scan_protein_domains
Read-only
De-novo protein domain and family annotation: submits a protein to EMBL-EBI InterProScan and returns every member-database signature that matches it — Pfam, CATH-Gene3D, SUPERFAMILY, PANTHER, PROSITE, SMART, CDD and the rest — with its InterPro entry, its GO terms, its coordinates and its E-value. This is the DOMAIN half of the Protein domains panel; for the short linear motifs a profile scan cannot see, use find_linear_motifs, which takes the domains this tool emits. The scan runs at EBI, takes minutes, and needs a contact address because EBI requires one.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| No | EBI requires a contact address on every submission (their abuse contact, not a login). Left empty, the one saved in any EMBL-EBI panel is used, which only the in-browser doors can read. It is sent to EBI with the job and stored nowhere by this tool. | ||
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| sortBy | No | row order of the returned matches. Values: length (longest first), position (position along the protein), evalue (best E-value first), library (by member database). | length |
| goTerms | No | ask InterPro to attach Gene Ontology terms to the integrated entries, so a match carries its function rather than only its accession. | |
| protein | Yes | the protein sequence, one-letter codes; wire it from translate_sequence or read it off a CDS. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| pathways | No | ask InterPro to attach pathway cross-references (Reactome, KEGG, MetaCyc) to the integrated entries. | |
| maxEvalue | No | drop matches whose E-value is worse than this. 0 applies no threshold. A match the member database scores no E-value for (Coils, MobiDB-lite, Phobius) is KEPT either way — it has not failed the threshold, it was never scored against one. | |
| applications | No | member databases to run, comma-separated, using InterProScan's own ids (Pfam, Gene3D, SUPERFAMILY, PANTHER, PROSITE …). Empty runs the service's own default set, which is every database it has enabled. An id the live service does not advertise is refused by name rather than dropped. | |
| integratedOnly | No | keep only signatures integrated into an InterPro entry, dropping member-database hits InterPro has not curated into one. | |
| visibleLibraries | No | keep only matches from these member databases, comma-separated, as the RESULT document spells them (PFAM, GENE3D, SUPERFAMILY, CDD, PANTHER, MOBIDB_LITE …). This narrows what comes back; `applications` narrows what is RUN, and they are not the same question — a caller reading one library out of the service's default set wants this one. Empty keeps every database that answered. | |
| representativeOnly | No | keep only the matches InterProScan itself marks representative — its own answer to “which of these overlapping signatures describes this region best”. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| count | Yes | matches returned, after the reading knobs | |
| jobId | Yes | EBI's own job id, which is re-fetchable at their dispatcher for as long as they keep it — the provenance of this result, not an internal handle | |
| domains | Yes | the FOLDED regions only — domains, as `start-end@label` residue ranges — ready to wire straight into find_linear_motifs.domains so its globular-domain filter can bury motifs in them. Families, signal peptides, transmembrane helices, coiled coils and disordered spans are excluded: those are not folds a motif can hide inside, and disorder is where linear motifs live | |
| matches | Yes | every signature that matched, after the reading knobs: member database, signature accession and name, the InterPro entry it is integrated into, its kind (domain, family, site, repeat, homologous superfamily…), 1-based inclusive aaStart/aaEnd, the fragments a discontinuous domain is made of, the E-value and the GO and pathway cross-references | |
| provenance | Yes | the InterProScan version that ran, the MD5 the service computed over the sequence it analyzed, the member databases asked for, how many matches the scan returned before the reading knobs, and which of those knobs ran |