Experiment set21IT030 for Pseudomonas fluorescens SBW25-INTG

Arabitol 10 mM carbon source

Group: carbon source
Media: MME_noNitrogen_noCarbon + Arabitol (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 17 genes in this experiment

For carbon source Arabitol in Pseudomonas fluorescens SBW25-INTG

For carbon source Arabitol across organisms

SEED Subsystems

Subsystem	#Specific
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	7
Xylose utilization	4
Transport of Zinc	2
Fatty Acid Biosynthesis FASII	1
Fructose utilization	1
Hemin transport system	1
L-Arabinose utilization	1
Mannitol Utilization	1
Nitrate and nitrite ammonification	1
mycolic acid synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fructose and mannose metabolism
• Pentose and glucuronate interconversions
• Ascorbate and aldarate metabolism
• Biosynthesis of unsaturated fatty acids
• Fatty acid biosynthesis
• C21-Steroid hormone metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine biosynthesis
• Bisphenol A degradation
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Linoleic acid metabolism
• Tetrachloroethene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Pantothenate and CoA biosynthesis
• Retinol metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of type II polyketide products
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
xylitol degradation I	2	2	2
D-xylose degradation I	2	2	1
D-arabinitol degradation I	2	1	1
ribitol degradation I	2	1	1
D-sorbitol degradation I	3	3	1
L-arabinose degradation III	6	5	2
L-lyxonate degradation	3	2	1
L-arabinose degradation II	3	1	1
erythritol degradation II	3	1	1
L-valine biosynthesis	4	4	1
gondoate biosynthesis (anaerobic)	4	4	1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	9	3
L-threitol degradation	4	1	1
palmitate biosynthesis III	29	21	7
tetradecanoate biosynthesis (mitochondria)	25	17	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	49	11
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	18	4
pyruvate fermentation to isobutanol (engineered)	5	4	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
cis-vaccenate biosynthesis	5	4	1
fatty acid elongation -- saturated	5	4	1
mannitol cycle	5	3	1
superpathway of fatty acid biosynthesis II (plant)	43	38	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
odd iso-branched-chain fatty acid biosynthesis	34	24	6
even iso-branched-chain fatty acid biosynthesis	34	24	6
anteiso-branched-chain fatty acid biosynthesis	34	24	6
(5Z)-dodecenoate biosynthesis II	6	6	1
(5Z)-dodecenoate biosynthesis I	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
L-isoleucine biosynthesis IV	6	4	1
stearate biosynthesis IV	6	4	1
L-arabinose degradation V	6	3	1
petroselinate biosynthesis	6	2	1
streptorubin B biosynthesis	34	20	5
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
superpathway of pentose and pentitol degradation	42	16	6
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	14	2
L-isoleucine biosynthesis II	8	5	1
L-arabinose degradation IV	8	5	1
2-allylmalonyl-CoA biosynthesis	8	2	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of L-threonine metabolism	18	11	1
mycolate biosynthesis	205	20	5
superpathway of mycolate biosynthesis	239	21	5