse transsulfuration) 7 4 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-phenylalanine biosynthesis 10 10 1
superpathway of L-tyrosine 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
superpathway of anaerobic sucrose degradation 19 14 1
hexitol fermentation to lactate, formate, ethanol and acetate 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