Experiment setATCH170 for Dickeya dianthicola ME23

PDB

Group: control
Media: Potato Dextrose Broth + kanamycin (50 ug/ml)
Culturing: DdiaME23, 24 well plate
By: Tyler Helmann on 11/16/20

Specific Phenotypes

For 7 genes in this experiment

For control kanamycin in Dickeya dianthicola ME23

For control kanamycin across organisms

SEED Subsystems

Subsystem	#Specific
D-gluconate and ketogluconates metabolism	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Redox-dependent regulation of nucleus processes	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:

• Nucleotide sugars metabolism
• Pentose and glucuronate interconversions
• Galactose metabolism
• Aminophosphonate metabolism
• Starch and sucrose metabolism
• High-mannose type N-glycan biosynthesis
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• Nicotinate and nicotinamide metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-glucose biosynthesis	2	2	1
cardiolipin biosynthesis I	3	3	1
cardiolipin biosynthesis II	3	3	1
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas)	4	3	1
sucrose degradation II (sucrose synthase)	5	4	1
NAD salvage pathway V (PNC V cycle)	5	3	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
superpathway of cardiolipin biosynthesis (bacteria)	13	10	2
stachyose degradation	7	7	1
NAD salvage pathway I (PNC VI cycle)	7	5	1
sucrose biosynthesis II	8	6	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
colanic acid building blocks biosynthesis	11	11	1
NAD salvage (plants)	11	5	1
superpathway of phospholipid biosynthesis III (E. coli)	12	11	1
superpathway of NAD biosynthesis in eukaryotes	14	7	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
superpathway of anaerobic sucrose degradation	19	17	1