Experiment set34S669 for Pseudomonas simiae WCS417

Plant=Zea_mays-B73; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days

Group: in planta
Media: + Plant=Zea_mays-B73; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days
Culturing: fluoroDangl_ML3b, pot, at 24 (C), (Solid)
By: Marta Torres on 2-Jul-24

Specific Phenotypes

For 24 genes in this experiment

For in planta Plant=Zea_mays-B73; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days in Pseudomonas simiae WCS417

For in planta Plant=Zea_mays-B73; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=outgrowth_LB; Time=7_days across organisms

SEED Subsystems

Subsystem	#Specific
Inositol catabolism	7
Biotin biosynthesis	2
Bacterial Cell Division	1
Bacterial Cytoskeleton	1
Cobalamin synthesis	1
Coenzyme B12 biosynthesis	1
Entner-Doudoroff Pathway	1
Flagellum in Campylobacter	1
Glycolysis and Gluconeogenesis	1
Lipid A modifications	1
Lysine Biosynthesis DAP Pathway	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Peptidoglycan Biosynthesis	1
Polyamine Metabolism	1
Pterin biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Inositol phosphate metabolism
• Streptomycin biosynthesis
• Propanoate metabolism
• Biotin metabolism
• Porphyrin and chlorophyll metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Glycolysis / Gluconeogenesis
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• Lysine biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• beta-Alanine metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Peptidoglycan biosynthesis
• Biphenyl degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Nicotinate and nicotinamide metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
myo-inositol degradation I	7	7	6
myo-, chiro- and scyllo-inositol degradation	10	7	6
β-alanine degradation II	2	2	1
trehalose degradation I (low osmolarity)	2	2	1
8-amino-7-oxononanoate biosynthesis III	2	1	1
8-amino-7-oxononanoate biosynthesis II	2	1	1
adenosylcobinamide-GDP salvage from assorted adenosylcobamides	2	1	1
trehalose degradation II (cytosolic)	2	1	1
β-alanine degradation I	2	1	1
adenosylcobinamide-GDP salvage from cobinamide I	5	5	2
GDP-α-D-glucose biosynthesis	3	2	1
trehalose degradation V	3	2	1
trehalose degradation IV	3	1	1
superpathway of adenosylcobalamin salvage from cobinamide I	8	8	2
biotin biosynthesis from 8-amino-7-oxononanoate I	4	4	1
sucrose degradation III (sucrose invertase)	4	3	1
glucose and glucose-1-phosphate degradation	5	4	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
acrylate degradation I	5	3	1
propanoyl-CoA degradation II	5	3	1
myo-inositol degradation II	5	1	1
adenosylcobinamide-GDP biosynthesis from cobyrinate a,c-diamide	6	6	1
glycogen degradation II	6	5	1
adenosylcobinamide-GDP salvage from cobinamide II	6	5	1
biotin biosynthesis II	6	4	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
2,4-dinitrotoluene degradation	7	3	1
biotin biosynthesis I	15	14	2
glycogen degradation I	8	6	1
L-valine degradation I	8	6	1
sucrose biosynthesis II	8	6	1
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
L-lysine biosynthesis I	9	9	1
superpathway of adenosylcobalamin salvage from cobinamide II	9	8	1
chitin biosynthesis	9	5	1
1,3-propanediol biosynthesis (engineered)	9	4	1
8-amino-7-oxononanoate biosynthesis I	11	10	1
glycolysis III (from glucose)	11	9	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	12	1
homolactic fermentation	12	9	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	1
Bifidobacterium shunt	15	12	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
heterolactic fermentation	18	14	1
streptomycin biosynthesis	18	3	1
aspartate superpathway	25	22	1
adenosylcobalamin biosynthesis II (aerobic)	33	31	1
adenosylcobalamin biosynthesis I (anaerobic)	36	28	1