CocoaCyc 1.0

Parent

Overview
Released: 
May 2017
Taxonomic Range: 
Theobroma cacao
Protein Sequence Source: 

Phytozome v12: Tcacao_233_v1.1.protein.fahttp://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Phytozome

Enzyme Functional Annotation Method: 

E2P2 v3.1

Enzyme Evidence: 
  • Almost exclusively large-scale computational predictions of enzyme function not subject to curator review
  • Small number of manually curated enzymes
Pathway Prediction Program: 
Pathway Tools v20.5 (primarily)
SAVI pathway validation lists: 
CAPP 4.0
AIPP 4.0
MCP 2.0
NPP 7.0
UPP 7.0
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.