petadex/petadex-corpus-full

PETadex corpus: full

Every ORF in the PETadex v1.1 catalytic corpus, 307,155,746 putative plastic-degrading enzyme ORFs (PAZy 211, NCBI nr 4,723,128, Logan/SRA 302,432,407), with every annotation that could be keyed to them. Built 2026-10-15.

The companion petadex/petadex-corpus-centroids90 has one row per 90%-identity cluster (18,172,960 rows) and is the place to start for most uses.

Not included, by design: protein-language-model embeddings (and anything derived from them, such as UMAP coordinates), and activity data (kinetics, curated activity labels). Activity labels are a separate PETai dataset.

Layout

All Parquet (zstd). Every table is a config: load_dataset("petadex/petadex-corpus-full", "signalp6"). For joins over the full corpus, querying the files directly with DuckDB or Polars is much faster than datasets.

orfs/: the spine, one row per ORF, sorted by orf_id. orf_id, origin (PAZy / NR / Logan), accession (NR/PAZy), library_id (SRA run, Logan), contig, orf_start, orf_end, orf_type, length, has_stop, md5, c90_id, c60_id, c30_id, is_c90_centroid, sequence.

md5 is the MD5 of the uppercase sequence with a trailing stop (*) removed; has_stop records the stop. md5(sequence) holds row by row.

layers/: annotations keyed on orf_id (an ORF can have several rows).

Layer	Rows	ORFs covered	Contents
afdb_structures	308,394	0.1%	AlphaFold DB structure pointers (S3 keys, UniProt) for ORFs whose NR accession matched an AFDB entry
biochem_full	307,155,746	100%	MW, pI, GRAVY, instability index, aromaticity of the full ORF
biochem_mature	42,522,458	13.8%	The same properties for the mature sequence, signal-peptide ORFs only
catalytic_domains	307,155,746	100%	PETadex HMM catalytic domain call per ORF: HMM, coordinates, catalytic residues
catalytic_domains_v260701	8,246,431	2.15%	Domain calls from the July 2026 rebuild: E-value, component, complete_catalytic_hit
family_v1	61,900	0.02%	Legacy 64,730-family membership (family representative = trimmed domain)
interproscan_family_reps	262,260	0.02%	InterProScan hits on the family representatives (coordinates are domain-relative)
nr_taxonomy	2,653,237	0.86%	Organism and lineage for NR-origin ORFs
plasticome	522	0%	Plasticome (known plastic-degrading enzymes) membership
signalp6	307,155,746	100%	SignalP 6 class probabilities and cleavage site

A missing row in a subset layer means not annotated, not absent.

dims/: tables keyed on something else, reached from the spine.

Table	Rows	Contents
biosamples	6,796,722	BioSample annotation: metadata profile, tier, environment, geography, temperature, pH
cluster90_profile_distribution	24,236,640	Profile counts per 90% cluster
cluster90_profiles	18,172,960	Dominant metadata profile per 90% cluster
clusters30	22,235	30% cluster table
clusters60	1,814,296	60% cluster table
clusters90	18,172,960	90% cluster table: centroid, size, composition
component_cath	42	Component to CATH lookup
hmms	45	PETadex HMMs and their catalytic positions
plasticome_reference	57	Plasticome reference residues per component
profiles	22	Metadata profile summary
runs	6,213,292	SRA run metadata for the runs that contribute Logan ORFs

Joins: orfs.library_id → runs.acc, runs.biosample → biosamples.biosample, orfs.c90_id → clusters90.cluster_id (and cluster90_profiles.pid90), c60_id → clusters60.cluster_id, c30_id → clusters30.cluster_id.

import duckdb
duckdb.sql("""
  select o.origin, s.prediction, count(*)
  from 'orfs/*.parquet' o join 'layers/signalp6.parquet' s using (orf_id)
  group by all""")

Things to know

• Redundancy. Only 123,966,734 ORFs (40.4%) are distinct sequences. Deduplicate on md5 before per-sequence work.
• Logan ORFs are called stop-to-stop: only ~3% start with M. N-terminal annotations (SignalP, biochem_mature) are unreliable for Logan rows.
• orf_type (Logan) is inherited and undocumented: types 0/2 end in a stop; 1/3 never do and are cut off by the contig end.
• HMM versions: catalytic_domains names _260407 models; dims/hmms lists _260507 models.
• Family layer / InterProScan coordinates are relative to the trimmed family-representative domain, not the ORF.
• centroid_domain_name in the cluster tables is known to be wrong for some representatives; prefer the HMM calls.
• Layers outside the orf_id key space were joined by sequence MD5, then accession (bridge_method). 44.5% of the July 2026 rebuild's NR proteins postdate this corpus and are not here.

Provenance

Corpus FASTA s3://petadex/logan/petadex.catalytic_orfs.v1.1.fa; PETadex RDS tables (clustering, catalytic domains, origins, metadata); PETadex v260701 rebuild; SignalP 6 and biochemical-property runs. Build code and checks: petadex-corpus-dataset (stages 01–06, notebook PETadex_Corpus_Dataset.ipynb).