Experiment set2IT080 for Agrobacterium fabrum C58

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Xylobiose carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Xylobiose (5 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 11 genes in this experiment

For carbon source Xylobiose in Agrobacterium fabrum C58

For carbon source Xylobiose 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
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:

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
D-arabinitol degradation I 2 1 1
linoleate biosynthesis II (animals) 2 1 1
γ-linolenate biosynthesis II (animals) 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
phosphatidylcholine acyl editing 4 1 1
wax esters biosynthesis II 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
stearate biosynthesis II (bacteria and plants) 6 5 1
fatty acid salvage 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
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
capsaicin biosynthesis 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