Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels - additional data

This repository stores additional data files for the article Rozenberg, Kaczmarczyk, Matzov, Vierock et al (2022) "Rhodopsin-bestrophin fusion proteins from unicellular algae form gigantic pentameric ion channels".

The files included are as follows:

• Inputs.zip - all input files to the workflow (also available there)
• Species phylogenies:
  • Chlorophyte_orthogroups.zip, Haptophyte_orthogroups.zip, Dinoflagellate_orthogroups.zip - zip files with the orthogroups used in species phylogeny. Each folder corresponds to an orthogroup (busco orthogroups for chlorophytes and dinoflagellate, proteinortho orthogroups for haptophytes):
    • mafft.faa - mafft alignment
    • trimal.faa - trimal trimmed alignment
    • iqtree.treefile and iqtree.log - iqtree tree and log file
    • treeshrink.treefile - treeshrink pruned tree
• Structural_alignment.zip includes structural alignments of the bestrhodopsin's rhodopsin and bestrophin domains with reference sequences:
  • rhodopsins.aln and bestrophins.aln- raw alignments from t_coffee
  • rhodopsins_modified.fasta and bestrophins_modified.fasta - curated alignments
  • rhodopsins.gff and bestrophins.gff - secondary structure features for the sequences
• Global phylogeny of bestrophins and rhodopsins:
  • Bestrophins_global_sequences.zip - sequence data for the bestrophin global phylogeny:
    • uniref50.txt - uniref50 tabular data matching bestrophins (Pfam PF01062)
    • ur50_long.cdhit, ur50_long.cdhit.clstr - cdhit clustering (50% identity)
    • ur50_trim.faa - filtered and trimmed alignment used as input to iqtree
  • Bestrophins_global_phylogeny.zip - global bestrophin phylogeny. Subfolders corresponding to different runs with names corresponding to the seed values, each containing iqtree output files, in particular the newick ur50.treefile files.
  • Rhodopsins_global_phylogeny.fasta, Rhodopsins_global_phylogeny.fasta.trimmed - alignment of rhodopsin sequences and its trimmed version as used for rhodopsin bestrophin phylogeny
  • Rhodopsins_global_phylogeny.zip - global rhodopsin phylogeny. Subfolders corresponding to different runs with names corresponding to the seed values, each containing iqtree output files, in particular the newick rhodopsins.treefile files
  • Rhodopsins_global_phylogeny_interproscan.zip - results of interproscan analysis of the rhodopsin sequences used for global phylogeny