Overview

This repository contains the "ground truth" dataset of the Minimum Information about a Tailoring Enzyme (MITE) data repository (mite_data/data).

Furthermore, the repository contains auxiliary files and scripts to automatically update them:

• Metadata files summarizing information of all MITE entries in a single file (mite_data/metadata)
• Protein FASTA-files for all active (i.e. non-retired) MITE entries and an accompanying up-to-date BLAST database (mite_data/fasta and mite_data/blast_lib)
• Alphafold-predicted enzyme structures and accompanying image files (mite_data/pdb and mite_data/img), if available.

When new data is added, auxiliary files must be updated too. Existing fasta and image files will not be overwritten.

For more information, see the README of the MITE-Standard organisation page.

Installation (for automated file updates)

Nota bene: This installation will only work on (Ubuntu) Linux.

• Install python 3.12.x
• Install hatch (e.g. with pipx install hatch)
• hatch env create
• sudo snap install pymol-oss (required for option --update_img)
• sudo apt install ncbi-blast+ (required for option --update_blast)

Quick-start

Update the MITE metadata files: mite_data

Update MITE files to the newest version of mite_schema: mite_data --update_mite

Update only enzyme visualization (re-downloads all AlphaFold PDBs): mite_data --update_img. Note that this module will fail if you have not installed PyMol-OSS.

Update only BLAST database (re-downloads all protein FASTA files): mite_data --update_blast

Update all files in repository: mite_data --update_all

Clean-up

If necessary, remove the environment again with hatch env remove