diff --git a/src/util/makepaddedseqdb.cpp b/src/util/makepaddedseqdb.cpp
index de2224159..6239fe226 100644
--- a/src/util/makepaddedseqdb.cpp
+++ b/src/util/makepaddedseqdb.cpp
@@ -5,6 +5,25 @@
 #include "Util.h"
 
 int makepaddedseqdb(int argc, const char **argv, const Command &command) {
+    const char AA_TO_20[256] = {
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+        20,  0, 20,  4,  3,  6, 13,  7,  8,  9, 20, 11, 10, 12,  2, 20,
+        14,  5,  1, 15, 16, 20, 19, 17, 20, 18, 20, 20, 20, 20, 20, 20,
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+        20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20
+    };
+
     Parameters &par = Parameters::getInstance();
     par.parseParameters(argc, argv, command, true, 0, 0);
     DBReader<unsigned int> dbr(par.db1.c_str(), par.db1Index.c_str(), 1,
@@ -19,11 +38,15 @@ int makepaddedseqdb(int argc, const char **argv, const Command &command) {
         char *data = dbr.getData(id, 0);
         size_t seqLen = dbr.getSeqLen(id);
         const size_t sequencepadding = (seqLen % ALIGN == 0) ? 0 : ALIGN - seqLen % ALIGN;
-        result.append(data, seqLen);
-        result.append(sequencepadding, ' ');
-        writer.writeData(data, seqLen + sequencepadding, key, 0, false);
+        for (size_t i = 0; i < seqLen; i++) {
+            result.append(1, AA_TO_20[(unsigned char)data[i]]);
+        }
+        result.append(sequencepadding, static_cast<char>(20));
+        writer.writeData(result.c_str(), result.size(), key, 0, false, false);
+        writer.writeIndexEntry(key, writer.getStart(0), seqLen, 0);
+        result.clear();
     }
-    writer.close(true);
+    writer.close(true, false);
     DBReader<unsigned int>::softlinkDb(par.db1, par.db2, DBFiles::SEQUENCE_ANCILLARY);
 
     dbr.close();