diff --git a/Model/lib/wdk/model/questions/geneQuestions.xml b/Model/lib/wdk/model/questions/geneQuestions.xml
index 7690d0569..d9b5e1ac1 100644
--- a/Model/lib/wdk/model/questions/geneQuestions.xml
+++ b/Model/lib/wdk/model/questions/geneQuestions.xml
@@ -931,6 +931,54 @@ In the analysis carried out by Alsford et al., pseudogenes, genes annotated as "
     </question>
 
 
+  <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
+  <!-- Genes By Secondary Metabolites (antiSMASH) -->
+  <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
+
+    <question name="GenesBySecondaryMetabolites"
+              includeProjects="FungiDB,UniDB"
+              displayName="Genes By Secondary Metabolites"
+              shortDisplayName="Sec Metabolites"
+              searchCategory="Function prediction"
+              queryRef="GeneId.GenesBySecondaryMetabolites"
+              recordClassRef="TranscriptRecordClasses.TranscriptRecordClass">
+
+      <paramRef ref="organismParams.antismash_organism"/>
+      <paramRef ref="geneParams.antismash_category"/>
+      <paramRef ref="geneParams.antismash_annotation"/>
+
+      <attributesList
+        summary="category,antismash_annotation,cluster_location,overlapping_clusters"
+        sorting="gene_source_id asc"/>
+
+      <dynamicAttributes>
+        <columnAttribute name="category" displayName="Cluster Category"/>
+        <columnAttribute name="antismash_annotation" displayName="Annotation"/>
+        <!--<columnAttribute name="sequence_id" displayName="Sequence"/>-->
+        <columnAttribute name="cluster_start" displayName="Cluster Start"/>
+        <columnAttribute name="cluster_end" displayName="Cluster End"/>
+        <columnAttribute name="org_abbrev" displayName="Organism Abbreviation" internal="true" inReportMaker="false"/>
+        <columnAttribute name="cluster_context_start" displayName="Cluster Context Start" inReportMaker="false"/>
+        <columnAttribute name="cluster_context_end" displayName="Cluster Context End" inReportMaker="false"/>
+        <columnAttribute name="overlapping_clusters" displayName="Overlapping Clusters"/>
+        <textAttribute name="cluster_location" displayName="View Cluster in JBrowse" inReportMaker="false" truncateTo="100000">
+          <text>
+            <![CDATA[
+              <a href="@JBROWSE_WEBPAGE_URL@?loc=$$sequence_id$$:$$cluster_context_start$$..$$cluster_context_end$$&data=@JBROWSE_SERVICE_URL@/tracks/$$org_abbrev$$&tracks=gene%2Cantibiotics%20and%20Secondary%20Metabolites%20Analysis%20SHell%20(antiSMASH)&highlight=$$sequence_id$$:$$gene_start_min$$..$$gene_end_max$$">$$sequence_id$$:$$cluster_start$$-$$cluster_end$$</a>
+            ]]>
+          </text>
+        </textAttribute>
+      </dynamicAttributes>
+
+      <summary><![CDATA[Find genes in secondary metabolite biosynthesis clusters.]]></summary>
+
+      <description><![CDATA[
+        Find genes associated with secondary metabolite biosynthesis clusters predicted by antiSMASH,
+        filtered by organism, cluster category, and annotation.
+      ]]></description>
+
+    </question>
+
 
   <!--++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++-->
   <!-- functional profiling growth rate Phenotype -->
diff --git a/Model/lib/wdk/model/questions/params/geneParams.xml b/Model/lib/wdk/model/questions/params/geneParams.xml
index fa686ea6a..6d05bb687 100644
--- a/Model/lib/wdk/model/questions/params/geneParams.xml
+++ b/Model/lib/wdk/model/questions/params/geneParams.xml
@@ -5104,6 +5104,29 @@ products of your selected type (or types).<br><br>
       <suggest default="1"/>
     </stringParam>
 
+    <!-- antiSMASH secondary metabolite params (FungiDB, UniDB only) -->
+    <flatVocabParam name="antismash_category"
+                    queryRef="GeneVQ.AntismashCategories"
+                    prompt="Cluster Category"
+                    multiPick="true"
+                    quote="true"
+                    dependedParamRef="organismParams.antismash_organism"
+                    includeProjects="FungiDB,UniDB">
+      <help>Select one or more secondary metabolite cluster categories.</help>
+      <suggest default="NRPS"/>
+    </flatVocabParam>
+
+    <flatVocabParam name="antismash_annotation"
+                    queryRef="GeneVQ.AntismashAnnotations"
+                    prompt="Annotation"
+                    multiPick="true"
+                    quote="true"
+                    dependedParamRef="geneParams.antismash_category, organismParams.antismash_organism"
+                    includeProjects="FungiDB,UniDB">
+      <help>Select an annotation. Options filter based on the selected category.</help>
+      <suggest default="biosynthetic"/>
+    </flatVocabParam>
+
     <stringParam name="genbank_accession"
                  prompt="GenBank Accession Number"
                  number="false">
@@ -9711,6 +9734,62 @@ end as term
       </sql>
     </sqlQuery>
 
