Experiment set2IT066 for Agrobacterium fabrum C58

Melibiose carbon source

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

For carbon source Melibiose in Agrobacterium fabrum C58

For carbon source Melibiose across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter oligopeptide (TC 3.A.1.5.1)	2
Fructooligosaccharides(FOS) and Raffinose Utilization	2
Galactosylceramide and Sulfatide metabolism	2
Lactose and Galactose Uptake and Utilization	2
Melibiose Utilization	2
Biotin biosynthesis	1
D-galactonate catabolism	1
Fatty Acid Biosynthesis FASII	1
Sex pheromones in Enterococcus faecalis and other Firmicutes	1
mycolic acid synthesis	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:

• Galactose metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Glycerolipid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - globo series
• Biosynthesis of unsaturated fatty acids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
melibiose degradation	1	1	1
long-chain fatty acid activation	1	1	1
D-galactose degradation II	2	2	1
γ-linolenate biosynthesis II (animals)	2	1	1
linoleate biosynthesis II (animals)	2	1	1
stearate biosynthesis II (bacteria and plants)	6	5	2
stearate biosynthesis IV	6	4	2
D-galactonate degradation	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
alkane biosynthesis II	3	1	1
oleate biosynthesis I (plants)	3	1	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	9
stachyose degradation	7	4	2
superpathway of fatty acid biosynthesis II (plant)	43	38	12
palmitate biosynthesis III	29	28	8
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	12	3
gondoate biosynthesis (anaerobic)	4	4	1
phytol degradation	4	3	1
long chain fatty acid ester synthesis (engineered)	4	1	1
phosphatidylcholine acyl editing	4	1	1
wax esters biosynthesis II	4	1	1
superpathway of fatty acids biosynthesis (E. coli)	53	49	13
tetradecanoate biosynthesis (mitochondria)	25	23	6
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
sporopollenin precursors biosynthesis	18	4	4
oleate biosynthesis IV (anaerobic)	14	13	3
fatty acid elongation -- saturated	5	5	1
8-amino-7-oxononanoate biosynthesis IV	5	5	1
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	18	4
cis-vaccenate biosynthesis	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
8-amino-7-oxononanoate biosynthesis I	11	9	2
anteiso-branched-chain fatty acid biosynthesis	34	30	6
even iso-branched-chain fatty acid biosynthesis	34	30	6
odd iso-branched-chain fatty acid biosynthesis	34	30	6
(5Z)-dodecenoate biosynthesis I	6	6	1
fatty acid salvage	6	5	1
(5Z)-dodecenoate biosynthesis II	6	5	1
petroselinate biosynthesis	6	2	1
6-gingerol analog biosynthesis (engineered)	6	2	1
stearate biosynthesis I (animals)	6	1	1
streptorubin B biosynthesis	34	20	5
L-glucose degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	15	2
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
2-allylmalonyl-CoA biosynthesis	8	2	1
2-deoxy-D-ribose degradation II	8	2	1
suberin monomers biosynthesis	20	3	2
cutin biosynthesis	16	1	1
oleate β-oxidation	35	27	1
mycolate biosynthesis	205	21	5
superpathway of mycolate biosynthesis	239	22	5