diff --git a/epauth/views.py b/epauth/views.py index 66b922c6..1eb3704d 100644 --- a/epauth/views.py +++ b/epauth/views.py @@ -87,6 +87,11 @@ def get_access_token_from_request(request, scopes=None): """ Get an access token from the request using MSAL token cache. """ + + # Check if auth via Access Token + if request.headers.get("Authorization"): + return {"access_token": request.headers.get("Authorization").split(" ")[1]} + if scopes is None: scopes = s.MS_ENTRA_SCOPES diff --git a/epdb/exceptions.py b/epdb/exceptions.py index 42cdcef1..e1d9f053 100644 --- a/epdb/exceptions.py +++ b/epdb/exceptions.py @@ -4,3 +4,7 @@ class InvalidSMILESException(Exception): class InvalidMolfileException(Exception): pass + + +class PackageImportException(Exception): + pass diff --git a/epdb/legacy_api.py b/epdb/legacy_api.py index 89e8ae58..93af425f 100644 --- a/epdb/legacy_api.py +++ b/epdb/legacy_api.py @@ -1635,24 +1635,10 @@ class PathwayNode(Schema): # TODO return [] - @staticmethod - def resolve_engineered_intermediate(obj: Node): - # TODO - return False - - @staticmethod - def resolve_image(obj: Node): - return f"{obj.default_node_label.url}?image=svg" - @staticmethod def resolve_image_size(obj: Node): return 400 - @staticmethod - def resolve_proposed_intermediate(obj: Node): - # TODO - return [] - class PathwaySchema(Schema): aliases: List[str] = Field([], alias="aliases") @@ -2282,3 +2268,26 @@ def get_setting(request, setting_uuid): return 403, { "message": f"Getting Setting with id {setting_uuid} failed due to insufficient rights!" } + + +######## +# Util # +######## +class NonPersistent(Schema): + smiles: str + setting_url: str = Field(..., alias="settingUri") + + +@router.post("/util", response={200: Any, 403: Error}) +def predict(request, np: Form[NonPersistent]): + try: + from epdb.logic import SPathway + + setting = SettingManager.get_setting_by_url(request.user, np.setting_url) + spw = SPathway(prediction_setting=setting, root_nodes=[np.smiles]) + spw.predict() + return spw.to_json() + except ValueError: + return 403, { + "message": f"Getting Setting with id {np.setting_url} failed due to insufficient rights!" + } diff --git a/epdb/logic.py b/epdb/logic.py index 6de2b73a..d6f974ad 100644 --- a/epdb/logic.py +++ b/epdb/logic.py @@ -1011,7 +1011,7 @@ class PackageManager(object): add_import_timestamp=True, trust_reviewed=False, ) -> Package: - importer = PackageImporter(data, preserve_uuids, add_import_timestamp, trust_reviewed) + importer = PackageImporter(data, preserve_uuids) imported_package = importer.do_import() up = UserPackagePermission() @@ -1828,6 +1828,11 @@ class SPathway(object): "to": to_indices, } + if edge.rule: + e["rule"] = edge.rule.simple_json() + if edge.probability: + e["probability"] = edge.probability + edges.append(e) return { diff --git a/epdb/models.py b/epdb/models.py index 599255a1..e6cc7d68 100644 --- a/epdb/models.py +++ b/epdb/models.py @@ -1241,8 +1241,12 @@ class CompoundStructure( if description is not None: cs.description = nh3.clean(description, tags=s.ALLOWED_HTML_TAGS).strip() - cs.smiles = smiles cs.compound = compound + cs.smiles = smiles + + # Check if molfile is present and valid + if molfile is not None and molfile.strip() != "": + cs.molfile = molfile if "normalized_structure" in kwargs: cs.normalized_structure = kwargs["normalized_structure"] @@ -2023,6 +2027,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix # add links start -> pseudo new_link = { "name": link["name"], + "plain_name": link["plain_name"], "id": link["id"], "url": link["url"], "image": link["image"], @@ -2032,6 +2037,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix "source": node_url_to_idx[link["start_node_urls"][0]], "target": pseudo_idx, "app_domain": link.get("app_domain", None), + "to_pseudo": True, } adjusted_links.append(new_link) @@ -2039,6 +2045,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix for target in link["end_node_urls"]: new_link = { "name": link["name"], + "plain_name": link["plain_name"], "id": link["id"], "url": link["url"], "image": link["image"], @@ -2049,6 +2056,7 @@ class Pathway(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMix "target": node_url_to_idx[target], "app_domain": link.get("app_domain", None), "multi_step": link["multi_step"], + "from_pseudo": True, } adjusted_links.append(new_link) @@ -2359,17 +2367,19 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin) def _url(self): return "{}/node/{}".format(self.pathway.url, self.uuid) - def get_name(self): + def get_name(self, include_suffix=True): non_generic_name = True - if self.name == "no name": + if self.name is None or self.name == "no name": non_generic_name = False - return ( - self.name - if non_generic_name - else f"{self.default_node_label.name} (taken from underlying structure)" - ) + if non_generic_name: + return self.name + else: + if include_suffix: + return f"{self.default_node_label.name} (taken from underlying structure)" + else: + return self.default_node_label.name def d3_json(self): app_domain_data = self.get_app_domain_assessment_data() @@ -2399,6 +2409,7 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin) ), "image_type": "svg", "name": self.get_name(), + "plain_name": self.get_name(include_suffix=False), "smiles": self.default_node_label.smiles, "scenarios": [{"name": s.get_name(), "url": s.url} for s in self.scenarios.all()], "app_domain": { @@ -2505,6 +2516,28 @@ class Node(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin) return res + def is_proposed_intermediate(self): + collected = defaultdict(dict) + for ai in self.additional_information.filter( + type__in=["ProposedIntermediate", "TransformationProductImportance", "Confidence"], + scenario__isnull=False, + ): + collected[str(ai.scenario.uuid)]["scenarioId"] = ai.scenario.url + collected[str(ai.scenario.uuid)]["scenarioName"] = ai.scenario.name + + if ai.type == "ProposedIntermediate": + collected[str(ai.scenario.uuid)]["proposed"] = True + + if ai.type == "Confidence": + collected[str(ai.scenario.uuid)]["Confidence"] = ai.get().level + + if ai.type == "TransformationProductImportance": + collected[str(ai.scenario.uuid)]["Transformation product importance"] = ( + ai.get().importance.value + ) + + return list(collected.values()) + class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin): pathway = models.ForeignKey( @@ -2526,6 +2559,7 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin) def d3_json(self): edge_json = { "name": self.get_name(), + "plain_name": self.get_name(include_suffix=False), "id": self.url, "url": self.url, "image": self.url + "?image=svg", @@ -2640,17 +2674,19 @@ class Edge(EnviPathModel, AliasMixin, ScenarioMixin, AdditionalInformationMixin) return res - def get_name(self): + def get_name(self, include_suffix=True): non_generic_name = True if self.name == "no name": non_generic_name = False - return ( - self.name - if non_generic_name - else f"{self.edge_label.name} (taken from underlying reaction)" - ) + if non_generic_name: + return self.name + else: + if include_suffix: + return f"{self.edge_label.name} (taken from underlying reaction)" + else: + return self.edge_label.name class EPModel(PolymorphicModel, EnviPathModel, AdditionalInformationMixin): diff --git a/epdb/views.py b/epdb/views.py index b42abe31..c6a9d361 100644 --- a/epdb/views.py +++ b/epdb/views.py @@ -775,13 +775,11 @@ def models(request): } if s.ENVIFORMER_PRESENT: - context["model_types"]["EnviFormer"] = ( - { - "type": "enviformer", - "requires_rule_packages": False, - "requires_data_packages": True, - }, - ) + context["model_types"]["EnviFormer"] = { + "type": "enviformer", + "requires_rule_packages": False, + "requires_data_packages": True, + } if