Experiment set2IT022 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 21 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
Branched-Chain Amino Acid Biosynthesis	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Folate Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Pyridoxin (Vitamin B6) 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
• Nicotinate and nicotinamide metabolism
• Pentose and glucuronate interconversions
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Biphenyl degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Vitamin B6 metabolism
• Folate biosynthesis
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of ansamycins
• Biosynthesis of phenylpropanoids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
long-chain fatty acid activation	1	1	1
L-glutamine degradation I	1	1	1
myo-inositol degradation I	7	6	4
pyridoxal 5'-phosphate salvage I	6	6	3
4-aminobenzoate biosynthesis I	2	2	1
L-glutamate 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
pyridoxal 5'-phosphate salvage II (plants)	9	9	3
ammonia assimilation cycle III	3	3	1
3-methyl-branched fatty acid α-oxidation	6	3	2
alkane biosynthesis II	3	1	1
oleate biosynthesis I (plants)	3	1	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	11	3
phytol degradation	4	3	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	5	2
long chain fatty acid ester synthesis (engineered)	4	1	1
wax esters biosynthesis II	4	1	1
phosphatidylcholine acyl editing	4	1	1
sporopollenin precursors biosynthesis	18	4	4
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
fatty acid salvage	6	5	1
stearate biosynthesis II (bacteria and plants)	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
L-glutamate and L-glutamine biosynthesis	7	4	1
ceramide degradation by α-oxidation	7	2	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
L-citrulline biosynthesis	8	7	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
2-deoxy-D-ribose degradation II	8	2	1
chloramphenicol biosynthesis	9	1	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
suberin monomers biosynthesis	20	3	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
superpathway of candicidin biosynthesis	11	4	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
superpathway of L-citrulline metabolism	12	9	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of fatty acids biosynthesis (E. coli)	53	49	2
palmitate biosynthesis III	29	28	1
oleate β-oxidation	35	27	1
superpathway of chorismate metabolism	59	38	1