Experiment set8IT087 for Klebsiella michiganensis M5al

RCH2_defined_noCarbon with Supernatant; Trichoderma harzianum M10 grown as spores in 0.5x MS_media_noCarbon with Brachypodium distachyon roots for 27 days 1x

Group: supernatant
Media: RCH2_defined_noCarbon + supernatant from Trichoderma harzianum M10 grown as spores in 0.5x MS_media_noCarbon with Brachypodium distachyon roots for 27 days (1 x), pH=7
Culturing: Koxy_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Trenton on 28-Feb-18
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 19 genes in this experiment

For supernatant Supernatant; Trichoderma harzianum M10 grown as spores in 0.5x MS_media_noCarbon with Brachypodium distachyon roots for 27 days in Klebsiella michiganensis M5al

For supernatant Supernatant; Trichoderma harzianum M10 grown as spores in 0.5x MS_media_noCarbon with Brachypodium distachyon roots for 27 days across organisms

SEED Subsystems

Subsystem	#Specific
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Murein hydrolase regulation and cell death	2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Acetoin, butanediol metabolism	1
Branched-Chain Amino Acid Biosynthesis	1
DNA-binding regulatory proteins, strays	1
Deoxyribose and Deoxynucleoside Catabolism	1
Entner-Doudoroff Pathway	1
Fermentations: Mixed acid	1
Formate hydrogenase	1
Ketoisovalerate oxidoreductase	1
Methylglyoxal Metabolism	1
Photorespiration (oxidative C2 cycle)	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Serine-glyoxylate cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Glyoxylate and dicarboxylate metabolism
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Biosynthesis of alkaloids derived from histidine and purine
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Ether lipid metabolism
• Sphingolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• 1,2-Dichloroethane degradation
• C5-Branched dibasic acid metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Pantothenate and CoA biosynthesis
• Retinol metabolism
• Limonene and pinene degradation
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ethanol degradation II	3	3	3
L-malate degradation I	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
acetate conversion to acetyl-CoA	1	1	1
acetaldehyde biosynthesis I	1	1	1
ethanol degradation IV	3	3	2
ethanol degradation III	3	2	2
glycolate and glyoxylate degradation II	2	2	1
ethanol degradation I	2	2	1
phenylethylamine degradation I	2	2	1
pyruvate fermentation to (R)-acetoin II	2	2	1
pyruvate fermentation to ethanol II	2	2	1
ethylene glycol degradation	2	2	1
putrescine degradation I	2	2	1
phytol degradation	4	3	2
chitin deacetylation	4	3	2
putrescine degradation V	2	1	1
phenylethylamine degradation II	2	1	1
phenylethanol degradation	2	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	2
glyoxylate cycle	6	6	2
pyruvate fermentation to (R)-acetoin I	3	3	1
pyruvate fermentation to ethanol III	3	3	1
pyruvate fermentation to (S)-acetoin	3	3	1
2-deoxy-D-ribose degradation I	3	3	1
pyruvate fermentation to ethanol I	3	3	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	3	1
superpathway of acetate utilization and formation	3	3	1
L-isoleucine biosynthesis IV	6	4	2
L-isoleucine degradation II	3	2	1
putrescine degradation IV	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-methionine degradation III	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-valine degradation II	3	2	1
hypotaurine degradation	3	2	1
styrene degradation	3	1	1
histamine degradation	3	1	1
noradrenaline and adrenaline degradation	13	4	4
superpathway of glycol metabolism and degradation	7	7	2
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	2
serotonin degradation	7	3	2
D-arabinose degradation II	4	4	1
L-valine biosynthesis	4	4	1
salidroside biosynthesis	4	2	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
putrescine degradation III	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
superpathway of (R,R)-butanediol biosynthesis	5	5	1
ethanolamine utilization	5	5	1
(S)-propane-1,2-diol degradation	5	5	1
acetylene degradation (anaerobic)	5	4	1
mitochondrial NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
2-methylcitrate cycle I	5	2	1
octane oxidation	5	2	1
phenylethanol biosynthesis	5	2	1
dopamine degradation	5	1	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	1
superpathway of glyoxylate bypass and TCA	12	11	2
superpathway of 2,3-butanediol biosynthesis	6	5	1
methylgallate degradation	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
2-methylcitrate cycle II	6	2	1
superpathway of bitter acids biosynthesis	18	3	3
alkane oxidation	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
β-alanine biosynthesis II	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
superpathway of purine deoxyribonucleosides degradation	7	7	1
3-methylbutanol biosynthesis (engineered)	7	6	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
L-isoleucine biosynthesis III	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
D-xylose degradation IV	7	3	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of ornithine degradation	8	8	1
protocatechuate degradation I (meta-cleavage pathway)	8	6	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	5	1
L-isoleucine biosynthesis II	8	4	1
L-arabinose degradation IV	8	4	1
aromatic biogenic amine degradation (bacteria)	8	3	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of fermentation (Chlamydomonas reinhardtii)	9	9	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	7	1
reductive glycine pathway of autotrophic CO2 fixation	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
cis-geranyl-CoA degradation	9	1	1
superpathway of vanillin and vanillate degradation	10	7	1
superpathway of coenzyme A biosynthesis II (plants)	10	5	1
superpathway of phenylethylamine degradation	11	11	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	11	1
syringate degradation	12	6	1
superpathway of L-arginine and L-ornithine degradation	13	13	1
superpathway of L-isoleucine biosynthesis I	13	13	1
gluconeogenesis I	13	13	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	7	1
L-tryptophan degradation V (side chain pathway)	13	1	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	2	1
mixed acid fermentation	16	16	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	9	1
superpathway of L-threonine metabolism	18	18	1
heterolactic fermentation	18	16	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	1
superpathway of anaerobic sucrose degradation	19	18	1
superpathway of pentose and pentitol degradation	42	21	2
superpathway of N-acetylneuraminate degradation	22	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1