diff --git a/CONFIG/RUNTIME_PARAMETERS.py b/CONFIG/RUNTIME_PARAMETERS.py
index 3732dc6..44b038f 100644
--- a/CONFIG/RUNTIME_PARAMETERS.py
+++ b/CONFIG/RUNTIME_PARAMETERS.py
@@ -14,6 +14,7 @@
 # parameters used to filter mmseqs2 search results before aligning
 MMSEQS_MIN_BIT_SCORE = -99999
 MMSEQS_MAX_EVAL = 99999
+MMSEQS_MIN_IDENTITY = 0.5
 
 # parameters used to calculate alignment score
 PAIRWISE_ALIGNMENT_MATCH = 2
diff --git a/CONFIG/get_config_dict.py b/CONFIG/get_config_dict.py
index 61f9fe8..41511fa 100644
--- a/CONFIG/get_config_dict.py
+++ b/CONFIG/get_config_dict.py
@@ -18,14 +18,15 @@ def runtime_config():
         "ANGSTROM_CONTACT_THRESHOLD": ANGSTROM_CONTACT_THRESHOLD,
         "GENERATE_CONTACTS": GENERATE_CONTACTS,
 
+        "MMSEQS_MIN_BIT_SCORE": MMSEQS_MIN_BIT_SCORE,
+        "MMSEQS_MAX_EVAL": MMSEQS_MAX_EVAL,
+        "MMSEQS_MIN_IDENTITY": MMSEQS_MIN_IDENTITY,
+
         "PAIRWISE_ALIGNMENT_MATCH": PAIRWISE_ALIGNMENT_MATCH,
         "PAIRWISE_ALIGNMENT_MISSMATCH": PAIRWISE_ALIGNMENT_MISSMATCH,
         "PAIRWISE_ALIGNMENT_GAP_OPEN": PAIRWISE_ALIGNMENT_GAP_OPEN,
         "PAIRWISE_ALIGNMENT_GAP_CONTINUATION": PAIRWISE_ALIGNMENT_GAP_CONTINUATION,
 
-        "MMSEQS_MIN_BIT_SCORE": MMSEQS_MIN_BIT_SCORE,
-        "MMSEQS_MAX_EVAL": MMSEQS_MAX_EVAL,
-
         "ALIGNMENT_MIN_SEQUENCE_IDENTITY": ALIGNMENT_MIN_SEQUENCE_IDENTITY,
     }
     return config
diff --git a/utils/search_alignments.py b/utils/search_alignments.py
index 270387b..ca94dd0 100644
--- a/utils/search_alignments.py
+++ b/utils/search_alignments.py
@@ -39,10 +39,14 @@ def search_alignments(query_seqs: dict, mmseqs_search_output: pd.DataFrame, targ
     if alignments_json_file.exists():
         return json.load(open(alignments_json_file, "r"))
 
+    print(f"MMseqs search output is {len(mmseqs_search_output)} long.")
     query_seqs_keys = list(query_seqs.keys())
     filtered_mmseqs_search = mmseqs_search_output[mmseqs_search_output['bit_score'] > job_config["MMSEQS_MIN_BIT_SCORE"]]
     filtered_mmseqs_search = filtered_mmseqs_search[filtered_mmseqs_search['e_value'] < job_config["MMSEQS_MAX_EVAL"]]
+    filtered_mmseqs_search = filtered_mmseqs_search[filtered_mmseqs_search['identity'] > job_config["MMSEQS_MIN_IDENTITY"]]
     filtered_mmseqs_search = filtered_mmseqs_search[filtered_mmseqs_search['query'].isin(query_seqs_keys)]
+    print(f"Filtered {len(mmseqs_search_output) - len(filtered_mmseqs_search)} mmseqs matches. "
+          f"Total alignments to check {len(filtered_mmseqs_search)}")
 
     queries = list(map(lambda x: query_seqs[x], filtered_mmseqs_search["query"]))
     targets = list(map(lambda x: target_seqs[x], filtered_mmseqs_search["target"]))
@@ -61,13 +65,14 @@ def search_alignments(query_seqs: dict, mmseqs_search_output: pd.DataFrame, targ
     alignments = dict()
     for i in range(len(all_alignments)):
         alignment = all_alignments[i]
-        query_id = filtered_mmseqs_search["query"].iloc[i]
-        target_id = filtered_mmseqs_search["target"].iloc[i]
+        # filter out bad alignments based on alignment sequences identity
         sequence_identity = alignment_sequences_identity(alignment)
         if sequence_identity > job_config["ALIGNMENT_MIN_SEQUENCE_IDENTITY"]:
+            query_id = filtered_mmseqs_search["query"].iloc[i]
+            target_id = filtered_mmseqs_search["target"].iloc[i]
             if query_id not in alignments.keys():
                 alignments[query_id] = {"target_id": target_id, "alignment": alignment, "sequence_identity": sequence_identity}
-            # select best alignment based on pairwise2.align.globalms.score, not sequence_identity?
+            # select best alignment based on pairwise2.align.globalms.score
             elif alignment.score > alignments[query_id]["alignment"].score:
                 alignments[query_id] = {"target_id": target_id, "alignment": alignment, "sequence_identity": sequence_identity}