Experiment set36IT080 for Pseudomonas putida KT2440

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: Putida_ML5, 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 57 genes in this experiment

For supernatant Supernatant; Trichoderma atroviride IMI dcr22mutant grown in Vogels_fungal_media, filtered in Pseudomonas putida KT2440

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

SEED Subsystems

Subsystem	#Specific
Iron acquisition in Vibrio	6
Transport of Iron	5
Campylobacter Iron Metabolism	3
Peptidoglycan Biosynthesis	3
Experimental tye	2
Heme and Siroheme Biosynthesis	2
ABC transporter oligopeptide (TC 3.A.1.5.1)	1
ATP-dependent RNA helicases, bacterial	1
Alginate metabolism	1
Ammonia assimilation	1
Arginine and Ornithine Degradation	1
Biogenesis of cytochrome c oxidases	1
Copper homeostasis	1
DNA-replication	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Lipid A modifications	1
Methionine Salvage	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Oxidative stress	1
Redox-dependent regulation of nucleus processes	1
Transcription factors bacterial	1
Transport of Zinc	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lipopolysaccharide biosynthesis
• Porphyrin and chlorophyll metabolism
• Peptidoglycan biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Methionine metabolism
• Geraniol degradation
• Arginine and proline metabolism
• Benzoxazinone biosynthesis
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Keratan sulfate biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Nicotinate and nicotinamide metabolism
• Folate biosynthesis
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Nitrogen metabolism
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation I	1	1	1
cis-cyclopropane fatty acid (CFA) biosynthesis	1	1	1
3-methylthiopropanoate biosynthesis	1	1	1
L-glutamine degradation II	1	1	1
acetate formation from acetyl-CoA (succinate)	1	1	1
ammonia assimilation cycle III	3	3	2
siroheme biosynthesis	4	4	2
sterculate biosynthesis	2	1	1
pyruvate fermentation to acetate V	3	3	1
pyruvate fermentation to acetate VI	3	2	1
L-glutamate and L-glutamine biosynthesis	7	6	2
factor 430 biosynthesis	7	3	2
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
heme b biosynthesis II (oxygen-independent)	4	3	1
tetrapyrrole biosynthesis II (from glycine)	4	3	1
L-arginine degradation II (AST pathway)	5	5	1
NAD salvage pathway V (PNC V cycle)	5	2	1
tetrapyrrole biosynthesis I (from glutamate)	6	6	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	4	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	2
cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation)	13	13	2
NAD salvage pathway I (PNC VI cycle)	7	4	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation I	7	2	1
succinate fermentation to butanoate	7	1	1
cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion)	15	13	2
L-citrulline biosynthesis	8	7	1
superpathway of heme b biosynthesis from glycine	8	6	1
TCA cycle VII (acetate-producers)	9	8	1
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	3	1
superpathway of heme b biosynthesis from glutamate	10	9	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	5	1
adenosylcobalamin biosynthesis II (aerobic)	33	31	3
L-methionine salvage cycle III	11	5	1
NAD salvage (plants)	11	4	1
L-methionine salvage cycle II (plants)	11	4	1
adenosylcobalamin biosynthesis I (anaerobic)	36	29	3
superpathway of L-citrulline metabolism	12	9	1
L-methionine salvage cycle I (bacteria and plants)	12	5	1
superpathway of bacteriochlorophyll a biosynthesis	26	6	2
superpathway of NAD biosynthesis in eukaryotes	14	5	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
mycolate biosynthesis	205	20	3
superpathway of mycolate biosynthesis	239	21	3