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.

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.

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 unrooted phylograms calculated with RAxML-NG v. 1.2.0 with parameters "--model LG+G4m" without bootstrapping.

Plots were generated from the resulting newick files using ete3.