Help & About

PlantSME is a database and online identification platform for plant secondary metabolism enzyme families. It unifies species-level annotations and provides in-site identification with official reference libraries.

• For result browsing: the site exposes multiple entry points across species, pathways, module nodes, enzyme families, and genes.
• For practical use: users can upload protein FASTA files, submit identification jobs, track Job IDs, and download result bundles.
• For local reuse: the download center provides the PathwayTools_V4 package and official libraries.

1. Open the Species page to inspect pathway coverage, family distributions, and gene lists for each species.
2. Open the Pathways page to inspect real pathways first, then drill down into functional modules and enzyme-step nodes.
3. The homepage serves as the main overview entry for the current public version; use it as the main hub before drilling down into species, pathway, and tool pages.

1. Open the Identify page and upload a protein FASTA file for one species; a complete proteome is recommended.
2. Select one or more official libraries; if none are selected, all public libraries are run by default.
3. After submission, the system generates a Job ID that can be used to track progress on the job detail page.
4. After completion, open the result page to inspect family/module summaries and download the standard output ZIP.

• The download center provides the PathwayTools_V4 package together with official reference libraries.
• The recommended order is to deploy the software first, load the libraries second, and then run local identification.
• If you need to understand how the current public dataset is organized, read the Methods page together with the download instructions.

• On this site, pathway statistics map to category and module statistics map to the pathway node.
• If an upper-level module page is configured as an overview page, its statistics aggregate all lower-level module results.
• To revisit an old task, use the Job ID lookup page to reopen the job detail or result page.