Alignments from "Evolutionary conservation of a core fungal phosphate homeostasis pathway tied to development in Blastocladiella emersonii"

Alignments used in phylogenetic tree reconstructions. Homologues of PHO proteins were identified in predicted proteomes using BLASTp (Altschul et al., 1997) and HMMer (Finn et al., 2011) homology searching algorithms. Proteins from diverse fungal predicted proteomes were considered orthologous when retrieved as reciprocal best hits when using S. cerevisiae PHO proteins as search queries. In some cases, (e.g. Pho4, Pho7, and Pho2 transcription factors) manual examination of alignments was used to identify putative orthologues based on sequence similarity or presence of unique motifs. In cases where orthologues could not be identified in a predicted proteome, tBLASTn was used to identify possible orthologues in corresponding genomes not identified during original annotations. In order to identify putative conserved phosphorylation motifs present in Pho4 orthologues, putative Pho4 proteins were collected from diverse fungal predicted proteomes. Pho4 proteins from more closely related species were aligned using MUSCLE (Edgar, 2004). These clade-specific alignments were then aligned to one another using the profile-profile alignment option in MUSCLE.