Experiment set1IT005 for Paraburkholderia graminis OAS925

D-Arabinose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Arabinose (20 mM)
Culturing: Burkholderia_OAS925_ML2, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Marta on 10-Apr-21
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 12 genes in this experiment

For carbon source D-Arabinose in Paraburkholderia graminis OAS925

For carbon source D-Arabinose across organisms

SEED Subsystems

Subsystem	#Specific
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	4
D-gluconate and ketogluconates metabolism	1
Fermentations: Mixed acid	1
Fructose utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Homogentisate pathway of aromatic compound degradation	1
L-fucose utilization temp	1
Lactose and Galactose Uptake and Utilization	1
Maltose and Maltodextrin Utilization	1
Xylose utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Fatty acid metabolism
• Puromycin biosynthesis
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Trinitrotoluene degradation
• 3-Chloroacrylic acid degradation
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Metabolism of xenobiotics by cytochrome P450
• Insect hormone biosynthesis
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
xylitol degradation I	2	2	1
D-arabinitol degradation I	2	2	1
D-xylose degradation I	2	2	1
trehalose degradation VI (periplasmic)	2	2	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation I	2	1	1
D-sorbitol degradation I	3	3	1
ethanol degradation II	3	3	1
L-leucine degradation III	3	2	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
1,2-propanediol biosynthesis from lactate (engineered)	6	2	2
L-methionine degradation III	3	1	1
pyruvate fermentation to ethanol III	3	1	1
pyruvate fermentation to ethanol I	3	1	1
phytol degradation	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
salidroside biosynthesis	4	1	1
D-altritol and galactitol degradation	4	1	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
ethanolamine utilization	5	4	1
acetylene degradation (anaerobic)	5	3	1
D-xylose degradation VI	5	3	1
(S)-propane-1,2-diol degradation	5	3	1
D-galactose degradation I (Leloir pathway)	5	3	1
phenylethanol biosynthesis	5	1	1
L-arabinose degradation V	6	5	1
D-arabinose degradation IV	6	4	1
noradrenaline and adrenaline degradation	13	4	2
3-methylbutanol biosynthesis (engineered)	7	6	1
L-rhamnose degradation III	7	6	1
serotonin degradation	7	3	1
L-fucose degradation III	8	5	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	6	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	12	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	9	1
heterolactic fermentation	18	15	1
superpathway of anaerobic sucrose degradation	19	15	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of N-acetylneuraminate degradation	22	15	1
superpathway of pentose and pentitol degradation	42	21	1