Prediction of Mtb-secreted eukaryotic-like proteins

Prediction of eukaryotic-like proteins in Mtb

1. The following databases were used:

Effective DB (http://effectivedb.org/)

UniProt (https://www.uniprot.org/)

SMART (http://smart.embl-heidelberg.de/)

2. The following software tool was used:

Python (https://repo.anaconda.com/archive/Anaconda3-4.2.0-Windows-x86_64.exe)

3. The following code was used:

  SMART.txt (see the attached file "SMART.txt")

4. Procedure:

  1) Download FASTA file which contains all sequences of Mtb-encoded proteins from UniProt database (https://www.uniprot.org/proteomes/UP000001584/), and name it as "H37rv.fasta".

  2) Download all eukaryotic-like domains (eld_search.csv) from Effective DB (https://effectivedb.org/reports/eld_search?minscore=4&maxscore=10000&maxavg=0.5)

  3) Install Selenium WebDriver (https://anaconda.org/conda-forge/selenium) in Python.

  4) Download SMART.txt and put it in the same directory as H37rv.fasta, and then rename "SMART.txt" as "SMART.py" to run it by python. A file named as "SMART.csv" containing all Mtb-encoded proteins with annotation of functional domains will be generated after ~1-week running. (NOTE: ensure the internet connection is stable and do NOT interrupt the internet connection.)

  5) In SMART.csv, Mtb-encoded proteins annotated with a PFAM ID that indicates a eukaryotic-like domain as listed in eld_search.csv were selected and considered as a eukaryotic-like protein.

Determination of subcellular localization of Mtb eukaryotic-like proteins

The subcellular localization of each Mtb protein was annotated according to the published articles (see the attached file “Refs. docx”).

Circular representation of Mtb H37Rv genome using Circos

1. The following databases were used:

NCBI (https://www.ncbi.nlm.nih.gov/)

PANTHER (http://www.pantherdb.org/)

Mycobrowser (https://mycobrowser.epfl.ch/)

2. The following software tool was used:

Circos (http://circos.ca/software/download/circos/)

3. The source code used for Circos plot is available on Zenodo:

Funtion annotation of MTB genome (https://doi.org/10.5281/zenodo.7021021)

4. Procedure:

  1) Install the Circos (http://circos.ca/software/download/circos/).

  2) Download all files from Zenodo (https://doi.org/10.5281/zenodo.7021021). [NOTE: these files include MTB.fas which contains entire genome sequence of Mtb H37Rv obtained from NCBI (RefSeq: NC_000962.3) and MTB_protein_class.xlsx which contains information of Mtb H37Rv genome location according to Mycobrowser database and functional classification of Mtb protein-encoding genes based on PANTHER database.]

  3) Run "circus -conf main.conf" in Shell or CMD.

  4) Get the output files "circos.svg" and "circos.png".