Experiment set10IT038 for Agrobacterium fabrum C58

4-Hydroxybenzoic Acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 4-Hydroxybenzoic Acid (2.5 mM), pH=7
Culturing: Agro_ML11, 24-well plate, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 1/6/22
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 11 genes in this experiment

For carbon source 4-Hydroxybenzoic Acid in Agrobacterium fabrum C58

For carbon source 4-Hydroxybenzoic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Protocatechuate branch of beta-ketoadipate pathway	5
Catechol branch of beta-ketoadipate pathway	3
Chloroaromatic degradation pathway	3
Peptidoglycan Biosynthesis	2
Phosphate metabolism	2
Pentose phosphate pathway	1
Type IV pilus	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Benzoate degradation via hydroxylation
• Peptidoglycan biosynthesis
• Lysine degradation
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lipopolysaccharide biosynthesis
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Fatty acid biosynthesis
• Fatty acid elongation in mitochondria
• Synthesis and degradation of ketone bodies
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Glutathione metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Keratan sulfate biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Glycerophospholipid metabolism
• 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
• Propanoate metabolism
• Nicotinate and nicotinamide metabolism
• Biotin metabolism
• Terpenoid biosynthesis
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-oxoadipate degradation	2	2	2
protocatechuate degradation II (ortho-cleavage pathway)	4	4	3
aromatic compounds degradation via β-ketoadipate	9	8	5
catechol degradation III (ortho-cleavage pathway)	6	5	3
acetoacetate degradation (to acetyl CoA)	2	1	1
toluene degradation III (aerobic) (via p-cresol)	11	7	5
superpathway of salicylate degradation	7	6	3
4-methylcatechol degradation (ortho cleavage)	7	3	3
adipate degradation	5	5	2
adipate biosynthesis	5	4	2
5,6-dehydrokavain biosynthesis (engineered)	10	6	4
pentose phosphate pathway (oxidative branch) I	3	3	1
benzoyl-CoA biosynthesis	3	3	1
polyhydroxybutanoate biosynthesis	3	2	1
ketolysis	3	2	1
catechol degradation to β-ketoadipate	4	3	1
4-sulfocatechol degradation	4	2	1
(2S)-ethylmalonyl-CoA biosynthesis	4	2	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	3	3
oleate β-oxidation	35	27	8
valproate β-oxidation	9	5	2
2-methyl-branched fatty acid β-oxidation	14	9	3
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	5	1
glutaryl-CoA degradation	5	3	1
4-hydroxybenzoate biosynthesis III (plants)	5	3	1
ketogenesis	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	2	2
fatty acid β-oxidation VII (yeast peroxisome)	5	1	1
pyruvate fermentation to acetone	5	1	1
isopropanol biosynthesis (engineered)	5	1	1
ethylbenzene degradation (anaerobic)	5	1	1
pyruvate fermentation to hexanol (engineered)	11	7	2
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	3
peptidoglycan biosynthesis II (staphylococci)	17	12	3
fatty acid salvage	6	5	1
L-isoleucine degradation I	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
NAD(P)/NADPH interconversion	6	3	1
propanoate fermentation to 2-methylbutanoate	6	3	1
mandelate degradation to acetyl-CoA	18	8	3
superpathway of aerobic toluene degradation	30	12	5
4-ethylphenol degradation (anaerobic)	6	2	1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast)	6	1	1
jasmonic acid biosynthesis	19	4	3
fatty acid β-oxidation I (generic)	7	4	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	15	5
pyruvate fermentation to butanoate	7	3	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
benzoyl-CoA degradation I (aerobic)	7	3	1
acetyl-CoA fermentation to butanoate	7	2	1
mevalonate pathway II (haloarchaea)	7	1	1
mevalonate pathway I (eukaryotes and bacteria)	7	1	1
pentose phosphate pathway	8	8	1
pyruvate fermentation to butanol I	8	4	1
2-methylpropene degradation	8	3	1
2-deoxy-D-ribose degradation II	8	2	1
isoprene biosynthesis II (engineered)	8	1	1
mevalonate pathway III (Thermoplasma)	8	1	1
mevalonate pathway IV (archaea)	8	1	1
androstenedione degradation I (aerobic)	25	6	3
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	3	1
phenylacetate degradation I (aerobic)	9	3	1
4-oxopentanoate degradation	9	2	1
superpathway of testosterone and androsterone degradation	28	6	3
L-glutamate degradation V (via hydroxyglutarate)	10	4	1
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)	10	4	1
3-phenylpropanoate degradation	10	4	1
methyl tert-butyl ether degradation	10	3	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
superpathway of phenylethylamine degradation	11	3	1
ethylmalonyl-CoA pathway	11	3	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	8	4
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	11	1
L-glutamate degradation VII (to butanoate)	12	4	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	1	1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	1	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
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
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
L-tryptophan degradation III (eukaryotic)	15	4	1
glycerol degradation to butanol	16	11	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	3	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	5	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	3	1
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
toluene degradation VI (anaerobic)	18	3	1
sitosterol degradation to androstenedione	18	1	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	2	1
superpathway of cholesterol degradation III (oxidase)	49	4	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	1
platensimycin biosynthesis	26	6	1
superpathway of ergosterol biosynthesis I	26	3	1
1-butanol autotrophic biosynthesis (engineered)	27	18	1
superpathway of cholesterol biosynthesis	38	3	1
superpathway of L-lysine degradation	43	10	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	18	1