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manifest-v5
Automated asset release: manifest-v5
manifest-v4
Automated asset release: manifest-v4
kegg120
manifest-v3
Index of the toolbox-assets releases: kegg118, wolfpsort-0.2, transporters-2026-07-01, brenda-2026.1-1 and the BLAST+, DIAMOND and HMMER binaries. Adds brenda-2026.1-1 to manifest-v2.
manifest-v2
Index of the toolbox-assets releases: kegg118, wolfpsort-0.2, transporters-2026-07-01 and the BLAST+, DIAMOND and HMMER binaries, at CompMetEng/toolbox-assets URLs. Replaces manifest-v1, which pointed to SysBioChalmers/raven-data URLs and did not list the transporter assets.
BRENDA 2026.1 (build 1)
BRENDA files for GECKO and geckopy, from BRENDA release 2026.1 (CC BY 4.0; Chang et al., BRENDA, https://doi.org/10.1093/nar/gkaa1025). Changes from the BRENDA data: values are converted to kcat in 1/s, grouped (kcat, sa, mw) or screened for unit errors (measurements).
| File | Contents | Used by |
|---|---|---|
kcat.tsv.gz |
kcat per EC number, substrate and organism: maximum, median, count, references | fuzzy matching (kcatsFromBrenda) |
sa.tsv.gz |
specific activity per EC number, substrate and organism | fuzzy matching |
mw.tsv.gz |
molecular weight per EC number and organism | fuzzy matching |
measurements.tsv.gz |
57,037 wild-type kcat measurements with an EC number, one row each, after the outlier screen; with substrate InChIKey, organism, UniProt accession, sequence id, temperature, pH, PubMed id | EC tree (kcatsFromECTree) |
sequences.fasta.gz |
the 6,577 sequences of the measurements, by sequence id | homologs |
substrates.tsv.gz |
ChEBI, MetaNetX and name keys per substrate InChIKey | matching model metabolites |
kcatCombineParams.tsv |
bias and error variance per source (EC tree, homologs, OpenKineticsPredictor methods) and evidence bin, fitted on the kcat benchmark's development split | combine stage |
The outlier screen leaves out values more than four orders of magnitude below their EC class, and clusters of values below 0.01 /s that sit three orders of magnitude under the other values of their EC number (423 values).
Transporter reference DBs (Pfam HMMs + TCDB)
Automated asset release: transporters-2026-07-01
manifest-v1
Automated asset release: manifest-v1
kegg118
hmmer-3.4.0
Automated asset release: hmmer-3.4.0