Experiment set2IT033 for Agrobacterium fabrum C58

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L-Xylose carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-Xylose (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 16 genes in this experiment

For carbon source L-Xylose in Agrobacterium fabrum C58

For carbon source L-Xylose across organisms

SEED Subsystems

Subsystem #Specific
Glycolate, glyoxylate interconversions 4
Photorespiration (oxidative C2 cycle) 3
4-Hydroxyphenylacetic acid catabolic pathway 1
Aromatic amino acid degradation 1
Biogenesis of cytochrome c oxidases 1
Chitin and N-acetylglucosamine utilization 1
Choline and Betaine Uptake and Betaine Biosynthesis 1
Fatty Acid Biosynthesis FASII 1
Gentisare degradation 1
Salicylate and gentisate catabolism 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:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
choline degradation I 2 2 1
glycolate and glyoxylate degradation II 2 2 1
glycine betaine biosynthesis I (Gram-negative bacteria) 2 2 1
glycine betaine biosynthesis II (Gram-positive bacteria) 2 2 1
choline-O-sulfate degradation 3 3 1
D-galactarate degradation II 3 3 1
D-arabinose degradation IV 6 4 2
gentisate degradation I 3 1 1
glycolate and glyoxylate degradation III 3 1 1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast) 12 12 3
gondoate biosynthesis (anaerobic) 4 4 1
D-galactarate degradation I 4 2 1
glycolate and glyoxylate degradation I 4 2 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
8-amino-7-oxononanoate biosynthesis IV 5 5 1
fatty acid elongation -- saturated 5 5 1
superpathway of unsaturated fatty acids biosynthesis (E. coli) 20 18 4
cis-vaccenate biosynthesis 5 4 1
D-xylose degradation VI 5 3 1
superpathway of D-glucarate and D-galactarate degradation 5 3 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
odd iso-branched-chain fatty acid biosynthesis 34 30 6
even 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
D-arabinose degradation III 6 3 1
L-arabinose degradation V 6 2 1
petroselinate biosynthesis 6 2 1
5-nitroanthranilate degradation 6 2 1
streptorubin B biosynthesis 34 20 5
superpathway of glycol metabolism and degradation 7 4 1
L-rhamnose degradation III 7 4 1
biotin biosynthesis I 15 13 2
superpathway of fatty acid biosynthesis I (E. coli) 16 15 2
L-fucose degradation III 8 5 1
4-hydroxyphenylacetate degradation 8 4 1
2-allylmalonyl-CoA biosynthesis 8 2 1
photorespiration I 9 6 1
photorespiration III 9 6 1
photorespiration II 10 6 1
3-phenylpropanoate degradation 10 4 1
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 22 1
mycolate biosynthesis 205 21 5
superpathway of pentose and pentitol degradation 42 16 1
superpathway of mycolate biosynthesis 239 22 5