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| Pathways deleted (MetaCyc hyperlink) |
Replaced by (in AraCyc) :
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A. Top
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| acetate fermentation |
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| acetate utilization |
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| acetyl-CoA assimilation |
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| aerobic respiration electron donor list |
-aerobic respiration |
| alanine degradation II |
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| allantoin degradation |
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| ammonia assimilation cycle |
-ammonia assimilation |
| anthocyanin biosynthesis (pathway ID 'PWY1F-823', now corresponds to leucopelargonidin and leucocyanidin biosynthesis) |
i)proanthocyanidin biosynthesis from flavonols
ii)anthocyanin biosynthesis(pelargonidin-3-O-glucoside, cyanidin-3-O-glucoside)
iii)leucopelargonidin and leucocyanidin biosynthesis
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| D-arabinose degradation II |
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| L-arabinose degradation |
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| arginine degradation II |
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| arginine degradation V |
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| arginine degradation IX |
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| asparagine degradation I |
-asparagine degradation I |
| aspartate degradation I |
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| aspartate degradation II |
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B. Top
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| bifidum pathway |
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| biotin biosynthesis I |
-biotin biosynthesis |
| butanediol fermentation |
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C. Top
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| C4 photosynthetic carbon assimilation cycle |
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| camalexin biosynthesis (pathway ID 'camalexin-biosynthesis', no longer exists in either MetaCyc or AraCyc) |
-camalexin biosynthesis |
| carbon monoxide dehydrogenase pathway |
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| carnitine degradation |
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| cobalamin biosynthesis II (aerobic pathway) |
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| colanic acid building blocks biosynthesis |
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| cyclopropane fatty acid biosynthesis |
-cyclopropane and cyclopropene fatty acid biosynthesis |
| cysteine biosynthesis II |
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D. Top
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| degradation of short-chain fatty acids |
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| 2-dehydro-D-gluconate degradation |
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| denitrification pathway |
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| diacetyl fermentation |
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| dissimilatory sulfate reduction |
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| dTDP-rhamnose biosynthesis |
-dTDP-L-rhamnose biosynthesis |
E. Top
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| enterobacterial common antigen biosynthesis |
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| Entner-Doudoroff pathway |
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F. Top
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| fatty acid -oxidation I |
-fatty acid -oxidation I (saturated) |
| fatty acid biosynthesis - initial steps |
-fatty acid biosynthesis - initial steps |
| fatty acid elongation-unsaturated |
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| formaldehyde assimilation I (serine pathway) |
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| formaldehyde oxidation I |
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| formaldehyde oxidation (thiol-independent) |
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| formylTHF biosynthesis |
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G. Top
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| GDP-mannose metabolism |
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| GDP-D-rhamnose biosynthesis |
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| geranylgeranyldiphosphate biosynthesis II (plastidic) (pathway ID 'PWY-5121' has been modified from its original structure in MetaCyc and two pathways have been substituted to match it) |
i)geranylgeranyldiphosphate biosynthesis
ii)trans,trans-farnesyl diphosphate biosynthesis
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| |
| gibberellin biosynthesis (pathway ID 'PWY1F-141', no longer exists in either MetaCyc or AraCyc) |
i)GA12 biosynthesis
ii)gibberellin biosynthesis I
iii)gibberellin biosynthesis II
iv)gibberellin biosynthesis III
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| gluconeogenesis |
-gluconeogenesis |
| glucosamine degradation |
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| glucose and glucose-1P degradation |
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| -D-glucuronide degradation |
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| glutamate biosynthesis I |
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| glutamate degradation I |
glutamate degradation II |
| glutamate degradation VII |
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| glutamate degradation VIII |
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| glutamine degradation III |
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| glyceraldehyde 3-phosphate degradation |
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| glycerol degradation II |
-glycerol degradation |
| glycerol teichoic acid biosynthesis |
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| glycerol metabolism |
-glycerol degradation |
| glycogen biosynthesis |
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| glycolate degradation I |
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| glycolysis II |
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| glycolysis III |
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H. Top
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| heterofermentative lactate fermentation |
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| homocysteine degradation I |
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I. Top
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| L-idonate degradation |
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| interconversion of arginine, ornithine and proline |
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| isoleucine degradation I |
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L. Top
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| lactate oxidation |
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| leucine degradation I |
