Experiment set4IT055 for Cupriavidus basilensis FW507-4G11

LB

Group: lb
Media: LB
Culturing: cupriavidus_4G11_ML11, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 5.6 generations
By: Mark on 5/13/2015
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: plate2 D6

Specific Phenotypes

For 18 genes in this experiment

SEED Subsystems

Subsystem	#Specific
2-phosphoglycolate salvage	1
Biogenesis of c-type cytochromes	1
Carotenoids	1
Cobalt-zinc-cadmium resistance	1
DNA repair, bacterial	1
DNA repair, bacterial UvrD and related helicases	1
Homogentisate pathway of aromatic compound degradation	1
Iron acquisition in Vibrio	1
Oxidative stress	1
Periplasmic disulfide interchange	1
Phosphate metabolism	1
Phosphonate metabolism	1
Photorespiration (oxidative C2 cycle)	1
TCA Cycle	1
Transport of Iron	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of plant hormones
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Citrate cycle (TCA cycle)
• Aminophosphonate metabolism
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Fatty acid biosynthesis
• Biosynthesis of steroids
• Ubiquinone and menaquinone biosynthesis
• Methionine metabolism
• Lysine biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Tryptophan metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Methane metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
epoxysqualene biosynthesis	3	2	2
superoxide radicals degradation	2	2	1
methanol oxidation to formaldehyde IV	2	1	1
2-aminoethylphosphonate degradation II	2	1	1
neurosporene biosynthesis	5	2	2
partial TCA cycle (obligate autotrophs)	8	7	3
TCA cycle II (plants and fungi)	9	9	3
glyoxylate cycle	6	6	2
2-aminoethylphosphonate biosynthesis	3	3	1
ethanol degradation IV	3	3	1
TCA cycle V (2-oxoglutarate synthase)	9	8	3
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	3
TCA cycle VII (acetate-producers)	9	6	3
TCA cycle VI (Helicobacter)	9	6	3
2-aminoethylphosphonate degradation I	3	2	1
trans-lycopene biosynthesis I	6	2	2
TCA cycle III (animals)	10	10	3
TCA cycle I (prokaryotic)	10	9	3
reductive TCA cycle I	11	7	3
reactive oxygen species degradation	4	4	1
superpathway of glyoxylate bypass and TCA	12	11	3
nitrogen remobilization from senescing leaves	8	7	2
reductive TCA cycle II	12	6	3
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)	8	3	2
β-carotene biosynthesis (engineered)	8	2	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	3
2-methylcitrate cycle I	5	5	1
mixed acid fermentation	16	12	3
TCA cycle VIII (Chlamydia)	6	6	1
2-methylcitrate cycle II	6	5	1
methylaspartate cycle	19	14	3
incomplete reductive TCA cycle	7	4	1
pyruvate fermentation to propanoate I	7	3	1
lycopadiene biosynthesis	7	1	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	3
cholesterol biosynthesis I	16	2	2
cholesterol biosynthesis II (via 24,25-dihydrolanosterol)	16	2	2
cholesterol biosynthesis III (via desmosterol)	16	2	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	3
photorespiration III	9	6	1
photorespiration I	9	6	1
botryococcenes and methylated squalene biosynthesis	9	1	1
4,4'-diapolycopenedioate biosynthesis	9	1	1
staphyloxanthin biosynthesis	9	1	1
peptidoglycan recycling II	10	7	1
photorespiration II	10	6	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	5	1
L-glutamate degradation VIII (to propanoate)	11	3	1
superpathway of carotenoid biosynthesis in plants	22	3	2
ethene biosynthesis V (engineered)	25	17	2
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	7	1
superpathway of ergosterol biosynthesis II	26	11	2
superpathway of ergosterol biosynthesis I	26	5	2
hopanoid biosynthesis (bacteria)	14	4	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
superpathway of cholesterol biosynthesis	38	5	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1