ECOD classification of the Vibrio parahaemolyticus RIMD 2210633 proteome (AlphaFold models)

Domain partitions and ECOD (Evolutionary Classification of protein Domains) classifications for AlphaFold Database (v3) models of the pandemic Vibrio parahaemolyticus strain RIMD 2210633 (TaxID 223926, UniProt proteome UP000002493). Models were partitioned and classified with the DPAM pipeline.

This is the data set behind Kinch et al. (2023) mSystems 8:e00796-23 (doi:10.1128/msystems.00796-23). It was previously served as a website (prodata.swmed.edu/ecod/index_rimd.php), which has been retired; this record is the archival copy of the classification and its database.

Contents: 8,490 domains (8,448 assigned to ECOD T-groups, 42 unassigned) from 4,402 proteins.

• ecod_rimd.domains.tsv: one row per domain, with protein annotation, residue range and full ECOD lineage (main table)
• ecod.af2_rimd.pdb.tar.gz: domain coordinates (PDB, pLDDT in the B-factor column)
• ecod.af2_rimd.fa.tar.gz and ecod.af2_rimd.unclassified.fa: domain sequences
• ecod.af2_rimd.domains.txt: the domain list as originally published (2023)
• ecod_rimd.tables.tar.zst and ecod_rimd.pgdump: the full PostgreSQL database, as per-table TSV and as a pg_dump

See README.md for column definitions and provenance. The domain structures are derived from AlphaFold DB models (CC BY 4.0).