Experiment set2S484 for Enterobacter sp. TBS_079

Plant=SorghumBicolor_Rtx430; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB_Kan50; Time=28_days; NumberPlantsPooled=4; CocultureWith=Inquilinus sp. 005-A5

Group: in planta
Media: + Plant=SorghumBicolor_Rtx430; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB_Kan50; Time=28_days; NumberPlantsPooled=4; CocultureWith=Inquilinus sp. 005-A5
Culturing: Enterobacter_TBS_079_ML3, pot, at 26 (C), (Solid)
By: Robin on 30-Aug-23

Specific Phenotypes

For 163 genes in this experiment

For in planta Plant=SorghumBicolor_Rtx430; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB_Kan50; Time=28_days; NumberPlantsPooled=4; CocultureWith=Inquilinus sp. 005-A5 in Enterobacter sp. TBS_079

For in planta Plant=SorghumBicolor_Rtx430; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB_Kan50; Time=28_days; NumberPlantsPooled=4; CocultureWith=Inquilinus sp. 005-A5 across organisms

SEED Subsystems

Subsystem	#Specific
Nitrate and nitrite ammonification	4
Cobalt-zinc-cadmium resistance	3
DNA repair, UvrABC system	3
Biotin biosynthesis	2
DNA repair, bacterial RecFOR pathway	2
Fatty Acid Biosynthesis FASII	2
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Glycine and Serine Utilization	2
Lactose and Galactose Uptake and Utilization	2
Pyruvate metabolism I: anaplerotic reactions, PEP	2
mycolic acid synthesis	2
Allantoin Utilization	1
Ammonia assimilation	1
Bacterial Chemotaxis	1
Beta-Glucoside Metabolism	1
Butanol Biosynthesis	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
DNA-binding regulatory proteins, strays	1
DNA-replication	1
DNA Repair Base Excision	1
Entner-Doudoroff Pathway	1
Fermentations: Mixed acid	1
Flagellar motility	1
Flagellum	1
Folate Biosynthesis	1
Fructooligosaccharides(FOS) and Raffinose Utilization	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutathione: Biosynthesis and gamma-glutamyl cycle	1
Glutathione: Non-redox reactions	1
Glycogen metabolism	1
Glycolysis and Gluconeogenesis	1
KDO2-Lipid A biosynthesis	1
Lipid A modifications	1
Lysine Biosynthesis DAP Pathway	1
Maltose and Maltodextrin Utilization	1
Methionine Biosynthesis	1
Orphan regulatory proteins	1
Oxidative stress	1
Peptidoglycan Biosynthesis	1
Photorespiration (oxidative C2 cycle)	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Serine-glyoxylate cycle	1
Serine Biosynthesis	1
Sialic Acid Metabolism	1
Sucrose utilization	1
Sucrose utilization Shewanella	1
Thiamin biosynthesis	1
Threonine and Homoserine Biosynthesis	1
Type III secretion systems, extended	1
Type IV pilus	1
Utilization of glutathione as a sulphur source	1
Xylose utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Fructose and mannose metabolism
• Galactose metabolism
• Glycine, serine and threonine metabolism
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Biotin metabolism
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Fatty acid biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Glycerophospholipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Butanoate metabolism
• Thiamine metabolism
• Folate biosynthesis
• Nitrogen metabolism
• Flavonoid biosynthesis
• Alkaloid biosynthesis I
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Glutamate metabolism
• Methionine metabolism
• Lysine biosynthesis
• Phenylalanine metabolism
• Benzoxazinone biosynthesis
• Taurine and hypotaurine metabolism
• Selenoamino acid metabolism
• Cyanoamino acid metabolism
• Glutathione metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Streptomycin biosynthesis
• Aminosugars metabolism
• Keratan sulfate biosynthesis
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Ether lipid metabolism
• Arachidonic acid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Ethylbenzene degradation
• One carbon pool by folate
• Methane metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Zeatin biosynthesis