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| lipoxygenase pathway |
-13-LOX and 13-HPL pathway |
| lysine biosynthesis |
-lysine biosynthesis |
M. Top
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| mannitol biosynthesis |
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| mannitol degradation |
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| mannose degradation |
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| menaquinone biosynthesis |
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| methanogenesis from CO2 |
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| methionine biosynthesis I |
-methionine biosynthesis |
| methionine biosynthesis III |
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| methionine biosynthesis IV |
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| methionine degradation I |
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| methylglyoxylate biosynthesis |
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| mevalonate degradation |
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| mixed acid fermentation |
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N. Top
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| N-acetylglucosamine , N-acetylmannosamine and N-acetylneuraminic acid dissimilation |
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| NAD biosynthesis II (from tryptophan) |
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| NAD biosynthesis II |
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| NAD biosynthesis III |
i)NAD biosynthesis I (from aspartate)
ii) NAD biosynthesis II (from tryptophan) (now also deleted from AraCyc) |
| non-phosphorylated glucose degradation |
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O. Top
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| O-antigen biosynthesis |
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| octane oxidation |
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P. Top
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| pantothenate biosynthesis I |
-pantothenate biosynthesis |
| peptidoglycan biosynthesis |
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| peptidoglycan and lipid A precursor biosynthesis |
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| phenylalanine biosynthesis II |
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| phenylalanine degradation |
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| phospholipid biosynthesis I |
-phospholipid biosynthesis II |
| polyamine biosynthesis |
-polyamine biosynthesis |
| polyisoprenoid biosynthesis |
-polyisoprenoid biosynthesis |
| ppGpp biosynthesis |
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| proline biosynthesis I |
-proline biosynthesis |
| proline degradation II |
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| proline degradation I |
-proline degradation |
| purine fermentation |
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| pyridoxal 5'-phosphate biosynthesis |
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| pyridine nucleotide cycling (pathway ID 'PYRNUCYC-PWY', no longer exists in either MetaCyc or AraCyc) |
-pyridine nucleotide cycling (plants) |
| pyruvate oxidation pathway |
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R. Top
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| respiration (anaerobic) |
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| ribitol degradation |
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S. Top
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| salvage pathways of adenine, hypoxanthine, and their nucleosides |
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| salvage pathways of purine and pyrimidine nucleotides |
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| salvage pathways of purine nucleosides |
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| salvage pathways of pyrimidine deoxyribonucleotides |
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| serine-isocitrate lyase pathway |
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| sorbitol fermentation |
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| succinate-propionate fermentation pathway |
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| sucrose degradation I |
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| sulfate assimilation |
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| sulfate assimilation II |
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T. Top
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| |
| TCA cycle - aerobic respiration |
-TCA cycle |
| TCA cycle variation VII |
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| TCA cycle variation VIII |
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| TCA cycle variation IV |
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| tetrahydrofolate biosynthesis II |
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| threonine degradation |
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| thiamine biosynthesis |
-thiamine biosynthesis |
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| trehalose biosynthesis and degradation -- low osmolarity |
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| trehalose biosynthesis II |
-trehalose biosynthesis |
| trehalose biosynthesis III |
-trehalose biosynthesis |
| tryptophan degradation |
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U. Top
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| ubiquinone biosynthesis |
-ubiquinone biosynthesis |
| ubiquinone-9 biosynthesis (pathway ID 'PWYQT-4448', no longer exists in either MetaCyc or AraCyc) |
-ubiquinone-9 biosynthesis
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| UDP-glucose conversion |
i)UDP-glucose biosynthesis (from glucose 6-P)
ii)UDP-galactose biosynthesis |
| UDP-N-acetylgalactosamine biosynthesis |
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| UDP-N-acetyl-D-glucosamine biosynthesis |
- UDP-N-acetyl-D-glucosamine biosynthesis |
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| ureide degradation |
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V. Top
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| valine degradation I |
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X. Top
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| xylulose-monophosphate cycle |
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Superpathways. Top
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| aspartate superpathway |
-superpathway of lysine, methionine and threonine biosynthesis |
| pantothenate/coenzymeA biosynthesis superpathway |
-superpathway of pantothenate/coenzymeA biosynthesis |
| superpathway of arginine, putrescine, and 4-aminobutyrate degradation |
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| superpathway of gluconate degradation |
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| superpathway of gluconate degradation |
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| superpathway glycolysis+Entner Doudoroff |
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| superpathway glycolysis+TCA variation VIII |
