AraCyc 12.0

Parent

Overview
Released: 
September 2014

AraCyc is the most highly curated species-specific database present at the PMN. It has a large number of experimentally supported enzymes and metabolic pathways, but it also houses a substantial number of computationally predicted enzymes and pathways.

More information on AraCyc curation is available.

Taxonomic Range: 
Arabidopsis thaliana col
Protein Sequence Source: 

Phytozome 9.0 (nuclear): Athaliana_167_peptide.fa and TAIR (organellar): various genome releases includingTAIR10_pep_20110103_representative_gene_model

Enzyme Functional Annotation Method: 

Primarily E2P2 v2.1

Enzyme Evidence: 
  • Substantial manual curation of enzymes
  • In addition, large-scale computational predictions of enzyme function not subject to curator review
Pathway Prediction Program: 
Pathway Tools v.17.5 (primarily)
SAVI pathway validation lists: 
MCP 1.0
UPP 5.0
NPP 5.0
AIPP 2.0
CAPP 2.0
Pathway Evidence: 
  • Substantial manual curation of pathways
  • Some computational prediction of pathways followed by curator review
  • Additional pathways imported from MetaCyc based on curator inference

The PMN is funded by the National Science Foundation (Grant #: 1546838, 1026003 and 0640769) and the Department of Energy (BER Grant #:  ER65472 ), governed by an Editorial Board composed of internationally renowned scientists, and executed at the Carnegie Institution for Science, Department of Plant Biology.