Experiment set8IT030 for Xanthomonas campestris pv. campestris strain 8004

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Pectin from apple 2 g/L carbon source

Group: carbon source
Media: CaMM_noCarbon + Pectin from apple (2 g/L)
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 14 genes in this experiment

For carbon source Pectin from apple in Xanthomonas campestris pv. campestris strain 8004

For carbon source Pectin from apple across organisms

SEED Subsystems

Subsystem #Specific
Cysteine Biosynthesis 2
D-Galacturonate and D-Glucuronate Utilization 1
D-galactonate catabolism 1
D-gluconate and ketogluconates metabolism 1
D-ribose utilization 1
Entner-Doudoroff Pathway 1
Fermentations: Mixed acid 1
Methionine Biosynthesis 1
One-carbon metabolism by tetrahydropterines 1
Peptidoglycan Biosynthesis 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:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
CO2 fixation into oxaloacetate (anaplerotic) 2 2 1
4-deoxy-L-threo-hex-4-enopyranuronate degradation 5 4 2
D-galactonate degradation 3 3 1
molybdenum cofactor biosynthesis 3 1 1
2-hydroxypenta-2,4-dienoate degradation 3 1 1
3,6-anhydro-α-L-galactopyranose degradation 7 4 2
D-fructuronate degradation 4 3 1
2-deoxy-D-glucose 6-phosphate degradation 4 2 1
D-galacturonate degradation I 5 3 1
catechol degradation I (meta-cleavage pathway) 5 2 1
toluene degradation II (aerobic) (via 4-methylcatechol) 6 1 1
folate transformations I 13 9 2
superpathway of β-D-glucuronosides degradation 7 5 1
C4 photosynthetic carbon assimilation cycle, NADP-ME type 7 4 1
alginate degradation 7 1 1
toluene degradation V (aerobic) (via toluene-cis-diol) 7 1 1
toluene degradation I (aerobic) (via o-cresol) 7 1 1
catechol degradation II (meta-cleavage pathway) 7 1 1
partial TCA cycle (obligate autotrophs) 8 7 1
nitrogen remobilization from senescing leaves 8 6 1
3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation 8 2 1
p-cumate degradation 8 1 1
folate transformations III (E. coli) 9 9 1
Entner-Doudoroff pathway III (semi-phosphorylative) 9 6 1
4-chloronitrobenzene degradation 9 1 1
superpathway of hexuronide and hexuronate degradation 10 6 1
reductive acetyl coenzyme A pathway I (homoacetogenic bacteria) 10 3 1
meta cleavage pathway of aromatic compounds 10 2 1
folate transformations II (plants) 11 10 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 7 1
p-cymene degradation 11 1 1
L-tryptophan degradation IX 12 5 1
L-tryptophan degradation XII (Geobacillus) 12 4 1
naphthalene degradation to acetyl-CoA 12 2 1
formaldehyde assimilation I (serine pathway) 13 8 1
toluene degradation IV (aerobic) (via catechol) 13 3 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 8 1
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 15 2
mixed acid fermentation 16 11 1
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 8 1
mandelate degradation to acetyl-CoA 18 6 1
ethene biosynthesis V (engineered) 25 17 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 19 2
superpathway of aerobic toluene degradation 30 10 1
superpathway of aromatic compound degradation via 3-oxoadipate 35 13 1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate 42 8 1