Experiment set4IT020 for Pseudomonas fluorescens SBW25-INTG

L-Arabinose carbon source; with MOPS

Group: carbon source
Media: soilextract_PNNL_Prosser_PlotA_B_20191220 + L-Arabinose (12 mM) + Ammonium chloride (10 mM) + 3-(N-morpholino)propanesulfonic acid (40 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1 mL volume, Aerobic, at 30 (C)
By: Joshua Elmore on 1/6/20

Specific Phenotypes

For 16 genes in this experiment

For carbon source L-Arabinose in Pseudomonas fluorescens SBW25-INTG

For carbon source L-Arabinose across organisms

SEED Subsystems

Subsystem	#Specific
D-Galacturonate and D-Glucuronate Utilization	1
D-galactonate catabolism	1
De Novo Pyrimidine Synthesis	1
Fructose and Mannose Inducible PTS	1
Fructose utilization	1
L-Arabinose utilization	1
LMPTP YwlE cluster	1
Mannitol Utilization	1
Nitrate and nitrite ammonification	1
Polyamine Metabolism	1
Proline, 4-hydroxyproline uptake and utilization	1
Transcription factors bacterial	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ascorbate and aldarate metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Glycolysis / Gluconeogenesis
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Galactose metabolism
• Pyrimidine metabolism
• Valine, leucine and isoleucine biosynthesis
• Aminosugars metabolism
• Pantothenate and CoA biosynthesis
• Caprolactam degradation
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyrimidine nucleobases salvage I	1	1	1
UDP-α-D-glucuronate biosynthesis (from UDP-glucose)	1	1	1
L-lyxonate degradation	3	2	2
pyrimidine nucleobases salvage II	2	2	1
L-arabinose degradation III	6	5	3
pyruvate fermentation to acetate VIII	2	1	1
UDP-α-D-xylose biosynthesis	2	1	1
D-galactarate degradation II	3	3	1
D-glucarate degradation II	3	3	1
L-carnitine degradation II	3	1	1
trans-4-hydroxy-L-proline degradation II	4	4	1
superpathway of pyrimidine nucleobases salvage	4	4	1
L-valine biosynthesis	4	4	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	2
1,2-dichloroethane degradation	4	3	1
D-glucuronate degradation II	5	4	1
mitochondrial NADPH production (yeast)	5	4	1
cytosolic NADPH production (yeast)	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
D-galacturonate degradation II	5	3	1
D-xylose degradation V	5	1	1
D-xylose degradation III	5	1	1
L-isoleucine biosynthesis IV	6	4	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
L-arabinose degradation V	6	3	1
D-arabinose degradation III	6	2	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
L-arabinose degradation IV	8	5	1
L-isoleucine biosynthesis II	8	5	1
superpathway of branched chain amino acid biosynthesis	17	17	2
UDP-sugars interconversion	9	2	1
teichuronic acid biosynthesis (B. subtilis 168)	9	2	1
superpathway of pyrimidine ribonucleosides salvage	10	6	1
superpathway of pentose and pentitol degradation	42	16	4
colanic acid building blocks biosynthesis	11	11	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-threonine metabolism	18	11	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	13	1