Experiment set54IT077 for Escherichia coli BW25113

vcDART vector transformation; agar assay

Group: plasmid transformation
Media: LB + Kanamycin sulfate (0.05 mg/ml) + Gentamicin sulfate salt (0.05 mg/ml)
Culturing: Keio_ML9a, Bioassay Dish, Aerobic, at 30 (C), (Solid)
By: Rachel Rovinsky on 3/30/22
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 15 genes in this experiment

For plasmid transformation Kanamycin sulfate in Escherichia coli BW25113

For plasmid transformation Kanamycin sulfate across organisms

SEED Subsystems

Subsystem	#Specific
Biogenesis of cytochrome c oxidases	1
Experimental tye	1
Heme and Siroheme Biosynthesis	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Proteolysis in bacteria, ATP-dependent	1
Serine-glyoxylate cycle	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Porphyrin and chlorophyll metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Citrate cycle (TCA cycle)
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Lipopolysaccharide biosynthesis
• Naphthalene and anthracene degradation
• Reductive carboxylate cycle (CO2 fixation)
• Folate biosynthesis
• 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 terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
heme b biosynthesis I (aerobic)	4	4	1
heme b biosynthesis V (aerobic)	4	4	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
pyruvate fermentation to propanoate I	7	5	1
incomplete reductive TCA cycle	7	5	1
superpathway of heme b biosynthesis from glycine	8	7	1
partial TCA cycle (obligate autotrophs)	8	7	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
TCA cycle VI (Helicobacter)	9	7	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	1
TCA cycle II (plants and fungi)	9	7	1
TCA cycle VII (acetate-producers)	9	6	1
3,8-divinyl-chlorophyllide a biosynthesis III (aerobic, light independent)	9	3	1
3,8-divinyl-chlorophyllide a biosynthesis I (aerobic, light-dependent)	9	3	1
superpathway of heme b biosynthesis from glutamate	10	10	1
TCA cycle I (prokaryotic)	10	9	1
TCA cycle III (animals)	10	8	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	7	1
reductive TCA cycle I	11	8	1
L-glutamate degradation VIII (to propanoate)	11	5	1
superpathway of glyoxylate bypass and TCA	12	11	1
reductive TCA cycle II	12	8	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
mixed acid fermentation	16	16	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
methylaspartate cycle	19	9	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1