+    <sqlQuery name="AntismashCategories" includeProjects="FungiDB,UniDB">
+      <paramRef ref="organismParams.antismash_organism"/>
+      <column name="display"/>
+      <column name="internal"/>
+      <column name="term"/>
+      <sql>
+        <![CDATA[
+        SELECT DISTINCT ac.category AS  display
+        , ac.category AS  internal
+        , ac.category AS  term
+        , CASE WHEN lower(ac.category) = 'other' THEN 1 ELSE 0 END AS sort_order
+        FROM apidb.antismashfeature af
+        JOIN apidb.antismashclusterfeature acf
+            ON acf.antismash_feature_id = af.antismash_feature_id
+        JOIN apidb.antismashcluster ac
+            ON ac.antismash_cluster_id = acf.antismash_cluster_id
+        JOIN apidbtuning.transcriptattributes ta
+            ON ta.gene_na_feature_id = af.na_feature_id
+        WHERE ta.org_abbrev in ($$antismash_organism$$)
+        AND ta.project_id = 'FungiDB'
+        ORDER BY sort_order, display
+        ]]>
+      </sql>
+    </sqlQuery>
+
+    <sqlQuery name="AntismashAnnotations" includeProjects="FungiDB,UniDB">
+      <paramRef ref="organismParams.antismash_organism"/>
+      <paramRef ref="geneParams.antismash_category"/>
+      <column name="display"/>
+      <column name="internal"/>
+      <column name="term"/>
+      <sql>
+        <![CDATA[
+        SELECT DISTINCT COALESCE (af.antismash_annotation, 'unknown') AS display
+        , COALESCE (af.antismash_annotation, 'unknown') AS internal
+        , CASE WHEN COALESCE(af.antismash_annotation, 'unknown') = 'biosynthetic'         THEN 0
+            WHEN COALESCE(af.antismash_annotation, 'unknown') = 'biosynthetic-additional' THEN 1
+            WHEN COALESCE(af.antismash_annotation, 'unknown') = 'other'                   THEN 3
+            WHEN COALESCE(af.antismash_annotation, 'unknown') = 'unknown'                 THEN 4
+            ELSE 2 END AS sort_order
+        , COALESCE (af.antismash_annotation, 'unknown') AS term
+        FROM apidb.antismashfeature af
+        JOIN apidb.antismashclusterfeature acf
+            ON acf.antismash_feature_id = af.antismash_feature_id
+        JOIN apidb.antismashcluster ac
+            ON ac.antismash_cluster_id = acf.antismash_cluster_id
+        JOIN apidbtuning.transcriptattributes ta
+            ON ta.gene_na_feature_id = af.na_feature_id
+        WHERE ta.org_abbrev in ($$antismash_organism$$)
+        AND ta.project_id = 'FungiDB'
+        AND ac.category in ($$antismash_category$$)
+        ORDER BY sort_order, display
+        ]]>
+      </sql>
+    </sqlQuery>
+
   </querySet>
 
   <groupSet name="geneParamGroupSet">
diff --git a/Model/lib/wdk/model/questions/params/organismParams.xml b/Model/lib/wdk/model/questions/params/organismParams.xml
index 5fb56512b..d3dae0663 100644
--- a/Model/lib/wdk/model/questions/params/organismParams.xml
+++ b/Model/lib/wdk/model/questions/params/organismParams.xml
@@ -438,6 +438,21 @@
       </enumList>
     </enumParam>
 
+    <flatVocabParam name="antismash_organism"
+                    queryRef="organismVQ.AntismashOrganisms"
+                    prompt="Organism"
+                    displayType="treeBox"
+                    multiPick="true"
+                    suppressNode="true"
+                    quote="true"
+                    includeProjects="FungiDB,UniDB">
+      <help>Select the organism(s) to search.</help>
+      <propertyList name="organismProperties">
+        <value>pruneNodesWithSingleExtendingChild</value>
+        <value>showOnlyPreferredOrganisms</value>
+      </propertyList>
+    </flatVocabParam>
+
   </paramSet>
 
 
@@ -1170,6 +1185,31 @@
       </sql>
     </sqlQuery>
 
+    <sqlQuery name="AntismashOrganisms" includeProjects="FungiDB,UniDB">
+      <column name="parentTerm"/>
+      <column name="internal"/>
+      <column name="term"/>
+      <sql>
+        <![CDATA[
+        WITH filter_query AS (
+            SELECT DISTINCT ga.organism, ga.org_abbrev
+            FROM apidbtuning.geneattributes ga
+            , apidb.antismashfeature af
+            WHERE ga.na_feature_id = af.na_feature_id
+            AND (ga.project_id = '@PROJECT_ID@' OR 'UniDB' = '@PROJECT_ID@')
+        )
+        SELECT DISTINCT term
+        , parentTerm
+        , string_agg(org_abbrev, ', ') AS internal
+        FROM apidbtuning.organismtree ot
+        , filter_query fq
+        WHERE ot.organism = fq.organism
+        GROUP BY term, parentTerm
+        ORDER BY parentTerm, term
+        ]]>
+      </sql>
+    </sqlQuery>
+
   </querySet>
 
