Experiment set10IT050 for Pseudomonas simiae WCS417

rhizosphere sample 8; outgrowth in LB

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

Specific Phenotypes

For 11 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Cysteine Biosynthesis	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Methionine Biosynthesis	2
Ammonia assimilation	1
Conserved gene cluster possibly involved in RNA metabolism	1
Nitrate and nitrite ammonification	1
Terminal cytochrome C oxidases	1
Thiamin biosynthesis	1
Threonine and Homoserine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Cysteine metabolism
• Glutamate metabolism
• Sulfur metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Oxidative phosphorylation
• Alanine and aspartate metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Selenoamino acid metabolism
• Carbon fixation in photosynthetic organisms
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

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-aspartate biosynthesis	1	1	1
L-glutamine degradation II	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-glutamine degradation I	1	1	1
L-aspartate degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
L-glutamate degradation II	2	2	1
L-tyrosine degradation II	2	1	1
arsenite to oxygen electron transfer	2	1	1
atromentin biosynthesis	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
seleno-amino acid biosynthesis (plants)	5	3	2
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
sulfolactate degradation III	3	1	1
(R)-cysteate degradation	3	1	1
L-glutamate and L-glutamine biosynthesis	7	6	2
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
L-cysteine biosynthesis VII (from S-sulfo-L-cysteine)	4	3	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
N-3-oxalyl-L-2,3-diaminopropanoate biosynthesis	4	1	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	2
L-tyrosine degradation I	5	5	1
trans-4-hydroxy-L-proline degradation I	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	2
superpathway of L-threonine biosynthesis	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
thiazole component of thiamine diphosphate biosynthesis I	6	4	1
Fe(II) oxidation	6	3	1
superpathway of sulfolactate degradation	6	2	1
D-cycloserine biosynthesis	6	1	1
coenzyme M biosynthesis II	6	1	1
hydrogen sulfide biosynthesis II (mammalian)	6	1	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
L-cysteine biosynthesis VI (reverse transsulfuration)	7	2	1
L-citrulline biosynthesis	8	8	1
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
superpathway of seleno-compound metabolism	19	8	2
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of thiamine diphosphate biosynthesis I	10	8	1
rosmarinic acid biosynthesis I	10	2	1
superpathway of thiamine diphosphate biosynthesis II	11	9	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
superpathway of L-citrulline metabolism	12	10	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	3	1
superpathway of anaerobic energy metabolism (invertebrates)	17	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of chorismate metabolism	59	44	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1