Experiment set2IT023 for Agrobacterium fabrum C58

m-Inositol carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + m-Inositol (10 mM)
Culturing: Agro_ML11, 24-well transparent microplate; Multitron, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 10/20/20
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 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 19 genes in this experiment

For carbon source m-Inositol in Agrobacterium fabrum C58

For carbon source m-Inositol across organisms

SEED Subsystems

Subsystem	#Specific
Inositol catabolism	5
D-ribose utilization	2
Phosphate metabolism	2
Biotin biosynthesis	1
Cysteine Biosynthesis	1
n-Phenylalkanoic acid degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Inositol phosphate metabolism
• Benzoate degradation via CoA ligation
• Nicotinate and nicotinamide metabolism
• Limonene and pinene degradation
• Pentose and glucuronate interconversions
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Cysteine metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Selenoamino acid metabolism
• alpha-Linolenic acid metabolism
• Biphenyl degradation
• Ethylbenzene degradation
• Sulfur metabolism
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of ansamycins
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
long-chain fatty acid activation	1	1	1
myo-inositol degradation I	7	6	4
L-cysteine biosynthesis I	2	2	1
linoleate biosynthesis II (animals)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
myo-, chiro- and scyllo-inositol degradation	10	6	4
3-methyl-branched fatty acid α-oxidation	6	3	2
oleate biosynthesis I (plants)	3	1	1
alkane biosynthesis II	3	1	1
phytol degradation	4	3	1
wax esters biosynthesis II	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
phosphatidylcholine acyl editing	4	1	1
sporopollenin precursors biosynthesis	18	4	4
seleno-amino acid biosynthesis (plants)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
stearate biosynthesis II (bacteria and plants)	6	5	1
fatty acid salvage	6	5	1
stearate biosynthesis IV	6	4	1
NAD(P)/NADPH interconversion	6	3	1
6-gingerol analog biosynthesis (engineered)	6	2	1
stearate biosynthesis I (animals)	6	1	1
ceramide degradation by α-oxidation	7	2	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
2-deoxy-D-ribose degradation II	8	2	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
suberin monomers biosynthesis	20	3	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of seleno-compound metabolism	19	8	1
superpathway of fatty acids biosynthesis (E. coli)	53	49	2
palmitate biosynthesis III	29	28	1
oleate β-oxidation	35	27	1