diff --git a/pkgs/applications/science/biology/mmseqs2/default.nix b/pkgs/applications/science/biology/mmseqs2/default.nix
deleted file mode 100644
index 18acee7a5f14..000000000000
--- a/pkgs/applications/science/biology/mmseqs2/default.nix
+++ /dev/null
@@ -1,51 +0,0 @@
-{ lib
-, stdenv
-, fetchFromGitHub
-, cmake
-, xxd
-, perl
-, installShellFiles
-, enableAvx2 ? stdenv.hostPlatform.avx2Support
-, enableSse4_1 ? stdenv.hostPlatform.sse4_1Support
-, enableMpi ? false
-, mpi
-, openmp
-, zlib
-, bzip2
-}:
-
-stdenv.mkDerivation rec {
-  pname = "mmseqs2";
-  version = "15-6f452";
-
-  src = fetchFromGitHub {
-    owner = "soedinglab";
-    repo = pname;
-    rev = version;
-    sha256 = "sha256-L+zOWrGkCLz/wqpBuji8H4/93sDFpcfnDOE8FHq1j84=";
-  };
-
-  nativeBuildInputs = [ cmake xxd perl installShellFiles ];
-  cmakeFlags =
-    lib.optional enableAvx2 "-DHAVE_AVX2=1"
-    ++ lib.optional enableSse4_1 "-DHAVE_SSE4_1=1"
-    ++ lib.optional enableMpi "-DHAVE_MPI=1";
-
-  buildInputs =
-    lib.optionals stdenv.cc.isClang [ openmp zlib bzip2 ]
-    ++ lib.optional enableMpi mpi;
-
-  postInstall = ''
-    installShellCompletion --bash --cmd mmseqs $out/util/bash-completion.sh
-    rm -r $out/util/
-  '';
-
-  meta = with lib; {
-    description = "Ultra fast and sensitive sequence search and clustering suite";
-    mainProgram = "mmseqs";
-    homepage = "https://mmseqs.com/";
-    license = licenses.gpl3;
-    maintainers = with maintainers; [ natsukium ];
-    platforms = platforms.unix;
-  };
-}
diff --git a/pkgs/by-name/mm/mmseqs2/package.nix b/pkgs/by-name/mm/mmseqs2/package.nix
new file mode 100644
index 000000000000..71be0aefcd91
--- /dev/null
+++ b/pkgs/by-name/mm/mmseqs2/package.nix
@@ -0,0 +1,96 @@
+{
+  lib,
+  config,
+  stdenv,
+  fetchFromGitHub,
+  cmake,
+  xxd,
+  perl,
+  installShellFiles,
+  enableAvx2 ? stdenv.hostPlatform.avx2Support,
+  enableSse4_1 ? stdenv.hostPlatform.sse4_1Support,
+  enableMpi ? false,
+  mpi,
+  cudaSupport ? config.cudaSupport,
+  cudaPackages,
+  llvmPackages,
+  zlib,
+  bzip2,
+  pkgsStatic,
+  runCommand,
+}:
+let
+  # require static library, libzstd.a
+  inherit (pkgsStatic) zstd;
+in
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "mmseqs2";
+  version = "16-747c6";
+
+  src = fetchFromGitHub {
+    owner = "soedinglab";
+    repo = "mmseqs2";
+    rev = "refs/tags/${finalAttrs.version}";
+    hash = "sha256-O7tx+gdVAmZLihPnWSo9RWNVzfPjI61LGY/XeaGHrI0=";
+  };
+
+  nativeBuildInputs =
+    [
+      cmake
+      xxd
+      perl
+      installShellFiles
+      zstd
+    ]
+    ++ lib.optionals cudaSupport [
+      cudaPackages.cuda_nvcc
+    ];
+
+  cmakeFlags =
+    [
+      (lib.cmakeBool "HAVE_AVX2" enableAvx2)
+      (lib.cmakeBool "HAVE_SSE4_1" enableSse4_1)
+      (lib.cmakeBool "HAVE_MPI" enableMpi)
+      (lib.cmakeBool "USE_SYSTEM_ZSTD" true)
+      (lib.cmakeBool "HAVE_ARM8" stdenv.hostPlatform.isAarch64)
+    ]
+    ++ lib.optionals cudaSupport [
+      (lib.cmakeBool "ENABLE_CUDA" true)
+      (lib.cmakeFeature "CMAKE_CUDA_ARCHITECTURES" cudaPackages.flags.cmakeCudaArchitecturesString)
+    ];
+
+  buildInputs =
+    lib.optionals stdenv.cc.isClang [
+      llvmPackages.openmp
+      zlib
+      bzip2
+    ]
+    ++ lib.optional enableMpi mpi
+    ++ lib.optionals cudaSupport [
+      cudaPackages.cuda_cudart
+      cudaPackages.cuda_cccl
+    ];
+
+  postInstall = ''
+    installShellCompletion --bash --cmd mmseqs $out/util/bash-completion.sh
+    rm -r $out/util/
+  '';
+
+  passthru.tests = {
+    example = runCommand "mmseqs2-test" { } ''
+      ${lib.getExe finalAttrs.finalPackage} createdb ${finalAttrs.src}/examples/DB.fasta targetDB > $out
+      ${lib.getExe finalAttrs.finalPackage} createindex targetDB tmp >> $out
+      ${lib.getExe finalAttrs.finalPackage} easy-search ${finalAttrs.src}/examples/QUERY.fasta targetDB alnRes.m8 tmp >> $out
+    '';
+  };
+
+  meta = with lib; {
+    description = "Ultra fast and sensitive sequence search and clustering suite";
+    mainProgram = "mmseqs";
+    homepage = "https://mmseqs.com/";
+    license = licenses.mit;
+    maintainers = with maintainers; [ natsukium ];
+    platforms = platforms.unix;
+  };
+})
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index db8d95490241..11df5e664fc9 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -17383,10 +17383,6 @@ with pkgs;
     inherit (perlPackages) perl TextFormat;
   };
 
-  mmseqs2 = callPackage ../applications/science/biology/mmseqs2 {
-    inherit (llvmPackages) openmp;
-  };
-
   obitools3 = callPackage ../applications/science/biology/obitools/obitools3.nix { };
 
   raxml-mpi = raxml.override { useMpi = true; };