Pantothenate and CoA biosynthesis in Apicomplexa and their promise as antiparasitic drug targets
Fig 5
Phylogenetic tree of ACS and AcAS.
Phylogeny of the ACS family and AcAS in Apicomplexa. The hits identified with the iterative jackhmmer search (S1 Table; [160]) were used for the phylogenetic analysis. PfACS1b was not identified based on its homology to the query sequences in the jackhmmr search but was added based on previous literature [154]. MegaX was used to align all hits with ClustalW, followed by building an unrooted tree using a maximum likelihood analysis with a bootstrap phylogeny test. In initial analyses, 5 hits were excluded because these sequences did not cluster with any of the annotated family members. (A) Phylogenetic tree of all identified ACS and AcAS family members. Different settings were tested, including the alignment of the full amino acid sequence or the AMP-binding enzyme (PF00501) domain sequence, followed by a maximum likelihood analysis using all sites or a 50% partial deletion, all leading to comparable results. Phylogenetic tree analyses with 50% partial deletion excluded 1 hit because this alignment aligned with less than 50% of the genes. The final phylogenetic tree presented here is based on the full amino acid sequence of the identified ACS and AcAS family members, analyzed by the maximum likelihood method, 50% partial deletion with a bootstrap phylogeny test with 500 replicates. (B) Phylogenetic tree of only ACS family members. The phylogeny of the clusters of ACS family members was further tested in a maximum likelihood analysis using all different approaches as under (A). In none of the analyses, TGME49_310080 and TGME49_310150 clustered with ACS9, while the Plasmodium ACS12 cluster only once included the additional sequences from (A). The final phylogenetic tree presented here is based on the full amino acid sequence, analyzed by the maximum likelihood method, 50% partial deletion with a bootstrap phylogeny test with 100 replicates. AcAS, acetyl-CoA synthetase; ACS, acyl-CoA synthetase; FASI, type I fatty acid synthase; PKS, polyketide synthase.