diff --git a/data/structureiterativesearch.sh b/data/structureiterativesearch.sh
index 9a59a61d..8cfe2177 100644
--- a/data/structureiterativesearch.sh
+++ b/data/structureiterativesearch.sh
@@ -19,13 +19,19 @@ while [ "$STEP" -lt "$NUM_IT" ]; do
     if notExists "$TMP_PATH/pref_tmp_${STEP}.done"; then
         PARAM="PREFILTER_PAR_$STEP"
         eval TMP="\$$PARAM"
+        TOOL="prefilter"
+        if [ "$PREFMODE" = "UNGAPPED" ]; then
+            TOOL="ungappedprefilter"
+            PARAM="UNGAPPEDPREFILTER_PAR_$STEP"
+            eval TMP="\$$PARAM"
+        fi
         if [ $STEP -eq 0 ]; then
             # shellcheck disable=SC2086
-            $RUNNER "$MMSEQS" prefilter "${QUERYDB}_ss" "${TARGET_PREFILTER}${INDEXEXT}" "$TMP_PATH/pref_${STEP}" ${TMP} \
+            $RUNNER "$MMSEQS" $TOOL "${QUERYDB}_ss" "${TARGET_PREFILTER}${INDEXEXT}" "$TMP_PATH/pref_${STEP}" ${TMP} \
                 || fail "Prefilter died"
         else
             # shellcheck disable=SC2086
-            $RUNNER "$MMSEQS" prefilter "${QUERYDB}_ss" "${TARGET_PREFILTER}${INDEXEXT}" "$TMP_PATH/pref_tmp_${STEP}" ${TMP} \
+            $RUNNER "$MMSEQS" $TOOL "${QUERYDB}_ss" "${TARGET_PREFILTER}${INDEXEXT}" "$TMP_PATH/pref_tmp_${STEP}" ${TMP} \
                 || fail "Prefilter died"
         fi
         touch "$TMP_PATH/pref_tmp_${STEP}.done"
diff --git a/src/workflow/StructureSearch.cpp b/src/workflow/StructureSearch.cpp
index fb180b5e..c2df6faf 100644
--- a/src/workflow/StructureSearch.cpp
+++ b/src/workflow/StructureSearch.cpp
@@ -152,6 +152,8 @@ int structuresearch(int argc, const char **argv, const Command &command) {
             par.compBiasCorrectionScale = 0.15;
             cmd.addVariable(std::string("PREFILTER_PAR_" + SSTR(i)).c_str(),
                             par.createParameterString(par.prefilter).c_str());
+            cmd.addVariable(std::string("UNGAPPEDPREFILTER_PAR_" + SSTR(i)).c_str(),
+                            par.createParameterString(par.ungappedprefilter).c_str());
             par.compBiasCorrectionScale = 0.5;
             if(par.alignmentType == LocalParameters::ALIGNMENT_TYPE_3DI){
                 cmd.addVariable(std::string("ALIGNMENT_PAR_" + SSTR(i)).c_str(), par.createParameterString(par.align).c_str());