Experiment set1IT059 for Phocaeicola vulgatus CL09T03C04

Sucrose 20 mM carbon source

Group: carbon source
Media: Varel_Bryant_medium + Sucrose (20 mM)
Culturing: Bvulgatus_CL09T03C04_ML5, 96 deep-well microplate; 0.5 mL volume, Anaerobic, at 34 (C), shaken=0 rpm
By: Surya Tripathi on 12/22/21
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 11 genes in this experiment

For carbon source Sucrose in Phocaeicola vulgatus CL09T03C04

For carbon source Sucrose across organisms

SEED Subsystems

Subsystem	#Specific
CMP-N-acetylneuraminate Biosynthesis	1
Entner-Doudoroff Pathway	1
Pentose phosphate pathway	1
Serine-glyoxylate cycle	1
Sialic Acid Metabolism	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Pentose phosphate pathway
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Glyoxylate and dicarboxylate metabolism
• 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 terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-N-acetyl-α-D-mannosamine biosynthesis	1	1	1
pentose phosphate pathway (oxidative branch) I	3	3	1
CMP-N-acetylneuraminate biosynthesis II (bacteria)	3	2	1
CMP-N-acetylneuraminate biosynthesis I (eukaryotes)	5	2	1
glyoxylate cycle	6	4	1
formaldehyde oxidation I	6	3	1
pentose phosphate pathway	8	8	1
nitrogen remobilization from senescing leaves	8	5	1
partial TCA cycle (obligate autotrophs)	8	5	1
Entner-Doudoroff pathway I	9	8	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
TCA cycle II (plants and fungi)	9	6	1
TCA cycle VI (Helicobacter)	9	6	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	6	1
TCA cycle VII (acetate-producers)	9	6	1
TCA cycle III (animals)	10	7	1
TCA cycle I (prokaryotic)	10	7	1
superpathway of glyoxylate bypass and TCA	12	7	1
superpathway of glyoxylate cycle and fatty acid degradation	14	6	1
superpathway of CMP-sialic acids biosynthesis	15	3	1
mixed acid fermentation	16	12	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
heterolactic fermentation	18	14	1
methylaspartate cycle	19	10	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	16	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	4	1
ethene biosynthesis V (engineered)	25	15	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	19	1