Experiment set2IT074 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 29 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
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Biogenesis of cytochrome c oxidases	1
Biotin biosynthesis	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
Glutathione-regulated potassium-efflux system and associated functions	1
Homogentisate pathway of aromatic compound degradation	1
Inositol catabolism	1
Maltose and Maltodextrin Utilization	1
Potassium homeostasis	1
Pyruvate Alanine Serine Interconversions	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
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Lysine degradation
• Arginine and proline metabolism
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Aminophosphonate metabolism
• D-Arginine and D-ornithine metabolism
• D-Alanine metabolism
• Glyoxylate and dicarboxylate metabolism
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
N-acetylglucosamine degradation I	2	2	2
D-alanine degradation	1	1	1
long-chain fatty acid activation	1	1	1
N-acetylglucosamine degradation II	3	2	2
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
choline degradation I	2	2	1
superpathway of N-acetylglucosamine, N-acetylmannosamine and N-acetylneuraminate degradation	6	3	3
arsenite to oxygen electron transfer	2	1	1
linoleate biosynthesis II (animals)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
choline-O-sulfate degradation	3	3	1
3-methyl-branched fatty acid α-oxidation	6	3	2
alkane biosynthesis II	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
oleate biosynthesis I (plants)	3	1	1
D-galactosamine and N-acetyl-D-galactosamine degradation	4	3	1
phytol degradation	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
chitin derivatives degradation	8	2	2
long chain fatty acid ester synthesis (engineered)	4	1	1
N-acetylneuraminate and N-acetylmannosamine degradation I	4	1	1
phosphatidylcholine acyl editing	4	1	1
wax esters biosynthesis II	4	1	1
sporopollenin precursors biosynthesis	18	4	4
tRNA processing	10	10	2
UDP-N-acetyl-D-glucosamine biosynthesis I	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
fatty acid salvage	6	5	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	4	1
UDP-N-acetyl-D-galactosamine biosynthesis III	6	2	1
Fe(II) oxidation	6	2	1
6-gingerol analog biosynthesis (engineered)	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
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
chitin degradation I (archaea)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	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 III	9	6	1
photorespiration I	9	6	1
chitin biosynthesis	9	5	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