diff --git a/src/util/pairaln.cpp b/src/util/pairaln.cpp
index 3e877875c..508f55366 100644
--- a/src/util/pairaln.cpp
+++ b/src/util/pairaln.cpp
@@ -9,110 +9,106 @@
 #include "NcbiTaxonomy.h"
 #include "MappingReader.h"
 
-#define ZSTD_STATIC_LINKING_ONLY
-#include <zstd.h>
-
 #include <map>
 
 #ifdef OPENMP
 #include <omp.h>
 #endif
 
+
+// need for sorting the results
+static bool compareByTaxId(const Matcher::result_t &first, const Matcher::result_t &second) {
+    return (first.dbOrfStartPos < second.dbOrfStartPos);
+}
+
 int pairaln(int argc, const char **argv, const Command& command) {
     Parameters &par = Parameters::getInstance();
     par.parseParameters(argc, argv, command, true, 0, 0);
 
-    const bool sameDB = par.db1.compare(par.db2) == 0 ? true : false;
-    const bool touch = (par.preloadMode != Parameters::PRELOAD_MODE_MMAP);
-
     std::string db2NoIndexName = PrefilteringIndexReader::dbPathWithoutIndex(par.db2);
     MappingReader* mapping = new MappingReader(db2NoIndexName);
-    const int dbaccessMode = (DBReader<unsigned int>::USE_INDEX | DBReader<unsigned int>::USE_DATA);
-    IndexReader qDbr(par.db1, par.threads,  IndexReader::SRC_SEQUENCES, (touch) ? (IndexReader::PRELOAD_INDEX | IndexReader::PRELOAD_DATA) : 0, dbaccessMode);
-    IndexReader *tDbr;
-    if (sameDB) {
-        tDbr = &qDbr;
-    } else {
-        tDbr = new IndexReader(par.db2, par.threads, IndexReader::SRC_SEQUENCES, (touch) ? (IndexReader::PRELOAD_INDEX | IndexReader::PRELOAD_DATA) : 0, dbaccessMode);
-    }
 
     DBReader<unsigned int> alnDbr(par.db3.c_str(), par.db3Index.c_str(), par.threads, DBReader<unsigned int>::USE_INDEX|DBReader<unsigned int>::USE_DATA);
     alnDbr.open(DBReader<unsigned int>::NOSORT);
-    if(alnDbr.getSize() % 2 != 0){
-        Debug(Debug::ERROR) << "Alignment database does not seem to be paired\n";
-        EXIT(EXIT_FAILURE);
-    }
-    size_t localThreads = 1;
-#ifdef OPENMP
-    localThreads = std::max(std::min((size_t)par.threads, alnDbr.getSize()), (size_t)1);
-#endif
 
-    DBWriter resultWriter(par.db4.c_str(), par.db4Index.c_str(), localThreads,  par.compressed, alnDbr.getDbtype());
+    DBWriter resultWriter(par.db4.c_str(), par.db4Index.c_str(), 1, par.compressed, alnDbr.getDbtype());
     resultWriter.open();
 
     Debug::Progress progress(alnDbr.getSize());
-#pragma omp parallel num_threads(localThreads)
-    {
-        unsigned int thread_idx = 0;
-#ifdef OPENMP
-        thread_idx = static_cast<unsigned int>(omp_get_thread_num());
-#endif
+    do {
+        int thread_idx = 0;
         char buffer[1024 + 32768*4];
-        std::string result;
-        result.reserve(1024 * 1024);
-        std::vector<Matcher::result_t> resultA;
-        resultA.reserve(100000);
-        std::vector<Matcher::result_t> resultB;
-        resultB.reserve(100000);
-        std::unordered_map<unsigned int, Matcher::result_t *> findPair;
-        std::string outputA;
-        outputA.reserve(100000);
-        std::string outputB;
-        outputB.reserve(100000);
-#pragma omp  for schedule(static, 2)
-        for (size_t i = 0; i < alnDbr.getSize(); i+=2) {
-            progress.updateProgress();
-            progress.updateProgress();
-            resultA.clear();
-            resultB.clear();
-            outputA.clear();
-            outputB.clear();
-            Matcher::readAlignmentResults(resultA, alnDbr.getData(i, thread_idx), true);
-            Matcher::readAlignmentResults(resultB, alnDbr.getData(i+1, thread_idx), true);
+        std::vector<Matcher::result_t> result;
+        result.reserve(100000);
+        std::unordered_map<unsigned int, size_t> findPair;
+        std::string output;
+        output.reserve(100000);
 