 </wdkModel>
diff --git a/Model/lib/wdk/model/questions/queries/geneQueries.xml b/Model/lib/wdk/model/questions/queries/geneQueries.xml
index c0163792a..6202067fe 100644
--- a/Model/lib/wdk/model/questions/queries/geneQueries.xml
+++ b/Model/lib/wdk/model/questions/queries/geneQueries.xml
@@ -5769,6 +5769,85 @@ select distinct ta.gene_source_id
       </sql>
     </sqlQuery>
 
+    <sqlQuery name="GenesBySecondaryMetabolites" includeProjects="FungiDB,UniDB">
+      <paramRef ref="organismParams.antismash_organism"/>
+      <paramRef ref="geneParams.antismash_category"/>
+      <paramRef ref="geneParams.antismash_annotation"/>
+      <column name="source_id"/>
+      <column name="gene_source_id"/>
+      <column name="project_id"/>
+      <column name="wdk_weight"/>
+      <column name="matched_result"/>
+      <column name="category"/>
+      <column name="antismash_annotation"/>
+      <column name="cluster_start"/>
+      <column name="cluster_end"/>
+      <column name="sequence_id"/>
+      <column name="org_abbrev"/>
+      <column name="cluster_context_start"/>
+      <column name="cluster_context_end"/>
+      <column name="overlapping_clusters"/>
+      <sql>
+        <![CDATA[
+        WITH gene_clusters AS (
+          SELECT DISTINCT
+            ta.source_id, ta.gene_source_id, ta.project_id, ta.sequence_id,
+            ta.org_abbrev,
+            ac.antismash_cluster_id, ac.category, af.antismash_annotation,
+            ac.cluster_start, ac.cluster_end,
+            (ac.cluster_end - ac.cluster_start) AS cluster_length
+          FROM apidb.antismashcluster ac
+          JOIN apidb.antismashclusterfeature acf ON acf.antismash_cluster_id = ac.antismash_cluster_id
+          JOIN apidb.antismashfeature af ON af.antismash_feature_id = acf.antismash_feature_id
+          JOIN apidbtuning.transcriptattributes ta ON ta.gene_na_feature_id = af.na_feature_id
+          WHERE ta.project_id = 'FungiDB'
+          AND ta.org_abbrev IN ($$antismash_organism$$)
+          AND ac.category IN ($$antismash_category$$)
+          AND (af.antismash_annotation IN ($$antismash_annotation$$)
+              OR ('unknown' IN ($$antismash_annotation$$) AND af.antismash_annotation IS NULL)
+          )
+        ),
+        ranked AS (
+          SELECT gc.*,
+            ROW_NUMBER() OVER (
+              PARTITION BY gc.source_id
+              ORDER BY gc.cluster_length DESC, gc.antismash_cluster_id
+            ) AS rn
+          FROM gene_clusters gc
+        ),
+        gene_overlaps AS (
+          SELECT r.source_id,
+            STRING_AGG(
+              CONCAT(
+                '<a href="@JBROWSE_WEBPAGE_URL@?loc=', gc2.sequence_id, ':',
+                GREATEST(gc2.cluster_start - 500, 1), '..', gc2.cluster_end + 500,
+                '&data=@JBROWSE_SERVICE_URL@/tracks/', gc2.org_abbrev,
+                '&tracks=gene%2Cantibiotics%20and%20Secondary%20Metabolites%20Analysis%20SHell%20(antiSMASH)">',
+                gc2.sequence_id, ':', gc2.cluster_start, '-', gc2.cluster_end, '</a>'
+              ),
+              ', ' ORDER BY gc2.cluster_start
+            ) AS overlapping_clusters
+          FROM ranked r
+          JOIN gene_clusters gc2
+            ON gc2.source_id = r.source_id
+            AND gc2.antismash_cluster_id != r.antismash_cluster_id
+          WHERE r.rn = 1
+          GROUP BY r.source_id
+        )
+        SELECT r.source_id, r.gene_source_id, r.project_id,
+          10 AS wdk_weight, 'Y' AS matched_result,
+          r.category, r.antismash_annotation, r.cluster_start, r.cluster_end, r.sequence_id,
+          r.org_abbrev,
+          GREATEST(r.cluster_start - 1000, 1) AS cluster_context_start,
+          r.cluster_end + 1000 AS cluster_context_end,
+          COALESCE(go.overlapping_clusters, 'No') AS overlapping_clusters
+        FROM ranked r
+        LEFT JOIN gene_overlaps go ON go.source_id = r.source_id
+        WHERE r.rn = 1
+        ]]>
+      </sql>
+    </sqlQuery>
+
 
 
   </querySet>