kegg-mcp-server

get_enzyme_info

Read-onlyIdempotent

Retrieve KEGG enzyme information by EC number and choose a compact summary or complete flat-file record for enzyme annotation and pathway analysis.

Instructions

Get detailed information for a KEGG enzyme (EC number).

Args: enzyme_id: EC number (e.g. '1.1.1.1') or prefixed ID (e.g. 'ec:1.1.1.1'). detail_level: 'summary' (default, compact) or 'full' (complete flat-file parse).

Input Schema

Name	Required	Description	Default
`enzyme_id`	Yes
`detail_level`	No		summary

Output Schema

Name	Required	Description	Default
`result`	Yes

Schema Changelog

Changes observed during successful MCP inspections.

Changed5 schema fields changedv0.5.0Oct 23, 2026

addedOutput schema / $defs / EntrySummary / properties / symbol

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Symbol"
+}

addedOutput schema / $defs / EnzymeInfo / properties / genes_truncated

Added value: +{
+  "default": false,
+  "title": "Genes Truncated",
+  "type": "boolean"
+}

removedOutput schema / $defs / ErrorResult

Removed value: -{
-  "description": "Structured error returned by a tool when the KEGG API fails.\n\nA tool returns this instead of raising so the model can reason about\nthe failure and decide whether to retry, change inputs, or give up.\nA point lookup that receives a 404 uses code ``not_found``; an empty search\nremains a successful result with no items.",
-  "properties": {
-    "code": {
-      "default": "kegg_api_error",
-      "title": "Code",
-      "type": "string"
-    },
-    "error": {
-      "title": "Error",
-      "type": "string"
-    },
-    "hint": {
-      "anyOf": [
-        {
-          "type": "string"
-        },
-        {
-          "type": "null"
-        }
-      ],
-      "default": null,
-      "title": "Hint"
-    },
-    "path": {
-      "anyOf": [
-        {
-          "type": "string"
-        },
-        {
-          "type": "null"
-        }
-      ],
-      "default": null,
-      "title": "Path"
-    },
-    "retryable": {
-      "default": false,
-      "title": "Retryable",
-      "type": "boolean"
-    },
-    "status": {
-      "anyOf": [
-        {
-          "type": "integer"
-        },
-        {
-          "type": "null"
-        }
-      ],
-      "default": null,
-      "title": "Status"
-    }
-  },
-  "required": [
-    "error"
-  ],
-  "title": "ErrorResult",
-  "type": "object"
-}

addedOutput schema / $defs / Reference / properties / sequence

Added value: +{
+  "anyOf": [
+    {
+      "type": "string"
+    },
+    {
+      "type": "null"
+    }
+  ],
+  "default": null,
+  "title": "Sequence"
+}

changedOutput schema / properties / result / anyOf

Previous value: -[
-  {
-    "$ref": "#/$defs/EnzymeInfo"
-  },
-  {
-    "$ref": "#/$defs/EntrySummary"
-  },
-  {
-    "$ref": "#/$defs/ErrorResult"
-  }
-]New value: +[
+  {
+    "$ref": "#/$defs/EnzymeInfo"
+  },
+  {
+    "$ref": "#/$defs/EntrySummary"
+  }
+]

First observedv0.1.0Jul 29, 2026

TDQS

A3.8/5.0

Behavior4/5

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

Annotations already declare readOnly, idempotent, non-destructive, open-world behavior, so the safety profile is covered. The description adds genuinely useful behavioral context beyond them: detail_level controls output verbosity ('summary' compact vs 'full' complete flat-file parse), which lets an agent reason about response size and cost. It omits error/not-found behavior and rate limits, keeping it below a 5.

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?

The one-line purpose is front-loaded, and the Args block is terse and scannable. Slight redundancy with the schema (restating the default for detail_level), but nothing wasteful.

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, return values needn't be described, and the tool's complexity is low (2 params, 1 required). The description covers ID formats and verbosity control, which is everything needed to invoke it correctly; only failure modes are unaddressed.

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

Parameters4/5

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

Schema description coverage is 0%, so the description carries the full burden and largely does: enzyme_id gets concrete format examples for both accepted forms ('1.1.1.1' and 'ec:1.1.1.1'), and detail_level is explained semantically with its default. It doesn't say whether prefixed/unprefixed forms are normalized or how partial EC numbers are treated.

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 ('Get detailed information for a KEGG enzyme (EC number)'), which is clearly a lookup-by-ID tool as opposed to the sibling search_enzymes. It doesn't name the sibling explicitly, so it stops short of a 5, but an agent can distinguish retrieval-by-identifier from search without opening either schema.

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?

Usage is implied through the Args block: the tool expects an EC number or prefixed ID, which tells the agent when it is applicable and implicitly routes discovery to search_enzymes. There is no explicit statement of when to prefer this over siblings or what happens with an invalid/unknown ID.

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