Experiment set1S511 for Paraburkholderia sabiae LMG 24235

2-Deoxy-D-Ribose carbon source

Group: carbon source
Media: AB_minimal medium + 2-Deoxy-D-Ribose (20 mM)
Culturing: Psabiae_ML3b, tube, Aerobic, at 30 (C), shaken=180 rpm
By: Marta Torres on 12/5/24

Specific Phenotypes

For 5 genes in this experiment

For carbon source 2-Deoxy-D-Ribose in Paraburkholderia sabiae LMG 24235

For carbon source 2-Deoxy-D-Ribose across organisms

SEED Subsystems

Subsystem	#Specific
Deoxyribose and Deoxynucleoside Catabolism	2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
D-ribose utilization	1
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Ketoisovalerate oxidoreductase	1
Methylglyoxal Metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Pyruvate metabolism
• Propanoate metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Glycerolipid metabolism
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate conversion to acetyl-CoA	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
ethanol degradation II	3	3	2
ethanol degradation IV	3	3	2
ethanol degradation III	3	2	2
2-deoxy-D-ribose degradation I	3	2	2
ethylene glycol degradation	2	2	1
putrescine degradation V	2	2	1
ribose phosphorylation	2	1	1
putrescine degradation I	2	1	1
superpathway of acetate utilization and formation	3	3	1
hypotaurine degradation	3	2	1
L-isoleucine biosynthesis V	3	2	1
putrescine degradation IV	3	2	1
histamine degradation	3	1	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	1	1
phytol degradation	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
chitin deacetylation	4	2	1
D-arabinose degradation II	4	2	1
putrescine degradation III	4	1	1
2-methylcitrate cycle I	5	5	1
mitochondrial NADPH production (yeast)	5	3	1
octane oxidation	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
2-methylcitrate cycle II	6	5	1
L-isoleucine biosynthesis IV	6	4	1
β-alanine biosynthesis II	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
superpathway of bitter acids biosynthesis	18	3	3
colupulone and cohumulone biosynthesis	6	1	1
alkane oxidation	6	1	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
noradrenaline and adrenaline degradation	13	4	2
superpathway of glycol metabolism and degradation	7	7	1
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
superpathway of purine deoxyribonucleosides degradation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
superpathway of ornithine degradation	8	5	1
aromatic biogenic amine degradation (bacteria)	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
cis-geranyl-CoA degradation	9	2	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	1
superpathway of L-arginine and L-ornithine degradation	13	8	1
superpathway of pentose and pentitol degradation	42	23	1