Experiment set24S531 for Agrobacterium fabrum C58

LB with Chloramphenicol 6.25 ug/mL

Group: stress
Media: LB + Chloramphenicol (6.25 ug/mL)
Culturing: Agro_ML11b, 24_well_plate, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 4/26/2025
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride

Specific Phenotypes

For 12 genes in this experiment

For stress Chloramphenicol in Agrobacterium fabrum C58

For stress Chloramphenicol across organisms

SEED Subsystems

Subsystem	#Specific
Multidrug Resistance Efflux Pumps	3
Conserved gene cluster associated with Met-tRNA formyltransferase	2
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	2
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Glycine and Serine Utilization	1
Pyruvate Alanine Serine Interconversions	1
Ribosome biogenesis bacterial	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Histidine metabolism
• Tyrosine metabolism
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Lysine degradation
• Phenylalanine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-serine degradation	3	3	3
D-serine degradation	3	3	2
L-tryptophan degradation II (via pyruvate)	3	2	2
L-cysteine degradation II	3	2	2
glycine betaine degradation III	7	4	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	6	3
glycine degradation	3	3	1
L-methionine biosynthesis II	6	5	2
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	3	2
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	2
purine nucleobases degradation II (anaerobic)	24	14	3