Experiment set2IT084 for Rahnella sp. WP5

D-Xylose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Xylose (20 mM)
Culturing: RahnellaWP5_ML7, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Robert Tournay on December 7, 2021
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 13 genes in this experiment

For carbon source D-Xylose in Rahnella sp. WP5

For carbon source D-Xylose across organisms

SEED Subsystems

Subsystem	#Specific
Xylose utilization	3
Acetoin, butanediol metabolism	2
Branched-Chain Amino Acid Biosynthesis	2
Fructose utilization	2
D-gluconate and ketogluconates metabolism	1
Folate Biosynthesis	1
Glycogen metabolism	1
Pentose phosphate pathway	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Ribosome biogenesis bacterial	1
cAMP signaling in bacteria	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
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Purine metabolism
• Pyrimidine metabolism
• Valine, leucine and isoleucine biosynthesis
• Starch and sucrose metabolism
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Pantothenate and CoA biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-xylose degradation I	2	2	2
pyruvate fermentation to (R)-acetoin II	2	2	1
D-arabinitol degradation I	2	1	1
xylitol degradation I	2	1	1
pseudouridine degradation	2	1	1
pyruvate fermentation to (S)-acetoin	3	3	1
pyruvate fermentation to (R)-acetoin I	3	3	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	4	1
L-valine biosynthesis	4	4	1
pentose phosphate pathway (non-oxidative branch) I	5	5	1
superpathway of (R,R)-butanediol biosynthesis	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
superpathway of glucose and xylose degradation	17	17	3
L-isoleucine biosynthesis IV	6	4	1
superpathway of 2,3-butanediol biosynthesis	6	4	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
pentose phosphate pathway	8	8	1
L-isoleucine biosynthesis II	8	5	1
superpathway of branched chain amino acid biosynthesis	17	17	2
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	7	1
Rubisco shunt	10	9	1
starch biosynthesis	10	6	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	11	1
superpathway of L-isoleucine biosynthesis I	13	13	1
Bifidobacterium shunt	15	13	1
superpathway of L-threonine metabolism	18	15	1
superpathway of pentose and pentitol degradation	42	13	2