Experiment set20IT049 for Pseudomonas simiae WCS417

Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered; 0.8X

Group: supernatant
Media: R2A + supernatant from Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered (0.8 X)
Culturing: fluoroDangl_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Cat_Manuel on 1-Feb-22
Media components: 0.5 g/L Bacto Peptone, 0.5 g/L casamino acids, 0.5 g/L Yeast Extract, 0.5 g/L D-Glucose, 0.5 g/L Starch, 0.3 g/L Potassium phosphate dibasic, 0.05 g/L Magnesium Sulfate Heptahydrate, 0.3 g/L Sodium pyruvate

Specific Phenotypes

For 48 genes in this experiment

For supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered in Pseudomonas simiae WCS417

For supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered across organisms

SEED Subsystems

Subsystem	#Specific
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	3
ABC transporter oligopeptide (TC 3.A.1.5.1)	2
Arginine and Ornithine Degradation	2
Campylobacter Iron Metabolism	2
Iron acquisition in Vibrio	2
Lysine degradation	2
Transport of Iron	2
2-Ketogluconate Utilization	1
DNA repair, bacterial	1
Glycogen metabolism	1
Heme, hemin uptake and utilization systems in GramPositives	1
Hemin transport system	1
Multidrug Resistance Efflux Pumps	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	1
Oxidative stress	1
Polyamine Metabolism	1
Protein degradation	1
Purine Utilization	1
Purine conversions	1
Pyruvate Alanine Serine Interconversions	1
Rhamnose containing glycans	1
Siderophore Pyoverdine	1
Ton and Tol transport systems	1
cAMP signaling in bacteria	1
dTDP-rhamnose synthesis	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Urea cycle and metabolism of amino groups
• Lysine biosynthesis
• Alanine and aspartate metabolism
• beta-Alanine metabolism
• Propanoate metabolism
• Purine metabolism
• Puromycin biosynthesis
• Glutamate metabolism
• Methionine metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Phenylalanine metabolism
• Tryptophan metabolism
• Aminophosphonate metabolism
• Cyanoamino acid metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Lipopolysaccharide biosynthesis
• Benzoate degradation via CoA ligation
• Styrene degradation
• Butanoate metabolism
• Caprolactam degradation
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
cis-cyclopropane fatty acid (CFA) biosynthesis	1	1	1
putrescine biosynthesis II	3	3	2
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	2
indole-3-acetate biosynthesis III (bacteria)	2	2	1
guanine and guanosine salvage II	2	2	1
adenine and adenosine salvage I	2	2	1
4-aminobutanoate degradation I	2	2	1
acrylonitrile degradation I	2	2	1
putrescine degradation V	2	2	1
indole-3-acetate biosynthesis IV (bacteria)	2	2	1
guanine and guanosine salvage I	2	2	1
β-alanine degradation II	2	2	1
adenine and adenosine salvage II	2	2	1
4-aminobutanoate degradation III	2	2	1
4-aminobutanoate degradation II	2	1	1
sterculate biosynthesis	2	1	1
L-arginine degradation I (arginase pathway)	3	3	1
L-ornithine biosynthesis II	3	3	1
L-proline biosynthesis III (from L-ornithine)	3	3	1
adenine salvage	3	2	1
superpathway of acrylonitrile degradation	3	2	1
superpathway of 4-aminobutanoate degradation	3	2	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
superpathway of guanine and guanosine salvage	3	2	1
L-arginine degradation VI (arginase 2 pathway)	4	4	1
superpathway of polyamine biosynthesis II	8	6	2
glycogen biosynthesis I (from ADP-D-Glucose)	4	3	1
GABA shunt II	4	3	1
GABA shunt I	4	2	1
L-arginine degradation XIII (reductive Stickland reaction)	5	5	1
L-arginine degradation II (AST pathway)	5	5	1
L-ornithine biosynthesis I	5	5	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
β-alanine biosynthesis II	6	5	1
superpathway of purine nucleotide salvage	14	13	2
L-Nδ-acetylornithine biosynthesis	7	6	1
glyphosate degradation III	7	3	1
4-aminobutanoate degradation V	7	2	1
L-citrulline biosynthesis	8	8	1
(aminomethyl)phosphonate degradation	8	3	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
starch biosynthesis	10	5	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	8	1
superpathway of L-citrulline metabolism	12	10	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of L-arginine and L-ornithine degradation	13	10	1
superpathway of arginine and polyamine biosynthesis	17	15	1
nicotine degradation I (pyridine pathway)	17	4	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	5	1
aspartate superpathway	25	22	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1
mycolate biosynthesis	205	20	3
superpathway of mycolate biosynthesis	239	21	3