• Phenylpropanoid biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of type II polyketide backbone
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
hydroxymethylpyrimidine salvage	2	2	2
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis I	2	2	2
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
glycogen degradation I	8	8	4
glutathione degradation (DUG pathway)	2	2	1
reductive monocarboxylic acid cycle	2	2	1
NADH to nitrate electron transfer	2	2	1
nitrate reduction IX (dissimilatory)	2	2	1
nitrate reduction VIIIb (dissimilatory)	2	2	1
trehalose degradation II (cytosolic)	2	2	1
nitrate reduction III (dissimilatory)	2	2	1
trehalose degradation I (low osmolarity)	2	2	1
2-O-α-mannosyl-D-glycerate degradation	2	2	1
nitrate reduction VIII (dissimilatory)	2	2	1
glycogen degradation II	6	4	3
8-amino-7-oxononanoate biosynthesis III	2	1	1
8-amino-7-oxononanoate biosynthesis II	2	1	1
thiamine diphosphate salvage II	5	5	2
8-amino-7-oxononanoate biosynthesis IV	5	4	2
dTMP de novo biosynthesis (mitochondrial)	3	3	1
L-homoserine biosynthesis	3	3	1
pyruvate fermentation to acetate IV	3	3	1
pyruvate fermentation to ethanol I	3	3	1
L-serine biosynthesis I	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
trehalose degradation IV	3	3	1
D-galactose detoxification	3	3	1
biotin biosynthesis II	6	4	2
GDP-α-D-glucose biosynthesis	3	2	1
trehalose degradation V	3	2	1
oleate biosynthesis III (cyanobacteria)	3	2	1
S-adenosyl-L-methionine salvage II	3	2	1
superpathway of thiamine diphosphate biosynthesis I	10	10	3
L-glutamate and L-glutamine biosynthesis	7	5	2
thiamine diphosphate salvage IV (yeast)	7	4	2
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	2
8-amino-7-oxononanoate biosynthesis I	11	11	3
superpathway of thiamine diphosphate biosynthesis II	11	9	3
biotin biosynthesis I	15	15	4
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	12	3
superpathway of L-homoserine and L-methionine biosynthesis	8	8	2
CDP-diacylglycerol biosynthesis I	4	4	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
biotin biosynthesis from 8-amino-7-oxononanoate I	4	4	1
CDP-diacylglycerol biosynthesis II	4	4	1
D-glucarate degradation I	4	4	1
sucrose degradation III (sucrose invertase)	4	4	1
gondoate biosynthesis (anaerobic)	4	4	1
D-galactarate degradation I	4	4	1
sucrose degradation IV (sucrose phosphorylase)	4	4	1
S-adenosyl-L-methionine salvage I	4	4	1
sucrose biosynthesis II	8	6	2
glycolate and glyoxylate degradation I	4	3	1
tetrahydromonapterin biosynthesis	4	3	1
dipicolinate biosynthesis	4	3	1
biotin biosynthesis from 8-amino-7-oxononanoate II	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
starch degradation V	4	3	1
L-asparagine biosynthesis III (tRNA-dependent)	4	3	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	6	3
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	4	2
L-methionine biosynthesis III	4	2	1
starch degradation III	4	2	1
spermidine biosynthesis II	4	2	1
L-methionine biosynthesis IV	4	2	1
palmitate biosynthesis III	29	28	7
tetradecanoate biosynthesis (mitochondria)	25	23	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
superpathway of L-methionine biosynthesis (transsulfuration)	9	9	2
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	9	2
superpathway of S-adenosyl-L-methionine biosynthesis	9	9	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	51	11
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	20	4
D-galactose degradation I (Leloir pathway)	5	5	1
cis-vaccenate biosynthesis	5	5	1
fatty acid elongation -- saturated	5	5	1
superpathway of D-glucarate and D-galactarate degradation	5	5	1
glucose and glucose-1-phosphate degradation	5	5	1
L-methionine biosynthesis I	5	5	1
ectoine biosynthesis	5	3	1
seleno-amino acid biosynthesis (plants)	5	3	1
phosphatidate biosynthesis (yeast)	5	3	1
biotin biosynthesis from 8-amino-7-oxononanoate III	5	3	1
