Experiment set2S482 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

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
Culturing: Enterobacter_TBS_079_ML3, pot, at 26 (C), (Solid)
By: Robin on 30-Aug-23

Specific Phenotypes

For 120 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 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 across organisms

SEED Subsystems

Subsystem	#Specific
Maltose and Maltodextrin Utilization	11
Phosphate metabolism	4
DNA repair, UvrABC system	3
Glycogen metabolism	3
Lactose and Galactose Uptake and Utilization	3
Nitrate and nitrite ammonification	3
Fatty Acid Biosynthesis FASII	2
mycolic acid synthesis	2
2-phosphoglycolate salvage	1
ABC transporter oligopeptide (TC 3.A.1.5.1)	1
Ammonia assimilation	1
Arginine and Ornithine Degradation	1
Bacterial Chemotaxis	1
Bacterial Cytoskeleton	1
Beta-Glucoside Metabolism	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Cobalt-zinc-cadmium resistance	1
DNA-replication	1
DNA Repair Base Excision	1
DNA repair, bacterial RecFOR pathway	1
Entner-Doudoroff Pathway	1
Flagellar motility	1
Folate Biosynthesis	1
Fructooligosaccharides(FOS) and Raffinose Utilization	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutathione: Non-redox reactions	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine and Serine Utilization	1
Glycolate, glyoxylate interconversions	1
Glycolysis and Gluconeogenesis	1
Methionine Biosynthesis	1
Methylglyoxal Metabolism	1
Photorespiration (oxidative C2 cycle)	1
Plasmid replication	1
Polyamine Metabolism	1
Potassium homeostasis	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Serine Biosynthesis	1
Sialic Acid Metabolism	1
Streptothricin resistance	1
Stringent Response, (p)ppGpp metabolism	1
Sucrose utilization	1
Sucrose utilization Shewanella	1
Thiamin biosynthesis	1
Trehalose Biosynthesis	1
Trehalose Uptake and Utilization	1
Two cell division clusters relating to chromosome partitioning	1
Type III secretion systems, extended	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
• Galactose metabolism
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Tryptophan metabolism
• Thiamine metabolism
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Arginine and proline metabolism
• Naphthalene and anthracene degradation
• Carotenoid biosynthesis - General
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones
• Fatty acid biosynthesis
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Methionine metabolism
• Geraniol degradation
• Lysine biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Benzoxazinone biosynthesis
• Glutathione metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Streptomycin biosynthesis
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• One carbon pool by folate
• Methane metabolism
• Nicotinate and nicotinamide metabolism
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Zeatin biosynthesis
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of terpenoids and steroids
• 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
glycogen degradation I	8	8	6
ammonia assimilation cycle III	3	3	2
thiamine diphosphate salvage II	5	5	3
trehalose degradation I (low osmolarity)	2	2	1
putrescine biosynthesis I	2	2	1
polyphosphate metabolism	2	2	1
trehalose degradation II (cytosolic)	2	2	1
glutathione degradation (DUG pathway)	2	2	1
pyruvate fermentation to acetate VIII	2	2	1
L-lactaldehyde degradation (aerobic)	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
trehalose degradation VI (periplasmic)	2	2	1
thiamine diphosphate biosynthesis II (Bacillus)	2	2	1
NAD phosphorylation and transhydrogenation	2	2	1
thiamine diphosphate biosynthesis I (E. coli)	2	2	1
starch degradation V	4	3	2
glycogen degradation II	6	4	3
thiamine diphosphate salvage IV (yeast)	7	4	3
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	3
D-galactose degradation I (Leloir pathway)	5	5	2
sucrose biosynthesis II	8	6	3
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	4	3
trehalose degradation IV	3	3	1
methylglyoxal degradation V	3	3	1
methylglyoxal degradation IV	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
thiamine diphosphate salvage V	3	3	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
D-galactose detoxification	3	3	1
L-serine biosynthesis I	3	3	1
NAD phosphorylation and dephosphorylation	3	3	1
trehalose degradation V	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
S-adenosyl-L-methionine salvage II	3	2	1
thiamine diphosphate biosynthesis III (Staphylococcus)	3	1	1
thiamine diphosphate biosynthesis IV (eukaryotes)	3	1	1
superpathway of thiamine diphosphate biosynthesis I	10	10	3
stachyose degradation	7	7	2
L-glutamate and L-glutamine biosynthesis	7	5	2
superpathway of thiamine diphosphate biosynthesis II	11	9	3
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	12	3
superpathway of L-serine and glycine biosynthesis I	4	4	1
S-adenosyl-L-methionine salvage I	4	4	1
sucrose degradation IV (sucrose phosphorylase)	4	4	1
sucrose degradation III (sucrose invertase)	4	4	1
gondoate biosynthesis (anaerobic)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
tetrahydromonapterin biosynthesis	4	3	1
L-asparagine biosynthesis III (tRNA-dependent)	4	3	1
superpathway of putrescine biosynthesis	4	3	1
starch degradation III	4	2	1
L-methionine biosynthesis III	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
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	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
glucose and glucose-1-phosphate degradation	5	5	1
fatty acid elongation -- saturated	5	5	1
cis-vaccenate biosynthesis	5	5	1
L-methionine biosynthesis I	5	5	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
cytosolic NADPH production (yeast)	5	4	1
seleno-amino acid biosynthesis (plants)	5	3	1
lactate biosynthesis (archaea)	5	2	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
8-amino-7-oxononanoate biosynthesis I	11	11	2
odd iso-branched-chain fatty acid biosynthesis	34	30	6
anteiso-branched-chain fatty acid biosynthesis	34	30	6
even iso-branched-chain fatty acid biosynthesis	34	30	6
(5Z)-dodecenoate biosynthesis I	6	6	1
ppGpp metabolism	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
γ-glutamyl cycle	6	5	1
(5Z)-dodecenoate biosynthesis II	6	5	1
L-methionine biosynthesis II	6	5	1
stearate biosynthesis IV	6	4	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
NAD(P)/NADPH interconversion	6	4	1
petroselinate biosynthesis	6	2	1
streptorubin B biosynthesis	34	20	5
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
β-(1,4)-mannan degradation	7	3	1
biotin biosynthesis I	15	15	2
superpathway of fatty acid biosynthesis I (E. coli)	16	16	2
superpathway of L-homoserine and L-methionine biosynthesis	8	8	1
superpathway of methylglyoxal degradation	8	7	1
superpathway of polyamine biosynthesis I	8	7	1
L-citrulline biosynthesis	8	6	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	5	1
chitin derivatives degradation	8	4	1
L-rhamnose degradation II	8	2	1
2-allylmalonyl-CoA biosynthesis	8	2	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	9	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	9	1
folate transformations III (E. coli)	9	9	1
1,3-propanediol biosynthesis (engineered)	9	7	1
chitin biosynthesis	9	6	1
photorespiration III	9	5	1
photorespiration I	9	5	1
starch degradation II	9	1	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
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	1
homolactic fermentation	12	11	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	11	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	10	1
superpathway of fucose and rhamnose degradation	12	8	1
superpathway of L-citrulline metabolism	12	8	1
superpathway of L-arginine and L-ornithine degradation	13	8	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
Bifidobacterium shunt	15	12	1
superpathway of arginine and polyamine biosynthesis	17	16	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	1
heterolactic fermentation	18	15	1
superpathway of seleno-compound metabolism	19	6	1
aspartate superpathway	25	24	1
mycolate biosynthesis	205	25	5
superpathway of mycolate biosynthesis	239	26	5
superpathway of chorismate metabolism	59	54	1