diff --git a/alphapulldown/objects.py b/alphapulldown/objects.py
index 70127479..feb1a10c 100644
--- a/alphapulldown/objects.py
+++ b/alphapulldown/objects.py
@@ -34,7 +34,13 @@ def _query_only_a3m(sequence: str, query_id: str = "query") -> str:
 
 def _query_only_stockholm(sequence: str, query_id: str = "query") -> str:
     """Return a single-sequence Stockholm alignment string."""
-    return f"# STOCKHOLM 1.0\n{query_id} {sequence}\n//\n"
+    rf_annotation = "x" * len(sequence)
+    return (
+        "# STOCKHOLM 1.0\n"
+        f"{query_id} {sequence}\n"
+        f"#=GC RF {rf_annotation}\n"
+        "//\n"
+    )
 
 
 class MonomericObject:
diff --git a/test/unit/test_objects.py b/test/unit/test_objects.py
index 1ce01ad6..edf8e7f3 100644
--- a/test/unit/test_objects.py
+++ b/test/unit/test_objects.py
@@ -278,6 +278,68 @@ def test_make_features_skip_msa_builds_query_only_features_and_templates(
     assert monomer.feature_dict["template_domain_names"].tolist() == [b"1abc_A"]
 
 
+def test_make_features_skip_msa_builds_stockholm_with_rf_for_hmmsearch(
+    monkeypatch, tmp_path
+):
+    monomer = MonomericObject("proteinA", "ACDE")
+    calls = {}
+
+    class FakeTemplateSearcher:
+        input_format = "sto"
+        output_format = "sto"
+
+        def query(self, alignment):
+            calls["template_query"] = alignment
+            return "template_hits"
+
+        def get_template_hits(self, output_string, input_sequence):
+            return ["hitA"]
+
+    class FakeTemplateFeaturizer:
+        def get_templates(self, query_sequence, hits):
+            return SimpleNamespace(
+                features={
+                    "template_aatype": np.ones((1, 4, 22), dtype=np.float32),
+                    "template_all_atom_masks": np.ones((1, 4, 37), dtype=np.float32),
+                    "template_all_atom_positions": np.ones(
+                        (1, 4, 37, 3), dtype=np.float32
+                    ),
+                    "template_domain_names": np.asarray([b"1abc_A"], dtype=object),
+                    "template_sequence": np.asarray([b"ACDE"], dtype=object),
+                    "template_sum_probs": np.asarray([0.5], dtype=np.float32),
+                }
+            )
+
+    class FakePipeline:
+        template_searcher = FakeTemplateSearcher()
+        template_featurizer = FakeTemplateFeaturizer()
+
+        def process(self, *_args, **_kwargs):
+            raise AssertionError("skip_msa should bypass pipeline.process")
+
+    monkeypatch.setattr(
+        MonomericObject, "unzip_msa_files", staticmethod(lambda _path: False)
+    )
+    monkeypatch.setattr(
+        MonomericObject,
+        "remove_msa_files",
+        staticmethod(lambda msa_output_path=None, **_kwargs: None),
+    )
+    monkeypatch.setattr(
+        MonomericObject, "zip_msa_files", staticmethod(lambda _path: None)
+    )
+
+    monomer.make_features(
+        pipeline=FakePipeline(),
+        output_dir=str(tmp_path),
+        save_msa=False,
+        skip_msa=True,
+    )
+
+    assert "#=GC RF xxxx" in calls["template_query"]
+    assert calls["template_query"].startswith("# STOCKHOLM 1.0\nquery ACDE\n")
+
+
 def test_make_mmseq_features_builds_all_seq_features_and_writes_a3m(
     monkeypatch, tmp_path
 ):