Experiment set10IT057 for Klebsiella michiganensis M5al

RCH2_defined_noCarbon with Supernatant; Trichoderma virens G41 grown in Fungal_growth_media_mCAFEs_v1, filtered and pH-adjusted 0.5x

Group: supernatant
Media: RCH2_defined_noCarbon (0.5x) + supernatant from Trichoderma virens G41 grown in Fungal_growth_media_mCAFEs_v1, filtered and pH-adjusted (0.5 x)
Culturing: Koxy_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Trenton on 5/2/18
Media components: 0.125 g/L Ammonium chloride, 0.05 g/L Potassium Chloride, 0.3 g/L Sodium phosphate monobasic monohydrate, 15 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.015 g/L Magnesium Sulfate Heptahydrate, 0.0075 g/L Nitrilotriacetic acid, 0.005 g/L Sodium Chloride, 0.0025 g/L Manganese (II) sulfate monohydrate, 0.0005 g/L Cobalt chloride hexahydrate, 0.0005 g/L Zinc sulfate heptahydrate, 0.0005 g/L Calcium chloride dihydrate, 0.0005 g/L Iron (II) sulfate heptahydrate, 0.000125 g/L Nickel (II) chloride hexahydrate, 0.0001 g/L Aluminum potassium sulfate dodecahydrate, 5e-05 g/L Copper (II) sulfate pentahydrate, 5e-05 g/L Boric Acid, 5e-05 g/L Sodium Molybdate Dihydrate, 0.0015 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.05 mg/L Pyridoxine HCl, 0.025 mg/L 4-Aminobenzoic acid, 0.025 mg/L Lipoic acid, 0.025 mg/L Nicotinic Acid, 0.025 mg/L Riboflavin, 0.025 mg/L Thiamine HCl, 0.025 mg/L calcium pantothenate, 0.01 mg/L biotin, 0.01 mg/L Folic Acid, 0.0005 mg/L Cyanocobalamin) (final concentrations)
Growth plate: Plate2a B3

Specific Phenotypes

For 12 genes in this experiment

For supernatant Supernatant; Trichoderma virens G41 grown in Fungal_growth_media_mCAFEs_v1, filtered and pH-adjusted in Klebsiella michiganensis M5al

For supernatant Supernatant; Trichoderma virens G41 grown in Fungal_growth_media_mCAFEs_v1, filtered and pH-adjusted across organisms

SEED Subsystems

Subsystem	#Specific
Campylobacter Iron Metabolism	1
Glutathione: Non-redox reactions	1
Iron acquisition in Vibrio	1
Lysine Biosynthesis DAP Pathway	1
Methylglyoxal Metabolism	1
Multidrug Resistance Efflux Pumps	1
Phenylalanine and Tyrosine Branches from Chorismate	1
Phosphate metabolism	1
Purine conversions	1
Stringent Response, (p)ppGpp metabolism	1
Threonine and Homoserine Biosynthesis	1
Transport of Iron	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Lysine biosynthesis
• Glycine, serine and threonine metabolism
• Methionine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Pyruvate metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• 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
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
L-phenylalanine biosynthesis I	3	3	1
L-homoserine biosynthesis	3	3	1
L-tyrosine biosynthesis I	3	3	1
methylglyoxal degradation VIII	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-leucine degradation III	3	2	1
methylglyoxal degradation I	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
L-phenylalanine biosynthesis II	4	3	1
dipicolinate biosynthesis	4	3	1
L-tyrosine biosynthesis III	4	3	1
spermidine biosynthesis II	4	2	1
L-tyrosine degradation III	4	2	1
L-methionine biosynthesis IV	4	2	1
L-phenylalanine degradation III	4	2	1
L-tyrosine biosynthesis II	4	2	1
L-tyrosine degradation I	5	4	1
superpathway of L-phenylalanine and L-tyrosine biosynthesis	5	3	1
ectoine biosynthesis	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-leucine biosynthesis	6	6	1
superpathway of L-threonine biosynthesis	6	6	1
ppGpp metabolism	6	6	1
norspermidine biosynthesis	6	4	1
L-leucine degradation I	6	2	1
L-lysine biosynthesis III	7	6	1
L-lysine biosynthesis VI	7	6	1
3-dehydroquinate biosynthesis II (archaea)	7	3	1
cremeomycin biosynthesis	7	2	1
superpathway of L-homoserine and L-methionine biosynthesis	8	8	1
superpathway of methylglyoxal degradation	8	5	1
superpathway of polyamine biosynthesis III	8	4	1
grixazone biosynthesis	8	2	1
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of S-adenosyl-L-methionine biosynthesis	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	9	1
L-lysine biosynthesis I	9	9	1
L-lysine biosynthesis II	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	2	1
tropane alkaloids biosynthesis	11	1	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	10	1
chorismate biosynthesis II (archaea)	12	8	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	3	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of branched chain amino acid biosynthesis	17	17	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	1
aspartate superpathway	25	24	1
platensimycin biosynthesis	26	6	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of chorismate metabolism	59	54	2
odd iso-branched-chain fatty acid biosynthesis	34	24	1