Experiment set5IT056 for Variovorax sp. OAS795

V2_100

Group: phage
Media: R2A + CaCl2, MgSO4 (5mM ), pH=7
Culturing: Variovorax_OAS795_ML2, 48-well_plate, Aerobic, at 30C (C), shaken=700 rpm
By: MM on 5/21/21
Media components: 0.5 g/L Bacto Peptone, 0.5 g/L casamino acids, 0.5 g/L Yeast Extract, 0.5 g/L D-Glucose, 0.5 g/L Starch, 0.3 g/L Potassium phosphate dibasic, 0.05 g/L Magnesium Sulfate Heptahydrate, 0.3 g/L Sodium pyruvate

Specific Phenotypes

For 21 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Conserved gene cluster associated with Met-tRNA formyltransferase	1
DNA-replication	1
Entner-Doudoroff Pathway	1
Glycine and Serine Utilization	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
KDO2-Lipid A biosynthesis	1
Maltose and Maltodextrin Utilization	1
Peptidoglycan Biosynthesis	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Serine Biosynthesis	1
Terminal cytochrome O ubiquinol oxidase	1
Terminal cytochrome oxidases	1
Ton and Tol transport systems	1
Transcription factors bacterial	1
Trehalose Biosynthesis	1
Type IV pilus	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lipopolysaccharide biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Glycolysis / Gluconeogenesis
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Starch and sucrose metabolism
• Peptidoglycan biosynthesis
• Naphthalene and anthracene degradation
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• 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
pyruvate to cytochrome bo oxidase electron transfer	2	2	1
glycerol-3-phosphate to cytochrome bo oxidase electron transfer	2	2	1
NADH to cytochrome bo oxidase electron transfer I	2	2	1
NADH to cytochrome bo oxidase electron transfer II	2	2	1
succinate to cytochrome bo oxidase electron transfer	2	2	1
proline to cytochrome bo oxidase electron transfer	2	1	1
pseudouridine degradation	2	1	1
D-lactate to cytochrome bo oxidase electron transfer	2	1	1
L-serine biosynthesis I	3	3	1
L-cysteine biosynthesis IX (Trichomonas vaginalis)	3	2	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
CMP-3-deoxy-D-manno-octulosonate biosynthesis	5	5	1
glycogen degradation II	6	5	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	2
CMP-8-amino-3,8-dideoxy-D-manno-octulosonate biosynthesis	7	4	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	6	1
Rubisco shunt	10	10	1
glycolysis IV	10	8	1
glycolysis V (Pyrococcus)	10	7	1
photorespiration II	10	6	1
glycolysis III (from glucose)	11	11	1
glycolysis II (from fructose 6-phosphate)	11	11	1
glycolysis VI (from fructose)	11	8	1
homolactic fermentation	12	11	1
glycolysis I (from glucose 6-phosphate)	13	12	1
gluconeogenesis I	13	11	1
Bifidobacterium shunt	15	14	1
glycerol degradation to butanol	16	10	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	16	1
superpathway of glucose and xylose degradation	17	14	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
superpathway of (Kdo)2-lipid A biosynthesis	17	12	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1
superpathway of hexitol degradation (bacteria)	18	13	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	12	1
superpathway of anaerobic sucrose degradation	19	16	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	15	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	20	1
superpathway of N-acetylneuraminate degradation	22	15	1
ethene biosynthesis V (engineered)	25	19	1
superpathway of Kdo2-lipid A biosynthesis	25	12	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	24	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	21	1
1-butanol autotrophic biosynthesis (engineered)	27	20	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	24	1