Experiment set22IT021 for Pseudomonas fluorescens SBW25-INTG

D-Xylose 10 mM carbon source

Group: carbon source
Media: MME_noNitrogen_noCarbon + D-Xylose (10 mM) + Ammonium chloride (10 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on 8-Mar-22
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 14 genes in this experiment

For carbon source D-Xylose in Pseudomonas fluorescens SBW25-INTG

For carbon source D-Xylose across organisms

SEED Subsystems

Subsystem	#Specific
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	4
Xylose utilization	3
D-galactonate catabolism	1
L-Arabinose utilization	1
Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway	1
Lactose and Galactose Uptake and Utilization	1
N-linked Glycosylation in Bacteria	1
Protocatechuate branch of beta-ketoadipate pathway	1
Rhamnose containing glycans	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Valine, leucine and isoleucine biosynthesis
• Nucleotide sugars metabolism
• Pantothenate and CoA biosynthesis
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-xylose degradation I	2	2	2
UDP-N-acetyl-D-galactosamine biosynthesis I	1	1	1
UDP-α-D-galactose biosynthesis	1	1	1
xylitol degradation I	2	2	1
D-glucuronate degradation III	2	2	1
D-galacturonate degradation III	2	2	1
UDP-α-D-galactofuranose biosynthesis	2	1	1
D-arabinitol degradation I	2	1	1
D-galactose detoxification	3	1	1
L-valine biosynthesis	4	4	1
D-glucuronate degradation II	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
D-galacturonate degradation II	5	3	1
D-galactose degradation I (Leloir pathway)	5	3	1
L-arabinose degradation III	6	5	1
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
L-isoleucine biosynthesis I (from threonine)	7	7	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	5	1
L-isoleucine biosynthesis III	7	4	1
stachyose degradation	7	2	1
L-isoleucine biosynthesis II	8	5	1
L-arabinose degradation IV	8	5	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of glucose and xylose degradation	17	16	2
teichuronic acid biosynthesis (B. subtilis 168)	9	2	1
UDP-sugars interconversion	9	2	1
colanic acid building blocks biosynthesis	11	11	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of pentose and pentitol degradation	42	16	3
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	13	2
superpathway of L-threonine metabolism	18	11	1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	18	1	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1