Experiment set3IT026 for Agrobacterium fabrum C58

6-aminocaproic acid nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Succinate_noNitrogen + e-Amino-N-Caproic Acid (10 mM)
Culturing: Agro_ML11, 24-well transparent microplate; Multitron, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 11/20/20
Media components: 10 mM Sodium succinate dibasic hexahydrate, 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 5 genes in this experiment

For nitrogen source e-Amino-N-Caproic Acid in Agrobacterium fabrum C58

For nitrogen source e-Amino-N-Caproic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Pyruvate Alanine Serine Interconversions	2
Fatty Acid Biosynthesis FASII	1
Respiratory dehydrogenases 1	1
mycolic acid synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid biosynthesis
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Phenylalanine metabolism
• beta-Alanine metabolism
• Propanoate metabolism
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Pantothenate and CoA biosynthesis
• Nitrogen metabolism
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-alanine degradation I	2	2	1
β-alanine degradation II	2	2	1
pyruvate fermentation to (R)-acetoin II	2	1	1
pyruvate fermentation to (R)-acetoin I	3	3	1
pyruvate fermentation to (S)-acetoin	3	2	1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	12	3
L-valine biosynthesis	4	4	1
gondoate biosynthesis (anaerobic)	4	4	1
palmitate biosynthesis III	29	28	7
tetradecanoate biosynthesis (mitochondria)	25	23	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	49	11
fatty acid elongation -- saturated	5	5	1
8-amino-7-oxononanoate biosynthesis IV	5	5	1
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	18	4
superpathway of (R,R)-butanediol biosynthesis	5	4	1
cis-vaccenate biosynthesis	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
superpathway of fatty acid biosynthesis II (plant)	43	38	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
anteiso-branched-chain fatty acid biosynthesis	34	30	6
even iso-branched-chain fatty acid biosynthesis	34	30	6
odd iso-branched-chain fatty acid biosynthesis	34	30	6
(5Z)-dodecenoate biosynthesis I	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
(5Z)-dodecenoate biosynthesis II	6	5	1
stearate biosynthesis IV	6	4	1
L-isoleucine biosynthesis IV	6	3	1
β-alanine biosynthesis II	6	3	1
petroselinate biosynthesis	6	2	1
superpathway of 2,3-butanediol biosynthesis	6	2	1
streptorubin B biosynthesis	34	20	5
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	15	2
L-isoleucine biosynthesis II	8	5	1
2-allylmalonyl-CoA biosynthesis	8	2	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of coenzyme A biosynthesis II (plants)	10	7	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	11	1
mycolate biosynthesis	205	21	5
superpathway of mycolate biosynthesis	239	22	5