Experiment set7IT002 for Pseudomonas simiae WCS417

LB 0.5x with Supernatant; Trichoderma harzanium TH1 grown as spores in 0.5x MS_media_noCarbon with Brachypodium distachyon roots for 27 days 0.5x

Group: supernatant
Media: LB (0.5x) + supernatant from Trichoderma harzanium TH1 grown as spores in 0.5x MS_media_noCarbon with Brachypodium distachyon roots for 27 days (0.5 x)
Culturing: fluoroDangl_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Trenton on 5/2/18
Media components: 5 g/L Tryptone, 2.5 g/L Yeast Extract, 2.5 g/L Sodium Chloride (final concentrations)
Growth plate: Plate3a A2

Specific Phenotypes

For 45 genes in this experiment

For supernatant Supernatant; Trichoderma harzanium TH1 grown as spores in 0.5x MS_media_noCarbon with Brachypodium distachyon roots for 27 days in Pseudomonas simiae WCS417

For supernatant Supernatant; Trichoderma harzanium TH1 grown as spores in 0.5x MS_media_noCarbon with Brachypodium distachyon roots for 27 days across organisms

SEED Subsystems

Subsystem	#Specific
Siderophore Pyoverdine	10
Iron acquisition in Vibrio	4
Transport of Iron	4
ABC transporter dipeptide (TC 3.A.1.5.2)	3
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	2
Campylobacter Iron Metabolism	2
Lysine degradation	2
Phosphate metabolism	2
Sodium Hydrogen Antiporter	2
Bacterial Chemotaxis	1
Biogenesis of cbb3-type cytochrome c oxidases	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Copper homeostasis	1
D-Sorbitol(D-Glucitol) and L-Sorbose Utilization	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
High affinity phosphate transporter and control of PHO regulon	1
Histidine Degradation	1
Homogentisate pathway of aromatic compound degradation	1
Isoleucine degradation	1
Leucine Degradation and HMG-CoA Metabolism	1
Queuosine-Archaeosine Biosynthesis	1
Threonine and Homoserine Biosynthesis	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tyrosine metabolism
• Biosynthesis of plant hormones
• Lysine degradation
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Biosynthesis of phenylpropanoids
• Pentose and glucuronate interconversions
• Fatty acid metabolism
• Biosynthesis of steroids
• Caffeine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Phenylalanine metabolism
• Novobiocin biosynthesis
• Lipopolysaccharide biosynthesis
• Benzoate degradation via CoA ligation
• Styrene degradation
• Carbon fixation in photosynthetic organisms
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
L-glutamate degradation II	2	2	1
3-dehydroquinate biosynthesis I	2	2	1
indole-3-acetate biosynthesis III (bacteria)	2	2	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
L-tyrosine degradation II	2	1	1
L-tyrosine degradation I	5	5	2
pyoverdine I biosynthesis	11	9	4
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
(R)-cysteate degradation	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
sulfolactate degradation III	3	1	1
queuosine biosynthesis I (de novo)	4	4	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
superpathway of L-tyrosine biosynthesis	10	10	2
superpathway of L-phenylalanine biosynthesis	10	10	2
L-histidine degradation II	5	5	1
L-lysine degradation IV	5	5	1
trans-4-hydroxy-L-proline degradation I	5	3	1
queuosine biosynthesis III (queuosine salvage)	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
ferrichrome A biosynthesis	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	2
superpathway of aromatic amino acid biosynthesis	18	18	3
superpathway of L-threonine biosynthesis	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
superpathway of sulfolactate degradation	6	2	1
coenzyme M biosynthesis II	6	1	1
chorismate biosynthesis I	7	7	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
rosmarinic acid biosynthesis I	10	2	1
mycobactin biosynthesis	11	2	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of L-tryptophan biosynthesis	13	13	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
superpathway of chorismate metabolism	59	44	3
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of L-lysine degradation	43	17	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1