Experiment set4IT021 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 18 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
Fructose and Mannose Inducible PTS	1
Fructose utilization	1
L-Arabinose utilization	1
Mannitol Utilization	1
Methylcitrate cycle	1
Nitrate and nitrite ammonification	1
Polyamine Metabolism	1
Proline, 4-hydroxyproline uptake and utilization	1
Propionate-CoA to Succinate Module	1
Queuosine-Archaeosine Biosynthesis	1
Transcription factors bacterial	1
tRNA processing	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
• Nucleotide sugars metabolism
• Starch and sucrose metabolism
• Propanoate metabolism
• Biosynthesis of alkaloids derived from histidine and purine
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Galactose metabolism
• Puromycin biosynthesis
• Pyrimidine metabolism
• Valine, leucine and isoleucine biosynthesis
• Aminosugars metabolism
• alpha-Linolenic acid metabolism
• Glyoxylate and dicarboxylate metabolism
• Trinitrotoluene degradation
• Reductive carboxylate cycle (CO2 fixation)
• Pantothenate and CoA biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-glucuronate biosynthesis (from UDP-glucose)	1	1	1
L-lyxonate degradation	3	2	2
L-arabinose degradation III	6	5	3
pseudouridine degradation	2	1	1
pyruvate fermentation to acetate VIII	2	1	1
UDP-α-D-xylose biosynthesis	2	1	1
2-methylcitrate cycle I	5	5	2
D-glucarate degradation II	3	3	1
D-galactarate degradation II	3	3	1
glyoxylate cycle	6	5	2
2-methylcitrate cycle II	6	5	2
L-carnitine degradation II	3	1	1
partial TCA cycle (obligate autotrophs)	8	8	2
L-valine biosynthesis	4	4	1
queuosine biosynthesis I (de novo)	4	4	1
trans-4-hydroxy-L-proline degradation II	4	4	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	2
nitrogen remobilization from senescing leaves	8	6	2
1,2-dichloroethane degradation	4	3	1
TCA cycle VI (Helicobacter)	9	7	2
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle VII (acetate-producers)	9	7	2
TCA cycle I (prokaryotic)	10	9	2
cytosolic NADPH production (yeast)	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
mitochondrial NADPH production (yeast)	5	4	1
D-glucuronate degradation II	5	4	1
TCA cycle III (animals)	10	7	2
queuosine biosynthesis III (queuosine salvage)	5	3	1
D-galacturonate degradation II	5	3	1
D-xylose degradation III	5	1	1
D-xylose degradation V	5	1	1
reductive TCA cycle I	11	6	2
superpathway of glyoxylate bypass and TCA	12	11	2
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
L-isoleucine biosynthesis IV	6	4	1
L-arabinose degradation V	6	3	1
reductive TCA cycle II	12	5	2
D-arabinose degradation III	6	2	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	2
L-isoleucine biosynthesis III	7	4	1
mixed acid fermentation	16	11	2
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
methylaspartate cycle	19	9	2
superpathway of pentose and pentitol degradation	42	16	4
colanic acid building blocks biosynthesis	11	11	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
ethene biosynthesis V (engineered)	25	18	2
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2
superpathway of L-threonine metabolism	18	11	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	13	1