Archives: AraCyc 6.0 Release Notes

The AraCyc 6.0 release contains 34 new pathways that have been added by PMN and MetaCyc curators. 4 pathways have been updated at the PMN and 5 pathways have been deleted from the previous version of AraCyc.

AraCyc 6.0 contains 360 pathways (excluding superpathways), 5501 enzymes*, and 2630compounds.

Detailed database content statistics are available for AraCyc 6.0 and the other PMN databases

Revised enzyme annotations and reaction assignments

The newly developed PMN enzyme annotation pipeline (to be published elsewhere) was applied to the TAIR9 sequence release to update the AraCyc computational predictions of enzyme function. Previous computational assignments had been made using the IEA annotations available at TAIR. The new pipeline resulted in a number of changes to the database:

  • New assignments to reactions were made for 1463 enzymes
  • Old assignments to reactions were removed for 1154 enzymes

In addition, over 100 protein modifying enzymes (e.g. ubiquitin ligases) were manully removed from the database to maintain the focus on small molecule metabolism.

In combination, these two processes led to the removal of 131 proteins from the AraCyc database.

New biochemical pathways

PMN curators worked to add new pathways based on published experimental results and to update existing pathways using new data.

Some highlights of the newly added AraCyc pathways:

  • Five new glucosinolate pathways:
    Glucosinolates are a class of nitrogen- and sulfur-containing secondary metabolites involved in plant pathogen defense that also give a sharp taste to many cruciferous plants such as mustard.

  • Three new hormone-modifying pathways:
    Indole-3-acetate (IAA) and jasmonic acid are important plant growth regulating hormones. New pathways for IAA methylation, IAA-amino acid conjugation, and jasmonoyl-amino acid conjugates biosynthesis provide insights into how plants can finely control the levels of these biologically active hormones.

Please check out our lists of the following items:


* Note: The term enzyme refers to both monomers and complexes found in the databases.

Information about all the current PMN releases can be found on the PMN Release Notes main page.

Please refer to our PMN Release Notes Archives to read about the details of past releases.