-            for (size_t resIdx = 0; resIdx < resultA.size(); ++resIdx) {
-                unsigned int taxon = mapping->lookup(resultA[resIdx].dbKey);
-                if(findPair.find(taxon) == findPair.end()){
-                    findPair.insert({taxon, &resultA[resIdx]});
+        unsigned int referenceDbKey = 0;
+        size_t id = alnDbr.getId(referenceDbKey);
+        if (id == UINT_MAX) {
+            break;
+        }
+        char* data = alnDbr.getData(id, thread_idx);
+        Matcher::readAlignmentResults(result, data, true);
+        for (size_t resIdx = 0; resIdx < result.size(); ++resIdx) {
+            unsigned int taxon = mapping->lookup(result[resIdx].dbKey);
+            if (findPair.find(taxon) == findPair.end()) {
+                findPair.emplace(taxon, 1);
+            }
+        }
+
+        // find intersection between all proteins
+        for (size_t i = 0; i < alnDbr.getSize(); i++) {
+            unsigned int dbKey = alnDbr.getDbKey(i);
+            if (dbKey == referenceDbKey) {
+                continue;
+            }
+            result.clear();
+            Matcher::readAlignmentResults(result, alnDbr.getData(i, thread_idx), true);
+            // find pairs
+            for (size_t resIdx = 0; resIdx < result.size(); ++resIdx) {
+                unsigned int taxon = mapping->lookup(result[resIdx].dbKey);
+                if (findPair.find(taxon) != findPair.end()) {
+                    findPair[taxon]++;
                 }
             }
+        }
+
+        for (size_t i = 0; i < alnDbr.getSize(); i++) {
+            progress.updateProgress();
+            result.clear();
+            output.clear();
+            Matcher::readAlignmentResults(result, alnDbr.getData(i, thread_idx), true);
             // find pairs
-            for (size_t resIdx = 0; resIdx < resultB.size(); ++resIdx) {
-                unsigned int taxon = mapping->lookup(resultB[resIdx].dbKey);
+            for (size_t resIdx = 0; resIdx < result.size(); ++resIdx) {
+                unsigned int taxon = mapping->lookup(result[resIdx].dbKey);
+                // we don't want to introduce a new field, reuse existing unused field here
+                result[resIdx].dbOrfStartPos = taxon;
+            }
+            // stable sort is required to assure that best hit is first per taxon
+            std::stable_sort(result.begin(), result.end(), compareByTaxId);
+            unsigned int prevTaxon = UINT_MAX;
+            for (size_t resIdx = 0; resIdx < result.size(); ++resIdx) {
+                unsigned int taxon = result[resIdx].dbOrfStartPos;
                 // found pair!
-                if(findPair.find(taxon) != findPair.end()) {
-                    bool hasBacktrace = (resultB[resIdx].backtrace.size() > 0);
-                    size_t len = Matcher::resultToBuffer(buffer, *findPair[taxon], hasBacktrace, false, false);
-                    outputA.append(buffer, len);
-                    len = Matcher::resultToBuffer(buffer, resultB[resIdx], hasBacktrace, false, false);
-                    outputB.append(buffer, len);
-                    findPair.erase (taxon);
+                if (taxon != prevTaxon
+                    && findPair.find(taxon) != findPair.end()
+                    && findPair[taxon] == alnDbr.getSize()) {
+                    bool hasBacktrace = result[resIdx].backtrace.size() > 0;
+                    size_t len = Matcher::resultToBuffer(buffer, result[resIdx], hasBacktrace, false, false);
+                    output.append(buffer, len);
                 }
+                prevTaxon = taxon;
             }
-            resultWriter.writeData(outputA.c_str(), outputA.length(), alnDbr.getDbKey(i), thread_idx);
-            resultWriter.writeData(outputB.c_str(), outputB.length(), alnDbr.getDbKey(i+1), thread_idx);
-            findPair.clear();
+            resultWriter.writeData(output.c_str(), output.length(), alnDbr.getDbKey(i), thread_idx);
         }
-    }
+    } while(false);
 
     resultWriter.close();
     // clean up
     delete mapping;
     alnDbr.close();
-    if (sameDB == false) {
-        delete tDbr;
-    }
-
-    return 0;
+    return EXIT_SUCCESS;
 }