Experiment set10IT039 for Pseudomonas simiae WCS417

root sample 6; outgrowth in LB

Group: root
Media:
Culturing: fluoroDangl_ML3, potted plant
By: Dawn Chiniquy on 4-Apr-19

Specific Phenotypes

For 35 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Widespread colonization island	3
Cysteine Biosynthesis	2
Methionine Biosynthesis	2
Ammonia assimilation	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Conserved gene cluster possibly involved in RNA metabolism	1
DNA-replication	1
Entner-Doudoroff Pathway	1
Folate Biosynthesis	1
Fructose utilization	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycolysis and Gluconeogenesis	1
Homogentisate pathway of aromatic compound degradation	1
Pentose phosphate pathway	1
Protein degradation	1
Thiamin biosynthesis	1
Zinc resistance	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Cysteine metabolism
• Sulfur metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Galactose metabolism
• Purine metabolism
• Pyrimidine metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Selenoamino acid metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Glycosaminoglycan degradation
• Nitrogen metabolism
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-cysteine biosynthesis I	2	2	2
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation I	1	1	1
L-glutamine degradation II	1	1	1
ammonia assimilation cycle III	3	3	2
trehalose degradation I (low osmolarity)	2	2	1
trehalose degradation II (cytosolic)	2	1	1
seleno-amino acid biosynthesis (plants)	5	3	2
trehalose degradation V	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
trehalose degradation IV	3	1	1
L-glutamate and L-glutamine biosynthesis	7	6	2
Arg/N-end rule pathway (eukaryotic)	14	8	4
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
L-cysteine biosynthesis VII (from S-sulfo-L-cysteine)	4	3	1
sucrose degradation III (sucrose invertase)	4	3	1
creatinine degradation I	4	2	1
N-3-oxalyl-L-2,3-diaminopropanoate biosynthesis	4	1	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	2
pentose phosphate pathway (non-oxidative branch) I	5	5	1
glucose and glucose-1-phosphate degradation	5	4	1
creatinine degradation II	5	2	1
glycogen degradation II	6	5	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
thiazole component of thiamine diphosphate biosynthesis I	6	4	1
hydrogen sulfide biosynthesis II (mammalian)	6	1	1
D-cycloserine biosynthesis	6	1	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
L-cysteine biosynthesis VI (reverse transsulfuration)	7	2	1
Bifidobacterium shunt	15	12	2
L-citrulline biosynthesis	8	8	1
pentose phosphate pathway	8	8	1
glycogen degradation I	8	6	1
glycine betaine degradation I	8	6	1
sucrose biosynthesis II	8	6	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	6	1
chitin biosynthesis	9	5	1
1,3-propanediol biosynthesis (engineered)	9	4	1
superpathway of seleno-compound metabolism	19	8	2
Rubisco shunt	10	8	1
superpathway of thiamine diphosphate biosynthesis I	10	8	1
glycolysis III (from glucose)	11	9	1
superpathway of thiamine diphosphate biosynthesis II	11	9	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	11	1
superpathway of L-citrulline metabolism	12	10	1
homolactic fermentation	12	9	1
superpathway of glucose and xylose degradation	17	16	1
heterolactic fermentation	18	14	1