Experiment set24S532 for Agrobacterium fabrum C58

LB with Chloramphenicol 12.5 ug/mL

Group: stress
Media: LB + Chloramphenicol (12.5 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 41 genes in this experiment

For stress Chloramphenicol in Agrobacterium fabrum C58

For stress Chloramphenicol across organisms

SEED Subsystems

Subsystem	#Specific
Multidrug Resistance Efflux Pumps	5
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	4
Conserved gene cluster associated with Met-tRNA formyltransferase	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Acetyl-CoA fermentation to Butyrate	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Butanol Biosynthesis	1
Experimental tye	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Heme and Siroheme Biosynthesis	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Peptidoglycan Biosynthesis	1
Polyhydroxybutyrate metabolism	1
Ribosome biogenesis bacterial	1
ZZ gjo need homes	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lipopolysaccharide biosynthesis
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Fatty acid metabolism
• Purine metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Glycerophospholipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Ethylbenzene degradation
• Porphyrin and chlorophyll metabolism
• Flavonoid biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid elongation in mitochondria
• Synthesis and degradation of ketone bodies
• Ubiquinone and menaquinone biosynthesis
• Glutamate metabolism
• Geraniol degradation
• Arginine and proline metabolism
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Benzoxazinone biosynthesis
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Keratan sulfate biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Pyruvate metabolism
• 2,4-Dichlorobenzoate degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Propanoate metabolism
• Folate biosynthesis
• Retinol metabolism
• Terpenoid biosynthesis
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Zeatin biosynthesis
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavone and flavonol biosynthesis
• Insect hormone biosynthesis
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate degradation I	1	1	1
acetoacetate degradation (to acetyl CoA)	2	1	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	5	2
5,6-dehydrokavain biosynthesis (engineered)	10	6	4
glutaryl-CoA degradation	5	3	2
L-alanine degradation II (to D-lactate)	3	3	1
benzoyl-CoA biosynthesis	3	3	1
pyruvate fermentation to butanol II (engineered)	6	4	2
polyhydroxybutanoate biosynthesis	3	2	1
ketolysis	3	2	1
ethene biosynthesis IV (engineered)	3	1	1
L-glutamate degradation V (via hydroxyglutarate)	10	4	3
pyruvate fermentation to butanoate	7	3	2
pyruvate fermentation to hexanol (engineered)	11	7	3
oleate β-oxidation	35	27	9
heme b biosynthesis II (oxygen-independent)	4	3	1
pyruvate fermentation to butanol I	8	4	2
(2S)-ethylmalonyl-CoA biosynthesis	4	2	1
2-methylpropene degradation	8	3	2
valproate β-oxidation	9	5	2
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	3	2
2-methyl-branched fatty acid β-oxidation	14	9	3
fatty acid β-oxidation II (plant peroxisome)	5	3	1
ketogenesis	5	3	1
4-hydroxybenzoate biosynthesis III (plants)	5	3	1
methyl tert-butyl ether degradation	10	3	2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	2	2
ethylbenzene degradation (anaerobic)	5	1	1
fatty acid β-oxidation VII (yeast peroxisome)	5	1	1
isopropanol biosynthesis (engineered)	5	1	1
pyruvate fermentation to acetone	5	1	1
fatty acid salvage	6	5	1
L-isoleucine degradation I	6	4	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	4	1
propanoate fermentation to 2-methylbutanoate	6	3	1
L-glutamate degradation VII (to butanoate)	12	4	2
4-ethylphenol degradation (anaerobic)	6	2	1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast)	6	1	1
jasmonic acid biosynthesis	19	4	3
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	2
fatty acid β-oxidation I (generic)	7	4	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
4-aminobutanoate degradation V	7	2	1
acetyl-CoA fermentation to butanoate	7	2	1
mevalonate pathway I (eukaryotes and bacteria)	7	1	1
mevalonate pathway II (haloarchaea)	7	1	1
L-glutamate degradation XI (reductive Stickland reaction)	7	1	1
L-tryptophan degradation III (eukaryotic)	15	4	2
glycerol degradation to butanol	16	11	2
2-deoxy-D-ribose degradation II	8	2	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	3	2
mevalonate pathway III (Thermoplasma)	8	1	1
mevalonate pathway IV (archaea)	8	1	1
isoprene biosynthesis II (engineered)	8	1	1
androstenedione degradation I (aerobic)	25	6	3
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	5	2
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	3	2
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	2
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	2	1
4-oxopentanoate degradation	9	2	1
toluene degradation VI (anaerobic)	18	3	2
superpathway of testosterone and androsterone degradation	28	6	3
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)	10	4	1
3-phenylpropanoate degradation	10	4	1
L-lysine fermentation to acetate and butanoate	10	2	1
superpathway of cholesterol degradation I (cholesterol oxidase)	42	8	4
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	1
ethylmalonyl-CoA pathway	11	3	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	8	4
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	1	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	1	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
1-butanol autotrophic biosynthesis (engineered)	27	18	2
androstenedione degradation II (anaerobic)	27	4	2
superpathway of glyoxylate cycle and fatty acid degradation	14	12	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
sitosterol degradation to androstenedione	18	1	1
methylaspartate cycle	19	12	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	2	1
superpathway of cholesterol degradation III (oxidase)	49	4	2
platensimycin biosynthesis	26	6	1
superpathway of bacteriochlorophyll a biosynthesis	26	6	1
superpathway of ergosterol biosynthesis I	26	3	1
superpathway of cholesterol biosynthesis	38	3	1
superpathway of L-lysine degradation	43	10	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	18	1