All Deleted Pathways

A number of pathways have been deleted from the database since the original AraCyc 1.0 release. In some cases, they have been replaced by an alternative form of the pathway*.

Pathways deleted following AraCyc 5.0

• adenosylmethionine biosynthesis [PWY-802]
  • Comment: This single-reaction pathway is contained within other larger pathways in PlantCyc. It no longer exists in MetaCyc.
• 2-O-alpha-mannosyl-D-glycerate degradation [ MetaCyc:PWY0-1300]
• 4-aminobutyrate degradation [4AMINOBUTMETAB-PWY-ARA]
  • Replaced with PWY-6473
• arginine biosynthesis III [MetaCyc:ARGININE-SYN4-PWY]
• carbon tetrachloride degradation II [MetaCyc:PWY-5372]
  • Comment: An alternative pathway for carbon tetracholride degradation exists in plants, but it has not been curated in AraCyc yet.
• (deoxy)ribose phosphate degradation [DRIBOPMET-PWY]
  • Replaced with PWY-6556
• glycine degradation [GLYCCAT-PWY]
  • Comment:This pathway has been removed from MetaCyc
• lysine biosynthesis I [MetaCyc:DAPLYSINESYN-PWY]
  • Comment: The lysine biosynthesis pathway VI is more appropriate for plants
• trans-lycopene biosynthesis I (bacteria) [ MetaCyc:PWY-5942]
  • Replaced by plant variant trans-lycopene biosynthesis II (plants)
• superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle [MetaCyc:PWY-5464]
• superpathway of ribose and deoxyribose phosphate degradation [RIB-DRIBMET-PWY]
  • Replaced with PWY-6556

 

 

All additional pathways deleted before AraCyc 5.0

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

*Note: Some of the pathways links above will broken if the pathways have subsequently been deleted from MetaCyc or AraCyc, or if their IDs have changed. Efforts will be made to remove these in the future.

 

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