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

Domain partitions and ECOD classifications for AlphaFold Database models of
the pandemic *V. parahaemolyticus* strain RIMD 2210633 (TaxID 223926, UniProt
proteome UP000002493). This is the data set behind:

> Kinch LN, Schaeffer RD, Zhang J, Cong Q, Orth K, Grishin NV (2023).
> Insights into virulence: structure classification of the *Vibrio
> parahaemolyticus* RIMD proteome. *mSystems* 8(6):e00796-23.
> https://doi.org/10.1128/msystems.00796-23

It used to be served as a website (`prodata.swmed.edu/ecod/index_rimd.php`).
That site has been retired, and this record is now the archival copy of the
classification and of the database behind it.

## How it was made

AlphaFold models (AFDB v3) for the RIMD proteome were downloaded in August 2022,
partitioned into domains, and assigned to ECOD with DPAM. The DPAM version used
merges neighbouring domains assigned to the same T-group, and flags domains with
simple topology or partial coverage. See the paper's Materials and Methods.
Each classified domain points at the ECOD reference domain that supported its
T-group assignment (`rep_ecod_uid`). The ECOD hierarchy is the one used in
2022-11 and is included in full (`cluster` table).

## Counts

| | |
|---|---|
| Domains | 8,490 (8,448 assigned to an ECOD T-group, 42 unassigned) |
| Proteins with at least one domain | 4,402 |
| Domain structures | 8,490 |

These are the counts of the database the website served. The paper's text
reports 7,696 domains from 4,822 proteins, and the database's own `info` table
gives 8,032 domains from 4,262 proteins. Use `ecod_rimd.domains.tsv` as the
authoritative list.

## Files

| File | Contents |
|---|---|
| `ecod_rimd.domains.tsv` | **Main table.** One row per domain, with protein annotation and the full ECOD lineage (see columns below). |
| `ecod.af2_rimd.domains.txt` | Domain list as published with the paper (2023-05-31), unchanged. |
| `ecod.af2_rimd.pdb.tar.gz` | Domain coordinates, one PDB file per domain (`<uid>.pdb`), 8,490 files. Cut from the AFDB v3 models; the B-factor column holds pLDDT. As published. |
| `ecod.af2_rimd.fa.tar.gz` | Domain sequences (`<uid>.fa`), 8,448 files: the assigned domains. As published. |
| `ecod.af2_rimd.unclassified.fa` | Sequences of the 42 unassigned domains, taken from their PDB files (added 2026). |
| `ecod_rimd.tables.tar.zst` | Every table of the database as TSV with a header row (`domain`, `cluster`, `cluster_relation`, `unp_info`, `rimd_gene_order`, `reference_domain`, `info`). Raw export: `domain` still contains 8 exact duplicate rows. |
| `ecod_rimd.pgdump` | `pg_dump -Fc` of the PostgreSQL database (PostgreSQL 17). Restore with `pg_restore -d <db> ecod_rimd.pgdump`. |
| `MANIFEST.tsv` | Size and MD5 of every file. |

Unpack the `.tar.zst` with `tar --zstd -xf` (or `zstd -dc FILE | tar -x`).

### `ecod_rimd.domains.tsv` columns

Tab-separated, UTF-8, one header row, no quoting. Empty fields are missing values.

| Column | Meaning |
|---|---|
| `uid` | ECOD domain uid (9 digits, zero-padded); the file name stem in the tarballs |
| `domain_id` | Domain identifier, `<UniProt acc>_nD<n>` |
| `unp_acc` | UniProt accession of the protein |
| `unp_name` | UniProt entry name |
| `locus_tag` | RIMD ordered locus name (VP / VPA numbers) |
| `gene_name` | Gene name, where UniProt gives one |
| `protein_name` | UniProt protein name |
| `gene_order` | Position of the gene in the RIMD genome order |
| `range` | Domain residue range on the UniProt sequence (segments separated by `,`) |
| `is_manual` | `t` if the assignment was set by hand (none in this set) |
| `a_id`, `x_id`, `h_id`, `t_id`, `f_id` | ECOD architecture, X-group, H-group, T-group and F-group ids. Empty `t_id` = unassigned; `f_id` is empty throughout (no F-group assignments were made for this set) |
| `a_name`, `x_name`, `h_name`, `t_name` | Names of those groups |
| `rep_ecod_uid`, `rep_ecod_domain_id` | ECOD reference domain that supported the T-group assignment |
| `comment` | Curator comment, if any |

## License and attribution

CC BY 4.0. The domain structures are derived from AlphaFold Database models
(Jumper et al. 2021, *Nature* 596:583; Varadi et al. 2022, *NAR* 50:D439),
which are themselves CC BY 4.0.

When using these data please cite the mSystems paper above and ECOD:
Schaeffer RD, Liao Y, Cheng H, Grishin NV (2017). ECOD: new developments in the
evolutionary classification of domains. *Nucleic Acids Res* 45:D296–D302.
https://doi.org/10.1093/nar/gkw1137

Contact: Grishin lab, UT Southwestern Medical Center (http://prodata.swmed.edu/ecod/).