Experiment set2TCH571 for Dickeya dianthicola ME23

Stem-Upstate

Group: plant
Media: Potato stem + cv.Upstate
Culturing: DdiaME23, Potato stem
By: Juliana Gonzalez-Tobon on 9/3/21

Specific Phenotypes

For 10 genes in this experiment

For plant cv.Upstate in Dickeya dianthicola ME23

For plant cv.Upstate across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter peptide (TC 3.A.1.5.5)	1
Experimental tye	1
Formate hydrogenase	1
Heme and Siroheme Biosynthesis	1
Lysine Biosynthesis DAP Pathway	1
Nitrate and nitrite ammonification	1
Threonine and Homoserine Biosynthesis	1
Type III secretion system orphans	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Lysine biosynthesis
• Glyoxylate and dicarboxylate metabolism
• Methane metabolism
• Porphyrin and chlorophyll metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
formate oxidation to CO2	1	1	1
L-homoserine biosynthesis	3	3	1
heme b biosynthesis II (oxygen-independent)	4	4	1
dipicolinate biosynthesis	4	3	1
L-methionine biosynthesis IV	4	2	1
oxalate degradation VI	4	2	1
spermidine biosynthesis II	4	2	1
ectoine biosynthesis	5	3	1
oxalate degradation III	5	2	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	6	1
superpathway of L-threonine biosynthesis	6	6	1
norspermidine biosynthesis	6	3	1
L-lysine biosynthesis VI	7	6	1
L-lysine biosynthesis III	7	6	1
3-dehydroquinate biosynthesis II (archaea)	7	3	1
cremeomycin biosynthesis	7	2	1
superpathway of L-homoserine and L-methionine biosynthesis	8	8	1
superpathway of polyamine biosynthesis III	8	3	1
grixazone biosynthesis	8	2	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	9	1
L-lysine biosynthesis I	9	9	1
L-lysine biosynthesis II	9	7	1
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	3	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
chorismate biosynthesis II (archaea)	12	8	1
superpathway of C1 compounds oxidation to CO2	12	4	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
purine nucleobases degradation I (anaerobic)	15	6	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	1
purine nucleobases degradation II (anaerobic)	24	13	1
aspartate superpathway	25	24	1
platensimycin biosynthesis	26	6	1
superpathway of bacteriochlorophyll a biosynthesis	26	6	1