Experiment set6IT008 for Paraburkholderia bryophila 376MFSha3.1

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Hydroxy-L-Proline carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Hydroxy-L-Proline (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 2 genes in this experiment

For carbon source Hydroxy-L-Proline in Paraburkholderia bryophila 376MFSha3.1

For carbon source Hydroxy-L-Proline across organisms

SEED Subsystems

Subsystem #Specific
Protocatechuate branch of beta-ketoadipate pathway 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
gallate degradation I 4 4 2
methylgallate degradation 6 5 2
protocatechuate degradation II (ortho-cleavage pathway) 4 4 1
protocatechuate degradation I (meta-cleavage pathway) 8 6 2
3,4-dichlorobenzoate degradation 4 3 1
4-sulfocatechol degradation 4 3 1
syringate degradation 12 7 3
gallate degradation II 5 4 1
superpathway of vanillin and vanillate degradation 10 7 2
3-chlorobenzoate degradation II (via protocatechuate) 6 3 1
aromatic compounds degradation via β-ketoadipate 9 9 1
toluene degradation III (aerobic) (via p-cresol) 11 7 1
superpathway of aerobic toluene degradation 30 16 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 22 1