Experiment set3IT010 for Ralstonia sp. UNC404CL21Col

rhizosphere sample 1; outgrowth in LB

Group: rhizosphere
Media:
Culturing: CL21_ML4, potted plant
By: Dawn Chiniquy on 4-Apr-19

Specific Phenotypes

For 3 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	1
DNA Repair Base Excision	1
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methylglyoxal Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• 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
• Glycerolipid metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
phenylethylamine degradation II	2	1	1
putrescine degradation I	2	1	1
ethylene glycol degradation	2	1	1
phenylethanol degradation	2	1	1
putrescine degradation V	2	1	1
phenylethylamine degradation I	2	1	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
hypotaurine degradation	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
putrescine degradation IV	3	2	1
ethanol degradation III	3	2	1
histamine degradation	3	1	1
styrene degradation	3	1	1
phytol degradation	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
putrescine degradation III	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
D-arabinose degradation II	4	1	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	1	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
superpathway of glycol metabolism and degradation	7	5	1
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	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	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
aromatic biogenic amine degradation (bacteria)	8	1	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	4	1
superpathway of phenylethylamine degradation	11	8	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	5	1
superpathway of L-arginine and L-ornithine degradation	13	7	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	5	1
superpathway of pentose and pentitol degradation	42	17	1