Experiment set2IT019 for Agrobacterium fabrum C58

methyl-beta-D-xylopyranoside carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + methyl-beta-D-xylopyranoside (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 13 genes in this experiment

For carbon source methyl-beta-D-xylopyranoside in Agrobacterium fabrum C58

For carbon source methyl-beta-D-xylopyranoside across organisms

SEED Subsystems

Subsystem	#Specific
Xylose utilization	3
Biotin biosynthesis	1
Chitin and N-acetylglucosamine utilization	1
D-ribose utilization	1
Fructooligosaccharides(FOS) and Raffinose Utilization	1
Inositol catabolism	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	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:

• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Fatty acid metabolism
• 1- and 2-Methylnaphthalene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-xylose degradation I	2	2	2
long-chain fatty acid activation	1	1	1
xylitol degradation I	2	2	1
γ-linolenate biosynthesis II (animals)	2	1	1
linoleate biosynthesis II (animals)	2	1	1
D-arabinitol degradation I	2	1	1
3-methyl-branched fatty acid α-oxidation	6	3	2
alkane biosynthesis II	3	1	1
oleate biosynthesis I (plants)	3	1	1
phytol degradation	4	3	1
wax esters biosynthesis II	4	1	1
phosphatidylcholine acyl editing	4	1	1
long chain fatty acid ester synthesis (engineered)	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
6-gingerol analog biosynthesis (engineered)	6	2	1
stearate biosynthesis I (animals)	6	1	1
ceramide degradation by α-oxidation	7	2	1
capsaicin biosynthesis	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-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 glucose and xylose degradation	17	16	2
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 pentose and pentitol degradation	42	16	2
superpathway of fatty acids biosynthesis (E. coli)	53	49	2
palmitate biosynthesis III	29	28	1
oleate β-oxidation	35	27	1