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Jean — Molecular Biology & Genomics

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.

Input Schema

NameRequiredDescriptionDefault
emailNoEBI 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.
_filesNoThe 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.
sortByNorow order of the returned matches. Values: length (longest first), position (position along the protein), evalue (best E-value first), library (by member database).length
goTermsNoask InterPro to attach Gene Ontology terms to the integrated entries, so a match carries its function rather than only its accession.
proteinYesthe protein sequence, one-letter codes; wire it from translate_sequence or read it off a CDS.
_subjectNoThe 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.
pathwaysNoask InterPro to attach pathway cross-references (Reactome, KEGG, MetaCyc) to the integrated entries.
maxEvalueNodrop 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.
applicationsNomember 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.
integratedOnlyNokeep only signatures integrated into an InterPro entry, dropping member-database hits InterPro has not curated into one.
visibleLibrariesNokeep 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.
representativeOnlyNokeep only the matches InterProScan itself marks representative — its own answer to “which of these overlapping signatures describes this region best”.

Output Schema

NameRequiredDescriptionDefault
countYesmatches returned, after the reading knobs
jobIdYesEBI'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
domainsYesthe 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
matchesYesevery 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
provenanceYesthe 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

Schema Changelog

Changes observed during successful MCP inspections.

  1. First observed

TDQS

A3.5/5.0
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint=true, openWorldHint=true and destructiveHint=false, so the description only needs to add context beyond that, and it does establish that this is an external submission to EMBL-EBI plus what comes back (InterPro entry, GO terms, coordinates, E-value). However, it omits genuinely important behavioural traits for a remote InterProScan job: expected latency, whether the call blocks or is asynchronous, failure/timeout behaviour, and result-size limits. Those gaps matter more than usual for a tool whose annotations already flag open-world cost.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

One dense opening sentence with the verb and scope front-loaded, then the payload enumeration in an em-dash clause. Every element earns its place, though the comma-separated database list is longer than strictly necessary and pushes the sentence toward run-on length.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

With an output schema present, the description need not explain return values and wisely only names them in passing. For a 12-parameter tool with nested _subject and an external service dependency, the remaining omission is operational — timing and failure modes — rather than conceptual. That is a real but modest gap, not a disqualifying one.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100% and the individual parameter descriptions are already unusually rich (applications vs visibleLibraries distinction, maxEvalue's never-scored exception, sortBy ordering semantics). The prose adds no parameter meaning beyond that, so the baseline of 3 applies; it does at least name the output fields the caller will filter on.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

States a specific verb and resource — submits a protein to EMBL-EBI InterProScan and returns every matching member-database signature — and enumerates the databases (Pfam, CATH-Gene3D, SUPERFAMILY, PANTHER, PROSITE, SMART, CDD). The 'every member-database signature' phrasing implicitly separates it from single-database siblings like rps_blast_cdd or rps_blast_smart, but no sibling is named explicitly, which keeps it just short of a 5.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

'De-novo' hints that this is for unannotated proteins rather than lookup_protein, but the hint is never spelled out. There is no explicit statement of when to choose this over the per-database scan tools (rps_blast_cdd, rps_blast_smart, protein_profile) or over lookup_protein for an already-annotated accession. Usage is implied, not stated.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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