Experiment set2IT088 for Rahnella sp. WP5

Sodium D,L-Lactate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Sodium D,L-Lactate (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 27 genes in this experiment

For carbon source Sodium D,L-Lactate in Rahnella sp. WP5

For carbon source Sodium D,L-Lactate across organisms

SEED Subsystems

Subsystem	#Specific
D-ribose utilization	2
Glycolysis and Gluconeogenesis	2
Glycolysis and Gluconeogenesis, including Archaeal enzymes	2
Lactate utilization	2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Respiratory dehydrogenases 1	2
Serine-glyoxylate cycle	2
TCA Cycle	2
Calvin-Benson cycle	1
Deoxyribose and Deoxynucleoside Catabolism	1
Fructose utilization	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Hfl operon	1
High affinity phosphate transporter and control of PHO regulon	1
Ketoisovalerate oxidoreductase	1
L-Arabinose utilization	1
L-rhamnose utilization	1
Lactose and Galactose Uptake and Utilization	1
Lactose utilization	1
Mannitol Utilization	1
Phosphate metabolism	1
Polyadenylation bacterial	1
Proteolysis in bacteria, ATP-dependent	1
Purine conversions	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Succinate dehydrogenase	1
Transport of Manganese	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of phenylpropanoids
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Pentose phosphate pathway
• Oxidative phosphorylation
• Carbon fixation in photosynthetic organisms
• Fructose and mannose metabolism
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Butanoate metabolism
• 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
acetate conversion to acetyl-CoA	1	1	1
pyruvate fermentation to (R)-lactate	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
ribose phosphorylation	2	2	1
succinate to cytochrome bd oxidase electron transfer	2	2	1
malate/L-aspartate shuttle pathway	2	2	1
polyphosphate metabolism	2	2	1
L-lactaldehyde degradation (aerobic)	2	2	1
succinate to cytochrome bo oxidase electron transfer	2	1	1
D-lactate to cytochrome bo oxidase electron transfer	2	1	1
methylglyoxal degradation IV	3	3	1
2-deoxy-D-ribose degradation I	3	3	1
aerobic respiration III (alternative oxidase pathway)	3	3	1
ethanol degradation II	3	3	1
methylglyoxal degradation V	3	3	1
superpathway of acetate utilization and formation	3	3	1
ethanol degradation IV	3	3	1
ethanol degradation III	3	2	1
L-alanine degradation II (to D-lactate)	3	2	1
vancomycin resistance I	3	2	1
L-isoleucine biosynthesis V	3	2	1
2-chloroacrylate degradation I	3	2	1
chitin deacetylation	4	3	1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	5	2
aerobic respiration I (cytochrome c)	4	2	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
gluconeogenesis I	13	13	3
TCA cycle III (animals)	10	8	2
2-methylcitrate cycle I	5	3	1
glycolysis II (from fructose 6-phosphate)	11	11	2
thiazole component of thiamine diphosphate biosynthesis I	6	6	1
glyoxylate cycle	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
gluconeogenesis III	12	9	2
L-isoleucine biosynthesis IV	6	4	1
2-methylcitrate cycle II	6	2	1
L-alanine degradation VI (reductive Stickland reaction)	6	2	1
superpathway of bitter acids biosynthesis	18	3	3
lupulone and humulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
β-alanine biosynthesis II	6	1	1
glycolysis I (from glucose 6-phosphate)	13	13	2
incomplete reductive TCA cycle	7	5	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
pyruvate fermentation to propanoate I	7	3	1
mixed acid fermentation	16	16	2
superpathway of methylglyoxal degradation	8	7	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	3
superpathway of hexitol degradation (bacteria)	18	18	2
superpathway of fermentation (Chlamydomonas reinhardtii)	9	9	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
TCA cycle II (plants and fungi)	9	7	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	1
reductive glycine pathway of autotrophic CO2 fixation	9	6	1
superpathway of L-alanine fermentation (Stickland reaction)	9	5	1
cis-geranyl-CoA degradation	9	1	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	2
superpathway of anaerobic sucrose degradation	19	18	2
superpathway of thiamine diphosphate biosynthesis I	10	10	1
TCA cycle I (prokaryotic)	10	9	1
glycolysis V (Pyrococcus)	10	7	1
superpathway of coenzyme A biosynthesis II (plants)	10	5	1
superpathway of N-acetylneuraminate degradation	22	20	2
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	8	1
reductive TCA cycle I	11	8	1
L-glutamate degradation VIII (to propanoate)	11	3	1
superpathway of glyoxylate bypass and TCA	12	11	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	11	1
superpathway of fucose and rhamnose degradation	12	9	1
reductive TCA cycle II	12	8	1
Calvin-Benson-Bassham cycle	13	10	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	8	1
formaldehyde assimilation I (serine pathway)	13	8	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
superpathway of glucose and xylose degradation	17	17	1
oxygenic photosynthesis	17	11	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
heterolactic fermentation	18	16	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
methylaspartate cycle	19	8	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
ethene biosynthesis V (engineered)	25	18	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	2