nitrate reduction I (denitrification)	5	2	1
nitrate reduction VII (denitrification)	5	2	1
superpathway of fatty acid biosynthesis II (plant)	43	38	8
anteiso-branched-chain fatty acid biosynthesis	34	30	6
even iso-branched-chain fatty acid biosynthesis	34	30	6
odd iso-branched-chain fatty acid biosynthesis	34	30	6
peptido-conjugates in tissue regeneration biosynthesis	17	5	3
(5Z)-dodecenoate biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis II	6	6	1
thiazole component of thiamine diphosphate biosynthesis I	6	6	1
L-threonine degradation I	6	6	1
superpathway of L-threonine biosynthesis	6	6	1
superpathway of phospholipid biosynthesis III (E. coli)	12	11	2
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	10	2
L-methionine biosynthesis II	6	5	1
(5Z)-dodecenoate biosynthesis II	6	5	1
stearate biosynthesis II (bacteria and plants)	6	5	1
γ-glutamyl cycle	6	5	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
stearate biosynthesis IV	6	4	1
norspermidine biosynthesis	6	4	1
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
palmitoyl ethanolamide biosynthesis	6	2	1
petroselinate biosynthesis	6	2	1
leukotriene biosynthesis	6	1	1
streptorubin B biosynthesis	34	20	5
stachyose degradation	7	7	1
L-lysine biosynthesis VI	7	6	1
L-lysine biosynthesis III	7	6	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
superpathway of glycol metabolism and degradation	7	5	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	1
diacylglycerol and triacylglycerol biosynthesis	7	3	1
β-(1,4)-mannan degradation	7	3	1
3-dehydroquinate biosynthesis II (archaea)	7	3	1
stigma estolide biosynthesis	7	2	1
cremeomycin biosynthesis	7	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	16	2
L-citrulline biosynthesis	8	6	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	5	1
chitin derivatives degradation	8	4	1
superpathway of polyamine biosynthesis III	8	4	1
2-deoxy-D-ribose degradation II	8	3	1
anandamide biosynthesis II	8	2	1
2-allylmalonyl-CoA biosynthesis	8	2	1
grixazone biosynthesis	8	2	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	2
folate transformations III (E. coli)	9	9	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	9	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
L-lysine biosynthesis I	9	9	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	8	1
1,3-propanediol biosynthesis (engineered)	9	7	1
L-lysine biosynthesis II	9	6	1
chitin biosynthesis	9	6	1
photorespiration III	9	5	1
photorespiration I	9	5	1
superpathway of tetrahydrofolate biosynthesis	10	9	1
photorespiration II	10	6	1
clavulanate biosynthesis	10	1	1
glycolysis III (from glucose)	11	11	1
folate transformations II (plants)	11	10	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
homolactic fermentation	12	11	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	11	1
superpathway of L-citrulline metabolism	12	8	1
chorismate biosynthesis II (archaea)	12	8	1
anandamide biosynthesis I	12	4	1
aspartate superpathway	25	24	2
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of cardiolipin biosynthesis (bacteria)	13	10	1
formaldehyde assimilation I (serine pathway)	13	8	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	7	1
superpathway of phospholipid biosynthesis II (plants)	28	10	2
hypoglycin biosynthesis	14	4	1
Bifidobacterium shunt	15	12	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
mixed acid fermentation	16	16	1
superpathway of L-threonine metabolism	18	16	1
heterolactic fermentation	18	15	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	18	1
superpathway of seleno-compound metabolism	19	6	1
superpathway of N-acetylneuraminate degradation	22	19	1
platensimycin biosynthesis	26	6	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	19	1
mycolate biosynthesis	205	25	5
superpathway of mycolate biosynthesis	239	26	5
superpathway of chorismate metabolism	59	54	1