active_sites v1.0: enzyme domain sequences with annotated active sites from Pfam v37.1 for benchmarking MSA tools

This dataset contains 772 enzyme domain families annotated with 1,376 active sites in Pfam v37.1. Protein sequences containing Pfam domains were retrieved from UniProt, and active site residues were predicted using Pfam’s pfam_scan.pl tool v1.626 together with the active site database active_site.dat v37.1. For each protein, only the sequence corresponding to the annotated domain was extracted from the full-length protein sequence Domain sequences were excluded if: the annotated domain was shorter than 25% of the length of the corresponding Pfam HMM model, or more than 10% of residues were non-standard amino acids. Directory structure The dataset contains two directories: families/ – domain protein sequences grouped by enzyme family [FASTA format] active_sites/ – active site residue annotations for each family [TSV format] A metadata file (metadata.tsv) is also included, providing detailed information for each enzyme family. Metadata A metadata file (metadata.tsv) provides: family_id – Pfam family identifier (e.g., PF02615) family_name – Pfam family name seqs_count – total number of domain sequences in the family seqs_with_active_sites – number of sequences containing at least one annotated active site seqs_with_active_sites_percent – percentage of sequences with active sites active_site_ids – comma-separated list of active site identifiers for the family min_seq_length – minimum domain sequence length mean_seq_length – average domain sequence length max_seq_length – maximum domain sequence length Active sites Each family has a corresponding TSV file in active_sites/ listing sequence-specific active site annotations: protein_id – protein sequence identifier site_id – active site identifier (e.g., 114_H, 42_H) protein_position – residue position within the sequence protein_residue – amino acid at the position