Experiment set2IT075 for Agrobacterium fabrum C58

N-Acetyl-D-Glucosamine carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + N-Acetyl-D-Glucosamine (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 27 genes in this experiment

For carbon source N-Acetyl-D-Glucosamine in Agrobacterium fabrum C58

For carbon source N-Acetyl-D-Glucosamine across organisms

SEED Subsystems

Subsystem	#Specific
Chitin and N-acetylglucosamine utilization	3
Sialic Acid Metabolism	2
UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis	2
Xylose utilization	2
Ammonia assimilation	1
Biogenesis of cytochrome c oxidases	1
Biotin biosynthesis	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
Inositol catabolism	1
Maltose and Maltodextrin Utilization	1
Molybdenum cofactor biosynthesis	1
RNA processing and degradation, bacterial	1
Terminal cytochrome C oxidases	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:

• Nucleotide sugars metabolism
• Aminosugars metabolism
• Galactose metabolism
• Fatty acid metabolism
• Oxidative phosphorylation
• Urea cycle and metabolism of amino groups
• Puromycin biosynthesis
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Benzoate degradation via hydroxylation
• Aminophosphonate metabolism
• Lipopolysaccharide biosynthesis
• Glyoxylate and dicarboxylate metabolism
• Atrazine degradation
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
N-acetylglucosamine degradation I	2	2	2
long-chain fatty acid activation	1	1	1
urea degradation I	3	3	2
N-acetylglucosamine degradation II	3	2	2
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
choline degradation I	2	2	1
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	6	3	3
linoleate biosynthesis II (animals)	2	1	1
arsenite to oxygen electron transfer	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
cyanuric acid degradation II	5	3	2
cyanuric acid degradation I	5	2	2
L-citrulline degradation	3	3	1
choline-O-sulfate degradation	3	3	1
cyanate degradation	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
superpathway of allantoin degradation in yeast	6	3	2
arsenite to oxygen electron transfer (via azurin)	3	1	1
alkane biosynthesis II	3	1	1
oleate biosynthesis I (plants)	3	1	1
aerobic respiration I (cytochrome c)	4	3	1
L-arginine degradation V (arginine deiminase pathway)	4	3	1
D-galactosamine and N-acetyl-D-galactosamine degradation	4	3	1
phytol degradation	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
superpathway of atrazine degradation	8	3	2
chitin derivatives degradation	8	2	2
wax esters biosynthesis II	4	1	1
N-acetylneuraminate and N-acetylmannosamine degradation I	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
phosphatidylcholine acyl editing	4	1	1
sporopollenin precursors biosynthesis	18	4	4
tRNA processing	10	10	2
UDP-N-acetyl-D-glucosamine biosynthesis I	5	5	1
uracil degradation III	5	5	1
N-acetyl-D-galactosamine degradation	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
CMP-N-acetylneuraminate biosynthesis I (eukaryotes)	5	1	1
stearate biosynthesis II (bacteria and plants)	6	5	1
fatty acid salvage	6	5	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
stearate biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	2	1
UDP-N-acetyl-D-galactosamine biosynthesis III	6	2	1
Fe(II) oxidation	6	2	1
stearate biosynthesis I (animals)	6	1	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
ceramide degradation by α-oxidation	7	2	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
chitin degradation I (archaea)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
superpathway of N-acetylneuraminate degradation	22	12	3
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
2-deoxy-D-ribose degradation II	8	2	1
photorespiration I	9	6	1
photorespiration III	9	6	1
chitin biosynthesis	9	5	1
allantoin degradation IV (anaerobic)	9	4	1
photorespiration II	10	6	1
CMP-legionaminate biosynthesis I	10	2	1
suberin monomers biosynthesis	20	3	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
O-antigen building blocks biosynthesis (E. coli)	11	11	1
peptidoglycan recycling I	14	8	1
superpathway of CMP-sialic acids biosynthesis	15	1	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	6	1
superpathway of fatty acids biosynthesis (E. coli)	53	49	2
palmitate biosynthesis III	29	28	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	13	1
oleate β-oxidation	35	27	1