Experiment set24S524 for Agrobacterium fabrum C58

LB with Erythromycin 12.5 ug/mL

Group: stress
Media: LB + Erythromycin (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 86 genes in this experiment

For stress Erythromycin in Agrobacterium fabrum C58

For stress Erythromycin across organisms

SEED Subsystems

Subsystem	#Specific
Peptidoglycan Biosynthesis	4
Heat shock dnaK gene cluster extended	3
Multidrug Resistance Efflux Pumps	3
Bacterial hemoglobins	2
Conserved gene cluster associated with Met-tRNA formyltransferase	2
Glycogen metabolism	2
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	2
Phosphate metabolism	2
ATP-dependent RNA helicases, bacterial	1
Anaerobic respiratory reductases	1
Arginine and Ornithine Degradation	1
Arsenic resistance	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Copper homeostasis: copper tolerance	1
Experimental tye	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine Biosynthesis	1
Glycine and Serine Utilization	1
Heme and Siroheme Biosynthesis	1
Hfl operon	1
Histidine Degradation	1
Maltose and Maltodextrin Utilization	1
NAD regulation	1
Oxidative stress	1
Potassium homeostasis	1
Protein degradation	1
Pyrimidine utilization	1
Pyruvate Alanine Serine Interconversions	1
RNA processing and degradation, bacterial	1
Sex pheromones in Enterococcus faecalis and other Firmicutes	1
Synechocystis experimental	1
Trehalose Biosynthesis	1
Triacylglycerol metabolism	1
Two cell division clusters relating to chromosome partitioning	1
Type IV pilus	1
Universal GTPases	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Peptidoglycan biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Lipopolysaccharide biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Pyrimidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Starch and sucrose metabolism
• Glycerophospholipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Porphyrin and chlorophyll metabolism
• Flavonoid biosynthesis
• Alkaloid biosynthesis I
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Benzoxazinone biosynthesis
• D-Arginine and D-ornithine metabolism
• D-Alanine metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Keratan sulfate biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Ether lipid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Methane metabolism
• Biotin metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Zeatin biosynthesis
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavone and flavonol 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
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate degradation I	1	1	1
D-alanine degradation	1	1	1
L-arginine degradation VII (arginase 3 pathway)	2	2	1
putrescine biosynthesis III	2	2	1
L-canavanine degradation I	2	1	1
pseudouridine degradation	2	1	1
arsenate detoxification III	2	1	1
L-threonine degradation II	2	1	1
glycogen degradation I	8	6	3
Arg/N-end rule pathway (eukaryotic)	14	8	5
L-alanine degradation II (to D-lactate)	3	3	1
glycogen degradation II	6	5	2
L-arginine degradation I (arginase pathway)	3	2	1
ethene biosynthesis IV (engineered)	3	1	1
Ac/N-end rule pathway	21	6	6
superpathway of putrescine biosynthesis	4	4	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	4	1
L-arginine degradation VI (arginase 2 pathway)	4	3	1
starch degradation III	4	2	1
arsenic detoxification (bacteria)	4	2	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
starch degradation V	4	2	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	3	3
glycogen biosynthesis II (from UDP-D-Glucose)	4	1	1
tRNA processing	10	10	2
L-histidine degradation II	5	5	1
urea cycle	5	4	1
starch biosynthesis	10	6	2
dibenzothiophene desulfurization	5	1	1
peptidoglycan biosynthesis II (staphylococci)	17	12	3
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	3
adenosylcobinamide-GDP biosynthesis from cobyrinate a,c-diamide	6	6	1
tetrapyrrole biosynthesis I (from glutamate)	6	5	1
arsenate detoxification I	6	3	1
arsenic detoxification (plants)	6	2	1
L-Nδ-acetylornithine biosynthesis	7	5	1
4-aminobutanoate degradation V	7	2	1
L-glutamate degradation XI (reductive Stickland reaction)	7	1	1
L-citrulline biosynthesis	8	7	1
superpathway of polyamine biosynthesis I	8	5	1
sucrose biosynthesis II	8	5	1
bacterial bioluminescence	8	4	1
superpathway of polyamine biosynthesis II	8	3	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	2	1
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
superpathway of heme b biosynthesis from glutamate	10	8	1
L-glutamate degradation V (via hydroxyglutarate)	10	4	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	11	1
superpathway of L-citrulline metabolism	12	9	1
arsenic detoxification (yeast)	12	3	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	4	1
adenosylcobalamin biosynthesis II (aerobic)	33	29	2
superpathway of arginine and polyamine biosynthesis	17	14	1
adenosylcobalamin biosynthesis I (anaerobic)	36	26	2
superpathway of L-threonine metabolism	18	11	1
methylaspartate cycle	19	12	1