Experiment set8S2 for Pantoea sp. MT58

Survival; Treatment=UGA synthetic gw pH7.4 with 1 mM Glucose and 0 mM NaH2PO4; TreatmentDuration=24hrs; Outgrowth=LBkan50

Group: survival
Media: + Treatment=UGA synthetic gw pH7.4 with 1 mM Glucose and 0 mM NaH2PO4; TreatmentDuration=24hrs; Outgrowth=LBkan50
Culturing: MT058_ML2, tube, Aerobic
By: Mike Thorgersen on 6/27/23

Specific Phenotypes

For 16 genes in this experiment

For survival Treatment=UGA synthetic gw pH7.4 with 1 mM Glucose and 0 mM NaH2PO4; TreatmentDuration=24hrs; Outgrowth=LBkan50 in Pantoea sp. MT58

For survival Treatment=UGA synthetic gw pH7.4 with 1 mM Glucose and 0 mM NaH2PO4; TreatmentDuration=24hrs; Outgrowth=LBkan50 across organisms

SEED Subsystems

Subsystem	#Specific
D-gluconate and ketogluconates metabolism	3
Allantoin Utilization	1
Biogenesis of c-type cytochromes	1
Calvin-Benson cycle	1
Cobalt-zinc-cadmium resistance	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
DNA structural proteins, bacterial	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine and Serine Utilization	1
Lysine Biosynthesis DAP Pathway	1
Methionine Biosynthesis	1
Nitrosative stress	1
Oxidative stress	1
Pentose phosphate pathway	1
Photorespiration (oxidative C2 cycle)	1
Protein chaperones	1
Proteolysis in bacteria, ATP-dependent	1
Rrf2 family transcriptional regulators	1
Serine-glyoxylate cycle	1
Threonine and Homoserine Biosynthesis	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:

• Glycine, serine and threonine metabolism
• Biosynthesis of plant hormones
• Pentose phosphate pathway
• Lysine biosynthesis
• Glycerolipid metabolism
• Glyoxylate and dicarboxylate metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of ansamycins
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pentose phosphate pathway (partial)	3	3	2
L-homoserine biosynthesis	3	3	2
2-O-α-mannosyl-D-glycerate degradation	2	1	1
pentose phosphate pathway (non-oxidative branch) I	5	5	2
superpathway of L-threonine biosynthesis	6	6	2
pentose phosphate pathway (non-oxidative branch) II	6	5	2
D-apiose degradation I	3	2	1
superpathway of L-homoserine and L-methionine biosynthesis	8	8	2
pentose phosphate pathway	8	8	2
D-galactarate degradation I	4	4	1
D-glucarate 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 L-methionine biosynthesis (transsulfuration)	9	9	2
superpathway of S-adenosyl-L-methionine biosynthesis	9	9	2
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	8	2
superpathway of D-glucarate and D-galactarate degradation	5	5	1
Rubisco shunt	10	9	2
glucose degradation (oxidative)	5	4	1
ectoine biosynthesis	5	3	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	11	2
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	10	2
norspermidine biosynthesis	6	4	1
superpathway of L-isoleucine biosynthesis I	13	13	2
Calvin-Benson-Bassham cycle	13	10	2
L-lysine biosynthesis III	7	6	1
superpathway of glycol metabolism and degradation	7	6	1
L-lysine biosynthesis VI	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
superpathway of polyamine biosynthesis III	8	4	1
2-deoxy-D-ribose degradation II	8	3	1
grixazone biosynthesis	8	2	1
superpathway of glucose and xylose degradation	17	16	2
oxygenic photosynthesis	17	11	2
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
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
photorespiration I	9	5	1
photorespiration III	9	5	1
photorespiration II	10	6	1
cytochrome c biogenesis (system I type)	11	9	1
chorismate biosynthesis II (archaea)	12	8	1
aspartate superpathway	25	24	2
ethene biosynthesis V (engineered)	25	18	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
formaldehyde assimilation I (serine pathway)	13	8	1
1-butanol autotrophic biosynthesis (engineered)	27	19	2
Bifidobacterium shunt	15	14	1
platensimycin biosynthesis	26	6	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	19	1