Experiment set8S9 for Pantoea sp. MT58

Survival; Treatment=UGA synthetic gw pH7.4 with 1 mM Glucose and 5 mM NaH2PO4; TreatmentDuration=24hrs; Outgrowth=LBkan50

Group: survival
Media: + Treatment=UGA synthetic gw pH7.4 with 1 mM Glucose and 5 mM NaH2PO4; TreatmentDuration=24hrs; Outgrowth=LBkan50
Culturing: MT058_ML2, tube, Aerobic
By: Mike Thorgersen on 06/27/2023

Specific Phenotypes

For 20 genes in this experiment

For survival Treatment=UGA synthetic gw pH7.4 with 1 mM Glucose and 5 mM NaH2PO4; TreatmentDuration=24hrs; Outgrowth=LBkan50 in Pantoea sp. MT58

For survival Treatment=UGA synthetic gw pH7.4 with 1 mM Glucose and 5 mM NaH2PO4; TreatmentDuration=24hrs; Outgrowth=LBkan50 across organisms

SEED Subsystems

Subsystem	#Specific
Biogenesis of c-type cytochromes	7
D-gluconate and ketogluconates metabolism	3
Glycine and Serine Utilization	2
Photorespiration (oxidative C2 cycle)	2
Allantoin Utilization	1
Copper homeostasis	1
D-Galacturonate and D-Glucuronate Utilization	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
Deoxyribose and Deoxynucleoside Catabolism	1
Fermentations: Lactate	1
Fermentations: Mixed acid	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine cleavage system	1
Lysine Biosynthesis DAP Pathway	1
Methionine Biosynthesis	1
Nitrosative stress	1
Oxidative stress	1
Periplasmic disulfide interchange	1
Rrf2 family transcriptional regulators	1
Serine-glyoxylate cycle	1
Threonine and Homoserine Biosynthesis	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
• Pentose phosphate pathway
• Lysine biosynthesis
• Biosynthesis of plant hormones
• Glycerolipid metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyruvate fermentation to (R)-lactate	1	1	1
L-homoserine biosynthesis	3	3	2
2-O-α-mannosyl-D-glycerate degradation	2	1	1
cytochrome c biogenesis (system I type)	11	9	5
superpathway of L-threonine biosynthesis	6	6	2
2-deoxy-α-D-ribose 1-phosphate degradation	3	3	1
glycine biosynthesis II	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
glycine cleavage	3	3	1
2-deoxy-D-ribose degradation I	3	3	1
vancomycin resistance I	3	2	1
superpathway of L-homoserine and L-methionine biosynthesis	8	8	2
D-glucarate degradation I	4	4	1
D-galactarate degradation I	4	4	1
glycolate and glyoxylate degradation I	4	3	1
dipicolinate biosynthesis	4	3	1
spermidine biosynthesis II	4	2	1
L-methionine biosynthesis IV	4	2	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	9	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	9	2
superpathway of D-glucarate and D-galactarate degradation	5	5	1
glucose degradation (oxidative)	5	4	1
ectoine biosynthesis	5	3	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	10	2
norspermidine biosynthesis	6	4	1
L-alanine degradation VI (reductive Stickland reaction)	6	2	1
superpathway of L-isoleucine biosynthesis I	13	13	2
superpathway of purine deoxyribonucleosides degradation	7	7	1
L-lysine biosynthesis III	7	6	1
L-lysine biosynthesis VI	7	6	1
superpathway of glycol metabolism and degradation	7	6	1
L-ascorbate biosynthesis VIII (engineered pathway)	7	5	1
3-dehydroquinate biosynthesis II (archaea)	7	3	1
cremeomycin biosynthesis	7	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	4	1
superpathway of polyamine biosynthesis III	8	4	1
2-deoxy-D-ribose degradation II	8	3	1
grixazone biosynthesis	8	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	2
L-lysine biosynthesis I	9	9	1
L-lysine biosynthesis II	9	7	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	7	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
photorespiration I	9	5	1
photorespiration III	9	5	1
superpathway of L-alanine fermentation (Stickland reaction)	9	4	1
photorespiration II	10	6	1
chorismate biosynthesis II (archaea)	12	8	1
aspartate superpathway	25	24	2
formaldehyde assimilation I (serine pathway)	13	8	1
mixed acid fermentation	16	14	1
superpathway of glucose and xylose degradation	17	16	1
heterolactic fermentation	18	16	1
platensimycin biosynthesis	26	6	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	19	1