diff --git a/.gitmodules b/.gitmodules
index 47906c66..08c43b92 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -17,4 +17,4 @@
 [submodule "alphafold3"]
 	path = alphafold3
 	url = https://github.com/KosinskiLab/alphafold3.git
-	branch = ap-gapped-discontinuous-chains-v3.0.2
+	branch = main
diff --git a/alphafold b/alphafold
index af1e26b4..5bf5b9f5 160000
--- a/alphafold
+++ b/alphafold
@@ -1 +1 @@
-Subproject commit af1e26b4ec844054e035de2d62e3c72baef49f71
+Subproject commit 5bf5b9f57dcd0e4919f4ff368788780f30be5d5e
diff --git a/alphafold3 b/alphafold3
index e3a1400c..86b9ea3f 160000
--- a/alphafold3
+++ b/alphafold3
@@ -1 +1 @@
-Subproject commit e3a1400ccc0bb2da2de19fd31cf50d088272175b
+Subproject commit 86b9ea3feacc8934e6e2a581c49eb4c37a2a3d20
diff --git a/alphapulldown/utils/mmseqs_species_identifiers.py b/alphapulldown/utils/mmseqs_species_identifiers.py
index 39ac232d..5525e079 100644
--- a/alphapulldown/utils/mmseqs_species_identifiers.py
+++ b/alphapulldown/utils/mmseqs_species_identifiers.py
@@ -388,12 +388,12 @@ def _write_identifier_rows_to_cache(
 def build_mmseq_identifier_features(
     a3m_string: str,
     *,
-    species_resolver: Callable[[Sequence[str]], dict[str, str]] = (
-        resolve_species_ids_by_accession
-    ),
+    species_resolver: Callable[[Sequence[str]], dict[str, str]] | None = None,
     cache_path: str | None = None,
     expected_rows: int | None = None,
 ) -> dict[str, np.ndarray]:
+    if species_resolver is None:
+        species_resolver = resolve_species_ids_by_accession
     stripped_a3m = strip_mmseq_comment_lines(a3m_string)
     source_sha256 = _calculate_mmseq_source_sha256(stripped_a3m)
 
@@ -431,9 +431,7 @@ def enrich_mmseq_feature_dict_with_identifiers(
     feature_dict: dict[str, np.ndarray],
     a3m_string: str,
     *,
-    species_resolver: Callable[[Sequence[str]], dict[str, str]] = (
-        resolve_species_ids_by_accession
-    ),
+    species_resolver: Callable[[Sequence[str]], dict[str, str]] | None = None,
     cache_path: str | None = None,
 ) -> None:
     msa = feature_dict.get("msa")
diff --git a/docker/alphafold3.dockerfile b/docker/alphafold3.dockerfile
index 7901b99b..f041eedf 100644
--- a/docker/alphafold3.dockerfile
+++ b/docker/alphafold3.dockerfile
@@ -68,7 +68,7 @@ RUN cd /hmmer_build && \
 COPY . /app/AlphaPulldown
 
 # ---------------------------------------------------------------------
-# Install AlphaFold3 from its locked v3.0.2/Tokamax environment
+# Install AlphaFold3 from its locked v3.0.3/Tokamax environment
 # ---------------------------------------------------------------------
 WORKDIR /app/AlphaPulldown/alphafold3
 
@@ -77,7 +77,8 @@ ENV PIP_INDEX_URL=${PIP_INDEX_URL} \
     PIP_DEFAULT_TIMEOUT=600 \
     PIP_RETRIES=10 \
     PIP_NO_CACHE_DIR=1 \
-    PIP_DISABLE_PIP_VERSION_CHECK=1
+    PIP_DISABLE_PIP_VERSION_CHECK=1 \
+    SETUPTOOLS_SCM_PRETEND_VERSION_FOR_ALPHAFOLD3=3.0.3
 
 ENV CMAKE_BUILD_PARALLEL_LEVEL=1
 ENV CFLAGS="-O2 -pipe"