Protein function annotation (ORFs and annotation outputs)

This item contains processed protein-level annotation files supporting our manuscript on the evolutionary relationships between HK97-fold viruses (Duplodnaviria) and encapsulins. The work was carried out in the Luque Lab (Department of Biology, University of Miami). These files capture predicted open reading frames (ORFs) and multiple complementary annotation strategies used for downstream analyses (protein function inference, remote homology assessment, and HK97-fold detection).<b>Contents:</b><b>data_file_S5_ORFs.gb</b><br>Multi-GenBank file containing all contigs with their predicted open reading frames (ORFs), including annotations used for downstream protein-level analyses.<br><b>data_file_S6_plm_annotation.zip</b><br>Protein function predictions generated with the Virus Protein Function Protein Language Model (VPF-PLM). Includes per-protein <code>.csv</code> outputs (predicted functions and probability matrices) and <code>.pkl</code> embedding files.<br><b>data_file_S7_vibrant_annotation.zip</b><br>VIBRANT-derived annotations for environmental viral contigs, including KEGG, Pfam, VOG, and VPFAM HMM scan results, plus summary outputs describing genome size, quality, and gene content.<br><b>data_file_S8_HK97_hmm_profiles.zip</b><br>Hidden Markov Model (HMM) profiles used to detect HK97-fold proteins, including Pfam clan CL0373 (“Phage_coat”) profiles and extended profile sets from the efam database.<br><b>data_file_S9_hhpred_annotation.zip</b><br>Archive of HHpred <code>.hhr</code> output files used for remote homology and function inference; these outputs were manually reviewed for key annotations used in the manuscript.<br><b>Notes on reuse:</b> These are processed outputs and profile resources assembled for the analyses reported in the manuscript. When reusing results, please cite the associated manuscript and this Figshare item DOI, and follow any relevant terms for third-party resources (e.g., database/profile sources) as applicable.