Experiment set2S417 for Phocaeicola vulgatus CL09T03C04

D-Glucose carbon source

Group: carbon source
Media: Varel_Bryant_medium + D-Glucose (20 mM)
Culturing: Bvulgatus_CL09T03C04_ML5, 24-well microplate; 1.2 mL volume, Anaerobic, at 34 (C), shaken=0 rpm
By: Surya Tripathi on 3-Jul-23
Media components: 15 uM Hemin, 134 uM L-Methionine, 15 uM Iron (II) sulfate heptahydrate, 8.25 mM L-Cysteine, 23.8 mM Sodium bicarbonate, Mineral 3B solution (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, 9.3 mM Ammonium chloride, 1.75 mM Sodium sulfate)

Specific Phenotypes

For 5 genes in this experiment

For carbon source D-Glucose in Phocaeicola vulgatus CL09T03C04

For carbon source D-Glucose across organisms

SEED Subsystems

Subsystem	#Specific
Entner-Doudoroff Pathway	1
Glycolysis and Gluconeogenesis	1
Pentose phosphate pathway	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Histidine metabolism
• beta-Alanine metabolism
• Glutathione metabolism
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Urea cycle and metabolism of amino groups
• Alanine and aspartate metabolism
• Arginine and proline metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pentose phosphate pathway (oxidative branch) I	3	3	1
cytosolic NADPH production (yeast)	5	3	1
formaldehyde oxidation I	6	3	1
L-lysine biosynthesis VI	7	7	1
pentose phosphate pathway	8	8	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	3	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	2
Entner-Doudoroff pathway I	9	8	1
L-lysine biosynthesis II	9	6	1
sucrose biosynthesis I (from photosynthesis)	9	6	1
L-lysine biosynthesis I	9	6	1
glycolysis II (from fructose 6-phosphate)	11	10	1
gluconeogenesis III	12	10	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
gluconeogenesis I	13	11	1
glycolysis I (from glucose 6-phosphate)	13	11	1
Calvin-Benson-Bassham cycle	13	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	12	1
superpathway of glucose and xylose degradation	17	16	1
oxygenic photosynthesis	17	9	1
heterolactic fermentation	18	14	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	12	1
superpathway of hexitol degradation (bacteria)	18	12	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
aspartate superpathway	25	19	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