AraCyc 11.5

Parent

Overview
Released: 
November 2013
July 2013

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.

** Please note: The initial PMN 8.0 release in June 2013 included AraCyc 11.0. Proteins not associated to reactions were removed from AraCyc 11.0 to produce this updated version (AraCyc 11.5).

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 2.0

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.16.5 (primarily)
SAVI pathway validation lists: 
MCP 1.0
CAPP 1.0
AIPP 1.0
NPP 4.0
UPP 4.0
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
Link to PGDB: 
AraCyc

Michigan State University  

The PMN is funded by the National Science Foundation (Grant #: 2312181, 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 Michigan State University's Department of Biochemistry & Molecular Biology and the Plant Resilience Institute