PKZILLA domain phylogenies with outgroup representatives from Uniprot

Source data files, executable code, and results for PKZILLA domain phylogenetic analysis, with inclusion of representative PKS domain outgroups from Uniprot.

Difference from previous version:

Difference between v1.0 to v1.1 of this Zenodo item series: is the text in the final plots has highlighting to allow the reader to quickly appreciate it without having to look closely at each taxonomic identifier, and KR11f0, KR20f0 were renamed in the plots to K11*, KR20*, respectively, based on new interpretations.  

Difference between v1.1 to v1.2: 

Domain phylogenetics method:

Representative PKS domains from bacteria, fungi, dinoflagellates, haptophytes, and human FAS were downloaded from the InterPro API using high level queries for taxonomically restricted polypeptides with the presence of PKS domains, and their Uniprot reviewed (Swiss-Prot) or unreviewed (TrEMBL) status, and then further filtered based on the presence of well known polyketide names in the metadata of the matching Uniprot entry (see impactful_polyketides.tsv):

erythromycinrapamycinsirolimusdoxorubicinamphotericintacrolimusfk506mupirocinnystatinivermectinsalinomycinmonensintetracyclinedoxorubicinplicamycindaunorubicinepothilonediscodermolidebrefeldinnarasinpikromycinactinorhodinaflatoxinlovastatinsaxitoxinquinolidomicincuracin

The PKS domains of the PKZILLAs and those PKS domains from the representative Uniprot PKS polypeptides were then multiple sequence aligned with kalign2 v2.0.4 and maximum likelihood phylograms calculated with RAxML-NG v. 1.2.2 (see manuscript for details)

Plots were generated from the resulting newick files using ete3 v3.1.3 (Huerta-Cepas et al. 2016). Text within PDF plots was highlighted with color using PyMuPDF v1.23.19.

References:

J. Huerta-Cepas, F. Serra, and P. Bork, “ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data,” Molecular Biology and Evolution, vol. 33, no. 6, pp. 1635–1638, Jun. 2016, doi: 10.1093/molbev/msw046.