An enzyme mining process based on python and multiple bioinformatics tools and exemplifies its application to methanol oxidase (AOX).
This is the online repository for the published paper "Sequence and taxonomic feature evaluation facilitated the discovery of alcohol oxidases"(doi:10.1016/j.synbio.2025.04.014).
conda create -n enzyme_mining python=3.8
conda activate enzyme_mining
conda install pandas
conda install ipykernel
pip install pymed
conda install biopython
conda install scipy
conda install scikit-learnTips: you will need another conda env for PyMol according to the version of PyMol distribution.
| Software | Version | URL |
|---|---|---|
| CD-HIT | 4.8.1 | https://github.com/weizhongli/cdhit/releases (linux) |
| T-Coffee | 11.00 | https://tcoffee.org/Projects/tcoffee/index.html (linux) https://tcoffee.crg.eu/ (online) |
| HMMER | 3.3 (2.41.2, online) |
http://hmmer.org/ (linux) https://www.ebi.ac.uk/Tools/hmmer/search/phmmer (online) |
| SWISS-MODEL | 2023.11.04 | https://swissmodel.expasy.org/ |
| USEARCH | 11.0.667 | http://www.drive5.com/usearch/ (linux, windows) |
| TM-align | 20190822 | https://zhanggroup.org/TM-align/ (linux) |
The repository contains the necessary intermediate files needed to reproduce the results, for development it is recommended to use the latest stable version of the softwares and online services.
| Software | Version | URL |
|---|---|---|
| Jalview | 2.11.2.7 | https://www.jalview.org/ |
| Cytoscape | 3.9.1 | https://cytoscape.org/ |
| iTOL | - | https://itol.embl.de/ (online) |
| Database | URL |
|---|---|
| BRENDA | https://www.brenda-enzymes.org/ |
| UniProt | https://www.uniprot.org/ |
| NCBI | https://www.ncbi.nlm.nih.gov/protein |
| NCBI Taxonomy | https://ftp.ncbi.nih.gov/pub/taxonomy/ |