Experiment set11IT069 for Klebsiella michiganensis M5al

2-Deoxy-D-ribonic acid lithium salt 10 mM carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 2-Deoxy-D-ribonic acid lithium salt (10 mM), pH=7
Culturing: Koxy_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 5/2/18
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)
Growth plate: Koxy_deoxyribosePlus_plate B4

Specific Phenotypes

For 5 genes in this experiment

For carbon source 2-Deoxy-D-ribonic acid lithium salt in Klebsiella michiganensis M5al

For carbon source 2-Deoxy-D-ribonic acid lithium salt across organisms

SEED Subsystems

Subsystem	#Specific
Acetyl-CoA fermentation to Butyrate	1
Allantoin Utilization	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine and Serine Utilization	1
Nitrate and nitrite ammonification	1
Photorespiration (oxidative C2 cycle)	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:

• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Butanoate metabolism
• Fatty acid elongation in mitochondria
• Synthesis and degradation of ketone bodies
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Lysine degradation
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Glycerolipid metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Ethylbenzene degradation
• Terpenoid biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetoacetate degradation (to acetyl CoA)	2	2	2
(R)-lactate fermentation to propanoate II (acrylate pathway)	4	2	2
5,6-dehydrokavain biosynthesis (engineered)	10	8	4
pyruvate fermentation to acetone	5	3	2
benzoyl-CoA biosynthesis	3	3	1
1,2-propanediol biosynthesis from lactate (engineered)	6	4	2
propanoate fermentation to 2-methylbutanoate	6	4	2
L-alanine degradation VI (reductive Stickland reaction)	6	4	2
polyhydroxybutanoate biosynthesis	3	2	1
ketolysis	3	1	1
acetyl-CoA fermentation to butanoate	7	5	2
(2S)-ethylmalonyl-CoA biosynthesis	4	2	1
oleate β-oxidation	35	32	8
superpathway of L-alanine fermentation (Stickland reaction)	9	7	2
valproate β-oxidation	9	5	2
2-methyl-branched fatty acid β-oxidation	14	9	3
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	4	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	2
fatty acid β-oxidation II (plant peroxisome)	5	3	1
glutaryl-CoA degradation	5	3	1
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	4	2
isopropanol biosynthesis (engineered)	5	2	1
4-hydroxybenzoate biosynthesis III (plants)	5	2	1
fatty acid β-oxidation VII (yeast peroxisome)	5	1	1
ethylbenzene degradation (anaerobic)	5	1	1
ketogenesis	5	1	1
pyruvate fermentation to hexanol (engineered)	11	8	2
gallate degradation III (anaerobic)	11	5	2
fatty acid salvage	6	5	1
L-isoleucine degradation I	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
4-ethylphenol degradation (anaerobic)	6	1	1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast)	6	1	1
jasmonic acid biosynthesis	19	4	3
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	7	2
fatty acid β-oxidation I (generic)	7	6	1
pyruvate fermentation to butanoate	7	4	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
4-aminobutanoate degradation V	7	3	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
mevalonate pathway II (haloarchaea)	7	2	1
mevalonate pathway I (eukaryotes and bacteria)	7	2	1
succinate fermentation to butanoate	7	1	1
pyruvate fermentation to butanol I	8	4	1
2-deoxy-D-ribose degradation II	8	4	1
2-methylpropene degradation	8	2	1
mevalonate pathway III (Thermoplasma)	8	2	1
mevalonate pathway IV (archaea)	8	2	1
isoprene biosynthesis II (engineered)	8	2	1
androstenedione degradation I (aerobic)	25	7	3
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	9	2
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	6	1
photorespiration I	9	5	1
photorespiration III	9	5	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	4	1
4-oxopentanoate degradation	9	1	1
superpathway of testosterone and androsterone degradation	28	7	3
3-phenylpropanoate degradation	10	6	1
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)	10	5	1
L-lysine fermentation to acetate and butanoate	10	3	1
methyl tert-butyl ether degradation	10	2	1
superpathway of cholesterol degradation I (cholesterol oxidase)	42	9	4
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	5	1
ethylmalonyl-CoA pathway	11	2	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	9	4
L-glutamate degradation VII (to butanoate)	12	7	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	2	1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	2	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
androstenedione degradation II (anaerobic)	27	4	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
L-tryptophan degradation III (eukaryotic)	15	4	1
glycerol degradation to butanol	16	12	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	3	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	3	1
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	10	1
toluene degradation VI (anaerobic)	18	3	1
sitosterol degradation to androstenedione	18	1	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	2	1
superpathway of cholesterol degradation III (oxidase)	49	4	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
platensimycin biosynthesis	26	6	1
superpathway of ergosterol biosynthesis I	26	4	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
superpathway of cholesterol biosynthesis	38	4	1
superpathway of L-lysine degradation	43	12	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	1