Experiment set4S65 for Pseudomonas segetis P6

Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=20h_outgrowth_LB; Time=7_days

Group: in planta
Media: + Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=20h_outgrowth_LB; Time=7_days
Culturing: Pseudo_segetis_P6_ML4b, pot, at 26 (C)
By: Marta Torres on 6-Nov-23

Specific Phenotypes

For 41 genes in this experiment

For in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=20h_outgrowth_LB; Time=7_days in Pseudomonas segetis P6

For in planta Plant=Zea_mays; PlantTreatment=None; Sample=rhizosphere; GrowthSubstrate=0.5X_MS_agar; Collection=20h_outgrowth_LB; Time=7_days across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	2
Glycine and Serine Utilization	2
Glycine cleavage system	2
Lysine degradation	2
Orphan regulatory proteins	2
Photorespiration (oxidative C2 cycle)	2
Bacterial Cytoskeleton	1
Entner-Doudoroff Pathway	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Lipid A modifications	1
Peptidoglycan Biosynthesis	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Ribosomal protein S12p Asp methylthiotransferase	1
ZZ gjo need homes	1
cAMP signaling in bacteria	1
tRNA processing	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
• Lysine degradation
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Glycolysis / Gluconeogenesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Puromycin biosynthesis
• Glutamate metabolism
• Alanine and aspartate metabolism
• Arginine and proline metabolism
• beta-Alanine metabolism
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Pyruvate metabolism
• Propanoate metabolism
• Butanoate metabolism
• One carbon pool by folate
• Carbon fixation in photosynthetic organisms
• Biotin metabolism
• Nitrogen metabolism
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• 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
cadaverine biosynthesis	1	1	1
cis-cyclopropane fatty acid (CFA) biosynthesis	1	1	1
arginine dependent acid resistance	1	1	1
glycine biosynthesis II	3	3	2
glycine cleavage	3	3	2
putrescine biosynthesis I	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
4-aminobutanoate degradation III	2	2	1
4-aminobutanoate degradation I	2	1	1
4-aminobutanoate degradation II	2	1	1
sterculate biosynthesis	2	1	1
putrescine biosynthesis II	3	3	1
aminopropylcadaverine biosynthesis	3	3	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
glycine degradation	3	3	1
L-lysine degradation X	6	5	2
2-chloroacrylate degradation I	3	2	1
superpathway of 4-aminobutanoate degradation	3	1	1
L-lysine degradation I	7	4	2
superpathway of polyamine biosynthesis I	8	7	2
glycine betaine degradation I	8	6	2
superpathway of putrescine biosynthesis	4	3	1
spermidine biosynthesis III	4	2	1
GABA shunt II	4	2	1
creatinine degradation I	4	1	1
GABA shunt I	4	1	1
L-lysine degradation IV	5	3	1
lupanine biosynthesis	5	1	1
creatinine degradation II	5	1	1
bisucaberin biosynthesis	5	1	1
desferrioxamine B biosynthesis	5	1	1
desferrioxamine E biosynthesis	5	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	2
L-lysine degradation III	6	2	1
superpathway of L-arginine and L-ornithine degradation	13	8	2
glycine betaine degradation III	7	7	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
4-aminobutanoate degradation V	7	3	1
superpathway of polyamine biosynthesis II	8	6	1
superpathway of arginine and polyamine biosynthesis	17	16	2
folate transformations III (E. coli)	9	9	1
Entner-Doudoroff pathway I	9	8	1
photorespiration I	9	5	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	5	1
photorespiration III	9	5	1
Rubisco shunt	10	8	1
glycolysis V (Pyrococcus)	10	7	1
glycolysis IV	10	7	1
photorespiration II	10	6	1
folate transformations II (plants)	11	10	1
glycolysis II (from fructose 6-phosphate)	11	9	1
glycolysis III (from glucose)	11	9	1
glycolysis VI (from fructose)	11	7	1
homolactic fermentation	12	10	1
glycolysis I (from glucose 6-phosphate)	13	10	1
folate transformations I	13	9	1
Bifidobacterium shunt	15	13	1
glycerol degradation to butanol	16	10	1
mixed acid fermentation	16	10	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of glucose and xylose degradation	17	14	1
superpathway of anaerobic energy metabolism (invertebrates)	17	9	1
nicotine degradation I (pyridine pathway)	17	5	1
heterolactic fermentation	18	13	1
superpathway of hexitol degradation (bacteria)	18	10	1
superpathway of anaerobic sucrose degradation	19	15	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	13	1
superpathway of L-lysine degradation	43	11	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	16	1
superpathway of N-acetylneuraminate degradation	22	12	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
mycolate biosynthesis	205	20	3
superpathway of mycolate biosynthesis	239	21	3