Experiment set8IT028 for Xanthomonas campestris pv. campestris strain 8004

D-Fructose 16.67 mM carbon source

Group: carbon source
Media: CaMM_noCarbon + D-Fructose (17 mM)
Culturing: Xantho_ML2, tube, Aerobic, at 28 (C)
By: Alice on 5/19/22
Media components: 10.5 g/L Potassium phosphate dibasic, 4.5 g/L Potassium phosphate monobasic, 1 g/L Ammonium Sulfate, 0.1 mM Calcium chloride, 1 mM Magnesium sulfate, 0.00625 g/L Iron (II) sulfate heptahydrate, 0.0625 g/L EDTA disodium dihydrate, 0.0225 g/L Zinc sulfate heptahydrate, 0.0143 g/L Boric Acid, 0.0063 g/L Manganese (II) chloride tetrahydrate, 0.002 g/L Cobalt chloride hexahydrate, 0.0019 g/L Copper (II) sulfate pentahydrate, 0.0014 g/L Ammonium heptamolybdate tetrahydrate

Specific Phenotypes

For 18 genes in this experiment

For carbon source D-Fructose in Xanthomonas campestris pv. campestris strain 8004

For carbon source D-Fructose across organisms

SEED Subsystems

Subsystem	#Specific
Cysteine Biosynthesis	2
Fructose utilization	2
Trehalose Biosynthesis	2
Fermentations: Mixed acid	1
Fructose and Mannose Inducible PTS	1
Glycogen metabolism	1
Maltose and Maltodextrin Utilization	1
Mannitol Utilization	1
Methionine Biosynthesis	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
One-carbon metabolism by tetrahydropterines	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Serine-glyoxylate cycle	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Nucleotide sugars metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Starch and sucrose metabolism
• Lipopolysaccharide biosynthesis
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Galactose metabolism
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Methionine metabolism
• Lysine biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Aminophosphonate metabolism
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Pyruvate metabolism
• One carbon pool by folate
• Methane metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Nicotinate and nicotinamide metabolism
• Folate biosynthesis
• Caprolactam degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
fructose degradation	1	1	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
molybdenum cofactor biosynthesis	3	1	1
D-galactosamine and N-acetyl-D-galactosamine degradation	4	2	1
dimethylsulfoniopropanoate biosynthesis III (algae and phytoplankton)	4	1	1
NAD salvage pathway II (PNC IV cycle)	5	5	1
galactitol degradation	5	2	1
N-acetyl-D-galactosamine degradation	5	2	1
lactose degradation I	5	1	1
folate transformations I	13	9	2
ethene biosynthesis III (microbes)	7	6	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
L-homomethionine biosynthesis	7	2	1
partial TCA cycle (obligate autotrophs)	8	7	1
nitrogen remobilization from senescing leaves	8	6	1
folate transformations III (E. coli)	9	9	1
reductive acetyl coenzyme A pathway I (homoacetogenic bacteria)	10	3	1
folate transformations II (plants)	11	10	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	1
formaldehyde assimilation I (serine pathway)	13	8	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	1
mixed acid fermentation	16	11	1
superpathway of hexitol degradation (bacteria)	18	13	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	8	1
ethene biosynthesis V (engineered)	25	17	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	19	2