# ECOD v293.1 Release Notes

**Release Date:** January 13, 2026

## Overview

ECOD v293.1 is a significant update featuring the migration from Pfam 37.4 to Pfam 38.1, introducing 3,358 new protein families and reclassifying approximately 47,000 domains based on updated Pfam clan and family definitions.

## Key Changes

### Pfam 38.1 Migration

This release incorporates Pfam database version 38.1 (released July 2024), which includes:
- Updated HMM profiles with improved sensitivity
- Revised clan memberships reflecting new evolutionary relationships
- New protein families discovered since Pfam 37.4

The migration involved:
- **47,095 domains** reclassified through updated Pfam-to-F-group mappings
- **3,358 new F-groups** created from novel Pfam 38.1 families
- Clan-aware assignment using `--cut_ga` (gathering threshold) for reliable domain boundaries

### New F-group Composition

The 3,358 new F-groups include families from Pfam 38.1 that were not present in the previous Pfam-to-F-group mappings. These families contain both experimental PDB structures and AlphaFold predicted models.

## Statistics

### Domain Coverage

| Metric | Count |
|--------|-------|
| Total domains | 2,626,470 |
| PDB domains | 1,110,671 |
| AlphaFold domains | 1,515,799 |
| Sequences | 2,709,251 |

### Classification Hierarchy

| Level | Count |
|-------|-------|
| X-groups (Possible Homology) | 2,455 |
| H-groups (Homology) | 3,948 |
| T-groups (Topology) | 3,948 |
| F-groups (Family) | 20,632 |

### Representatives

| Type | Count |
|------|-------|
| Manual representatives | 26,664 |
| F40 clustering representatives | 483,474 |
| F70 clustering representatives | 851,573 |
| F99 clustering representatives | 1,434,264 |

## Distribution Files

All distribution files are available at: http://prodata.swmed.edu/ecod/distributions/

### Main Files
- `ecod.v293.1.domains.txt` - Complete domain list with classifications
- `ecod.v293.1.names.txt` - Simplified domain index
- `ecod.v293.1.fa` - FASTA sequences for all domains
- `ecod.v293.1.hierarchy.txt` - Classification hierarchy with domain counts

### Clustering Representatives
- `ecod.v293.1.F40.*` - 40% sequence identity representatives
- `ecod.v293.1.F70.*` - 70% sequence identity representatives
- `ecod.v293.1.F99.*` - 99% sequence identity representatives

### BLAST Database
- `ecod.v293.1.blast.*` - BLAST-formatted database for sequence searches

### Checksums
- `ecod.v293.1.md5` - MD5 checksums for all files

## Technical Details

### Pfam Assignment Parameters
- Pfam-A HMM database version: 38.1
- hmmscan with `--cut_ga` (gathering threshold)
- Clan-aware assignment respecting Pfam clan definitions

### Clustering Parameters
- CD-HIT used for sequence clustering within F-groups
- F40: 40% sequence identity, 80% alignment coverage
- F70: 70% sequence identity, 80% alignment coverage
- F99: 99% sequence identity, 80% alignment coverage

### Data Sources
- PDB structures through July 2025
- AlphaFold DB v4 (48 proteomes + SwissProt set)
- UniProt 2024_06 annotations

## Changes from v293

| Metric | v293 | v293.1 | Change |
|--------|------|--------|--------|
| Total domains | 2,626,478 | 2,626,470 | -8 |
| F-groups | 17,274 | 20,632 | +3,358 |
| Pfam mappings | 17,274 | 20,632 | +3,358 |

Note: The slight decrease in total domains reflects obsolescence of 8 domains, while F-group count increases due to Pfam 38.1 migration.

## Acknowledgments

This release was developed using the ECOD release management infrastructure with automated Pfam clan integration and per-F-group clustering pipelines.

## Citation

Please cite ECOD as:
> Cheng H, Schaeffer RD, Liao Y, Kinch LN, Pei J, Shi S, Kim BH, Grishin NV. (2014) ECOD: An evolutionary classification of protein domains. PLoS Comput Biol 10(12): e1003926.

## Contact

For questions or issues, please contact: ecod.database@gmail.com