Supplementary data for "Mass spectrometry reveals the evolutionary conservation of phycobiliprotein complexes"

This repository contains sequence data and protein structures predicted using AlphaFold. The data files are organised as follows: Phylogenomics.zip: contains the sequences and alignments used to infer the phylogenomic tree. 1_Sequences: contains the unaligned sequence files for 136 marker genes. 2_Alignments: contains the aligned sequences. 3_FilteredAlignments: contains filtered alignments. 4_Trees: contains the trees produced by the phylogenomic analysis. partitions.nex: IQ-TREE partition file specifying the evolutionary model for each marker gene. Structures.zip: contains data for protein structures predicted using AlphaFold. 1_apcAAABBB_1403_21: hexamer containing three apcA and three apcB subunits from Dolichospermum circinale CCAP 1403/21. 2_cpcAAABBB_1403_21: hexamer containing three cpcA and three cpcB subunits from Dolichospermum circinale CCAP 1403/21. 3_apcAABB_1403_21_apcAB_1437_1: mixed hexamer containing two apcA and two apcB subunits from Dolichospermum circinale CCAP 1403/21, and one apcA and apcB subunit from Gloeomargarita litophora CCAP 1437/1. 4_cpcAABB_1403_21_cpcAB_1437_1: mixed hexamer containing two cpcA and two cpcB subunits from Dolichospermum circinale CCAP 1403/21, and one cpcA and cpcB subunit from Gloeomargarita litophora CCAP 1437/1. 5_apcAABB_cpcAB_1403_21: mixed hexamer containing two apcA, two apcB, one cpcA, and one cpcB subunits from Dolichospermum circinale CCAP 1403/21. 6_apcAABB_cpcAsBs_1403_21_2: mixed hexamer containing two apcA, two apcB, one modified cpcA, and one modified cpcB subunits from Dolichospermum circinale CCAP 1403/21. Each folder contains four files: [name].fas: the sequences used for AlphaFold structure prediction, in FASTA format. [name].pdb: the structure predicted by AlphaFold, in PDB format. [name].confidence.json: per-residue confidence values produced by AlphaFold, in JSON format. [name].pae.json: pairwise predicted aligned error values produced by AlphaFold, in JSON format.