diff --git a/src/MMseqsBase.cpp b/src/MMseqsBase.cpp
index e5a6751fc..788a6e245 100644
--- a/src/MMseqsBase.cpp
+++ b/src/MMseqsBase.cpp
@@ -1134,11 +1134,11 @@ std::vector<Command> baseCommands = {
                                           {"resultDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::resultDb },
                                           {"resultDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::resultDb },
                                           {"profileDB", DbType::ACCESS_MODE_OUTPUT, DbType::NEED_DATA, &DbValidator::profileDb }}},
-        {"pairaln",      pairaln,        &par.threadsandcompression,       COMMAND_EXPERT,
-                "Pair sequences to match best protein A and B from an species",
+        {"pairaln",             pairaln,               &par.pairaln,              COMMAND_EXPERT,
+                "Pair sequences to match best protein A and B from a species",
                 NULL,
                 "Martin Steinegger <martin.steinegger@snu.ac.kr>",
-                "<i:queryDB> <i:targetDB> <i:alnDB> <o:alnDB|ca3mDB>",
+                "<i:queryDB> <i:targetDB> <i:alnDB> <o:alnDB>",
                 CITATION_MMSEQS2, {{"queryDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::sequenceDb },
                                           {"targetDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA|DbType::NEED_TAXONOMY, &DbValidator::sequenceDb },
                                           {"alnDB", DbType::ACCESS_MODE_INPUT, DbType::NEED_DATA, &DbValidator::alignmentDb },
diff --git a/src/commons/Parameters.cpp b/src/commons/Parameters.cpp
index 328fd2808..0eed6f07f 100644
--- a/src/commons/Parameters.cpp
+++ b/src/commons/Parameters.cpp
@@ -1132,6 +1132,11 @@ Parameters::Parameters():
     expand2profile.push_back(&PARAM_THREADS);
     expand2profile.push_back(&PARAM_V);
 
+    pairaln.push_back(&PARAM_PRELOAD_MODE);
+    pairaln.push_back(&PARAM_COMPRESSED);
+    pairaln.push_back(&PARAM_THREADS);
+    pairaln.push_back(&PARAM_V);
+
     sortresult.push_back(&PARAM_COMPRESSED);
     sortresult.push_back(&PARAM_THREADS);
     sortresult.push_back(&PARAM_V);
diff --git a/src/commons/Parameters.h b/src/commons/Parameters.h
index 1dd7dd20e..390f78183 100644
--- a/src/commons/Parameters.h
+++ b/src/commons/Parameters.h
@@ -1101,6 +1101,7 @@ class Parameters {
     std::vector<MMseqsParameter*> multihitsearch;
     std::vector<MMseqsParameter*> expandaln;
     std::vector<MMseqsParameter*> expand2profile;
+    std::vector<MMseqsParameter*> pairaln;
     std::vector<MMseqsParameter*> sortresult;
     std::vector<MMseqsParameter*> enrichworkflow;
     std::vector<MMseqsParameter*> databases;