Experiment set6IT029 for Paraburkholderia bryophila 376MFSha3.1

4-Hydroxybenzoic Acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 4-Hydroxybenzoic Acid (10 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Burk376_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700rpm
By: RobinH_and_TrentonO on 13-Feb-19
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 34 genes in this experiment

For carbon source 4-Hydroxybenzoic Acid in Paraburkholderia bryophila 376MFSha3.1

For carbon source 4-Hydroxybenzoic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	2
Phosphate metabolism	2
Arginine Biosynthesis extended	1
Aromatic Amin Catabolism	1
CO Dehydrogenase	1
Carbon monoxide dehydrogenase maturation factors	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycine reductase, sarcosine reductase and betaine reductase	1
Hfl operon	1
Maltose and Maltodextrin Utilization	1
Multidrug Resistance Efflux Pumps	1
Polyadenylation bacterial	1
Proline Synthesis	1
Thioredoxin-disulfide reductase	1
Trehalose Biosynthesis	1
Wyeosine-MimG Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Fatty acid metabolism
• Lysine biosynthesis
• Histidine metabolism
• Tryptophan metabolism
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Pyrimidine metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Tyrosine metabolism
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Benzoxazinone biosynthesis
• beta-Alanine metabolism
• Aminophosphonate metabolism
• Starch and sucrose metabolism
• High-mannose type N-glycan biosynthesis
• Nucleotide sugars metabolism
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Sphingolipid metabolism
• Pyruvate metabolism
• Biphenyl degradation
• Toluene and xylene degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Fluorene degradation
• Carbazole degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Ethylbenzene degradation
• Styrene degradation
• Butanoate metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
long-chain fatty acid activation	1	1	1
phytol degradation	4	3	2
3-methyl-branched fatty acid α-oxidation	6	3	3
linoleate biosynthesis II (animals)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
thioredoxin pathway	2	1	1
octane oxidation	5	4	2
sphingosine and sphingosine-1-phosphate metabolism	10	4	4
2-hydroxypenta-2,4-dienoate degradation	3	3	1
L-ornithine biosynthesis II	3	3	1
ethanol degradation IV	3	3	1
cardiolipin biosynthesis II	3	3	1
ethanol degradation II	3	3	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
histamine degradation	3	1	1
oleate biosynthesis I (plants)	3	1	1
alkane biosynthesis II	3	1	1
ceramide degradation by α-oxidation	7	2	2
L-proline biosynthesis I (from L-glutamate)	4	4	1
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas)	4	3	1
putrescine degradation III	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	4
long chain fatty acid ester synthesis (engineered)	4	1	1
phosphatidylcholine acyl editing	4	1	1
wax esters biosynthesis II	4	1	1
sporopollenin precursors biosynthesis	18	4	4
L-ornithine biosynthesis I	5	5	1
catechol degradation I (meta-cleavage pathway)	5	4	1
mitochondrial NADPH production (yeast)	5	3	1
dopamine degradation	5	1	1
stearate biosynthesis II (bacteria and plants)	6	5	1
fatty acid salvage	6	5	1
glycogen degradation II	6	5	1
stearate biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	3	1
toluene degradation II (aerobic) (via 4-methylcatechol)	6	1	1
stearate biosynthesis I (animals)	6	1	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
catechol degradation II (meta-cleavage pathway)	7	6	1
L-Nδ-acetylornithine biosynthesis	7	5	1
capsaicin biosynthesis	7	4	1
toluene degradation V (aerobic) (via toluene-cis-diol)	7	3	1
serotonin degradation	7	3	1
toluene degradation I (aerobic) (via o-cresol)	7	3	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
limonene degradation IV (anaerobic)	7	1	1
L-citrulline biosynthesis	8	7	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation	8	5	1
p-cumate degradation	8	3	1
aromatic biogenic amine degradation (bacteria)	8	2	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
phenylacetate degradation I (aerobic)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
4-chloronitrobenzene degradation	9	2	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
meta cleavage pathway of aromatic compounds	10	9	1
suberin monomers biosynthesis	20	3	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
superpathway of phenylethylamine degradation	11	9	1
p-cymene degradation	11	4	1
superpathway of L-citrulline metabolism	12	9	1
L-tryptophan degradation XII (Geobacillus)	12	8	1
L-tryptophan degradation IX	12	8	1
naphthalene degradation to acetyl-CoA	12	5	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
toluene degradation IV (aerobic) (via catechol)	13	9	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of arginine and polyamine biosynthesis	17	14	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	15	1
mandelate degradation to acetyl-CoA	18	13	1
aspartate superpathway	25	22	1
superpathway of fatty acids biosynthesis (E. coli)	53	50	2
palmitate biosynthesis III	29	28	1
superpathway of aerobic toluene degradation	30	16	1
oleate β-oxidation	35	29	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	22	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	18	1