Experiment set15IT070 for Shewanella oneidensis MR-1

C.elegans, mixed culture-2

Group: micoeukaryotes
Media: LB (0.1x) + Pelleted after growth overnight in LB+Kan50 + CaCl2, MgSO4 (10mM ), pH=7
Culturing: MR1_ML3b, 48-well_plate, Aerobic, at 30 (C), shaken=700 rpm
By: VM on 6/23/21
Media components: 1 g/L Tryptone, 0.5 g/L Yeast Extract, 0.5 g/L Sodium Chloride (final concentrations)

Specific Phenotypes

For 21 genes in this experiment

For micoeukaryotes Pelleted after growth overnight in LB+Kan50 in Shewanella oneidensis MR-1

For micoeukaryotes Pelleted after growth overnight in LB+Kan50 across organisms

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Bacterial hemoglobins	1
Ribosome biogenesis bacterial	1
Ton and Tol transport systems	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ubiquinone and menaquinone biosynthesis
• Glutamate metabolism
• Arginine and proline metabolism
• Nitrogen metabolism
• Fatty acid biosynthesis
• Urea cycle and metabolism of amino groups
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• alpha-Linolenic acid metabolism
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• 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
ammonia assimilation cycle III	3	3	3
L-glutamate biosynthesis I	2	2	2
L-glutamine biosynthesis I	1	1	1
L-glutamine degradation I	1	1	1
L-glutamine degradation II	1	1	1
ammonia assimilation cycle I	2	2	1
ammonia assimilation cycle II	2	2	1
L-glutamate and L-glutamine biosynthesis	7	6	3
superpathway of ammonia assimilation (plants)	3	3	1
L-aspartate degradation III (anaerobic)	3	1	1
L-aspartate degradation II (aerobic)	3	1	1
putrescine degradation II	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	1	1
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
2-carboxy-1,4-naphthoquinol biosynthesis	7	7	1
L-citrulline biosynthesis	8	7	1
superpathway of ornithine degradation	8	6	1
superpathway of demethylmenaquinol-8 biosynthesis I	9	9	1
superpathway of demethylmenaquinol-6 biosynthesis I	9	8	1
superpathway of demethylmenaquinol-9 biosynthesis	9	8	1
superpathway of menaquinol-8 biosynthesis I	10	10	1
superpathway of menaquinol-6 biosynthesis	10	9	1
superpathway of menaquinol-9 biosynthesis	10	9	1
L-arginine biosynthesis II (acetyl cycle)	10	9	1
superpathway of menaquinol-10 biosynthesis	10	9	1
superpathway of menaquinol-13 biosynthesis	10	9	1
superpathway of menaquinol-12 biosynthesis	10	9	1
superpathway of menaquinol-7 biosynthesis	10	9	1
superpathway of menaquinol-11 biosynthesis	10	9	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of L-arginine and L-ornithine degradation	13	8	1
superpathway of phylloquinol biosynthesis	15	8	1
superpathway of chorismate metabolism	59	50	1