diff --git a/08-submission/gff-02-functional_annot.ipynb b/08-submission/gff-02-functional_annot.ipynb
index 590383ece54fcc4ebe7a66416a100342a1ad451e..dd80c03bce8534a7ddbd5ddc06fee57cfce0ebe4 100644
--- a/08-submission/gff-02-functional_annot.ipynb
+++ b/08-submission/gff-02-functional_annot.ipynb
@@ -136,6 +136,55 @@
     "    return None"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def find_EC(gene_id, lookup): # expects a protein-coding gene as input\n",
+    "    \"\"\"Retrieve the EC number assigned by EggNOG-mapper for a certain gene ID.\n",
+    "\n",
+    "    Parameters\n",
+    "    ----------\n",
+    "    gene_id : str\n",
+    "        a P. litorale protein-coding gene ID\n",
+    "    lookup : pd.DataFrame\n",
+    "        the eggNOG-mapper output file, filtered to maximum one entry per gene ID\n",
+    "\n",
+    "    Returns\n",
+    "    -------\n",
+    "    str\n",
+    "        the EC number (if available) for the current gene (product).\n",
+    "    \"\"\"\n",
+    "    if gene_id in lookup.index:\n",
+    "        ec = lookup.loc[gene_id]['EC']\n",
+    "        if ec != '-':\n",
+    "            return ec.split(',')\n",
+    "    return None\n",
+    "\n",
+    "def find_PFAMs(gene_id, lookup): # expects a protein-coding gene as input\n",
+    "    \"\"\"Retrieve the PFAM domains assigned by EggNOG-mapper for a certain gene ID.\n",
+    "\n",
+    "    Parameters\n",
+    "    ----------\n",
+    "    gene_id : str\n",
+    "        a P. litorale protein-coding gene ID\n",
+    "    lookup : pd.DataFrame\n",
+    "        the eggNOG-mapper output file, filtered to maximum one entry per gene ID\n",
+    "\n",
+    "    Returns\n",
+    "    -------\n",
+    "    list\n",
+    "        a list of PFAM domains (if available) associated with the gene (product).\n",
+    "    \"\"\"\n",
+    "    if gene_id in lookup.index:\n",
+    "        pfam = lookup.loc[gene_id]['PFAMs']\n",
+    "        if pfam != '-':\n",
+    "            return pfam.split(',')\n",
+    "    return None"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -157,6 +206,15 @@
     "emapper.set_index('gene', inplace=True)"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "emapper.columns"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -203,6 +261,8 @@
     "                    name = find_protein(gene, emapper)\n",
     "                    line = f'{line};gene={name}'\n",
     "                    description = find_description(gene, emapper)\n",
+    "                    ec_list = find_EC(gene, emapper)\n",
+    "                    pfams = find_PFAMs(gene, emapper)\n",
     "                    if description:\n",
     "                        line = f'{line};function={description}'\n",
     "                    if name != f'Uncharacterised protein {gene}' or description:\n",
@@ -223,6 +283,12 @@
     "                        line = f'{line};function={description}'\n",
     "                    if name != f'Uncharacterised protein {gene}' or description:\n",
     "                        line = f'{line};note=function predicted by EggNOG-mapper'\n",
+    "                    if ec_list is not None:\n",
+    "                        for ec in ec_list:\n",
+    "                            line = f'{line};EC_number=\"{ec}\"'\n",
+    "                    if pfams is not None:\n",
+    "                        for pfam in pfams:\n",
+    "                            line = f'{line};Dbxref=\"PFAM:{pfam}\"'\n",
     "            named.write(line + '\\n')"
    ]
   }
diff --git a/08-submission/gff-04-convert_to_embl.sh b/08-submission/gff-04-convert_to_embl.sh
index 4b39f04bf8e07f4d23ece7edef930419b25b1041..05d8ce752fe426e2b16d15ce6f2c9090db42cfb5 100644
--- a/08-submission/gff-04-convert_to_embl.sh
+++ b/08-submission/gff-04-convert_to_embl.sh
@@ -23,4 +23,6 @@ EMBLmyGFF3 $GFF $GENOME \
         -v \
         -o result.embl
 
-gzip result.embl
\ No newline at end of file
+# when zipping: overwrite file if it already exists,
+# else the command will hang while waiting for confirmation
+gzip -f result.embl
\ No newline at end of file