Experiment set2IT082 for Rahnella sp. WP5

D-Mannitol carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Mannitol (20 mM)
Culturing: RahnellaWP5_ML7, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Robert Tournay on December 7, 2021
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 9 genes in this experiment

For carbon source D-Mannitol in Rahnella sp. WP5

For carbon source D-Mannitol across organisms

SEED Subsystems

Subsystem	#Specific
Alkanesulfonate assimilation	2
Alkanesulfonates Utilization	2
2-Ketogluconate Utilization	1
Folate Biosynthesis	1
Fructose utilization	1
Glycogen metabolism	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Mannitol Utilization	1
Pentose phosphate pathway	1
Putative sulfate assimilation cluster	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Starch and sucrose metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Pyruvate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
two-component alkanesulfonate monooxygenase	2	2	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	4	1
pentose phosphate pathway (non-oxidative branch) I	5	5	1
dimethyl sulfide degradation II (oxidation)	5	2	1
pentose phosphate pathway	8	8	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	7	1
Rubisco shunt	10	9	1
glycolysis V (Pyrococcus)	10	7	1
starch biosynthesis	10	6	1
glycolysis II (from fructose 6-phosphate)	11	11	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	11	1
gluconeogenesis I	13	13	1
glycolysis I (from glucose 6-phosphate)	13	13	1
Bifidobacterium shunt	15	13	1
superpathway of glucose and xylose degradation	17	17	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
superpathway of hexitol degradation (bacteria)	18	18	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	1
superpathway of anaerobic sucrose degradation	19	18	1
superpathway of N-acetylneuraminate degradation	22	20	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	1