s.FLAGS.get("PLUGINS", False): for k, v in s.CLASSIFIER_PLUGINS.items(): @@ -2102,12 +2100,14 @@ def package_pathways(request, package_uuid): else: prediction_setting = current_user.prediction_settings() + is_predict_mode = pw_mode in {"predict", "incremental"} + pw = Pathway.create( current_package, - stand_smiles, + stand_smiles if is_predict_mode else smiles, name=name, description=description, - predicted=pw_mode in {"predict", "incremental"}, + predicted=is_predict_mode, ) # set mode @@ -2466,7 +2466,26 @@ def package_pathway_node(request, package_uuid, pathway_uuid, node_uuid): return JsonResponse({"success": current_node.url}) - return HttpResponseBadRequest() + new_node_name = request.POST.get("node-name") + new_node_description = request.POST.get("node-description") + + if any([new_node_name, new_node_description]): + if new_node_name is not None and new_node_name.strip() != "": + new_node_name = nh3.clean(new_node_name.strip(), tags=s.ALLOWED_HTML_TAGS).strip() + current_node.name = new_node_name + + if new_node_description is not None and new_node_description.strip() != "": + new_node_description = nh3.clean( + new_node_description.strip(), tags=s.ALLOWED_HTML_TAGS + ).strip() + current_node.description = new_node_description + + current_node.save() + + return redirect(current_node.url) + + return error(request, "Node update failed!", "No changes were made to the node") + else: return HttpResponseNotAllowed(["GET", "POST"]) diff --git a/fixtures/EAWAG-BBD_32de3cf4-e3e6-4168-956e-32fa5ddb0ce1.json b/fixtures/EAWAG-BBD_32de3cf4-e3e6-4168-956e-32fa5ddb0ce1.json new file mode 100644 index 00000000..bb2f3403 --- /dev/null +++ b/fixtures/EAWAG-BBD_32de3cf4-e3e6-4168-956e-32fa5ddb0ce1.json @@ -0,0 +1 @@ +{"name": "EAWAG-BBD", "description": "Migration package for pathways, reactions and compounds from the EAWAG-BBD database", "uuid": "32de3cf4-e3e6-4168-956e-32fa5ddb0ce1", "reviewed": true, "license": {"cc_string": "by-nc-sa", "link": "https://creativecommons.org/licenses/by-nc-sa/4.0/", "image_link": "https://licensebuttons.net/l/by-nc-sa/4.0/88x31.png"}, "compounds": [{"uuid": "aba0117a-6afc-4373-83a0-64433e96b4ee", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/aba0117a-6afc-4373-83a0-64433e96b4ee", "name": 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"description": "Carbonochloridate + Acid chloride > mono Carbonate + Carboxylate", "aliases": [], "smirks": "Cl[#6:1](-[#6,#8:4])=[O:5]>>[#8-]-[#6:1](-[#6,#8:4])=[O:5]", "reactant_filter_smarts": null, "product_filter_smarts": null, "scenarios": [{"uuid": "d0b44ace-ba6a-47f7-9f68-f78ed3141658", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/d0b44ace-ba6a-47f7-9f68-f78ed3141658"}]}, {"uuid": "53647c10-4607-4a38-8196-d7d817ac50a3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/53647c10-4607-4a38-8196-d7d817ac50a3", "enzymes": [], "name": "bt0420-3794", "description": "Nitroguanidine derivative > Urea derivative", "aliases": [], "smirks": "[#7:7]\\[#6:1](-[#7:8])=[#7]\\?[#7+](-[#8-])=O>>[#7:8]-[#6:1](-[#7:7])=O", "reactant_filter_smarts": null, "product_filter_smarts": null, "scenarios": [{"uuid": "9e51c3f0-699e-4e4d-b443-6bcc436a1ea6", "url": 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"http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/dc490113-910e-437c-92d4-2c9ff19f6452"}], "edge_evidence": []}, {"uuid": "a180989c-c5b8-4342-8967-3da8fa852351", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/4ff285e5-4c8d-4cd8-a2a7-cdf0430869b9/enzymelink/a180989c-c5b8-4342-8967-3da8fa852351", "ec_number": "4.5.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "5103b7fb-ca4a-4717-9ecf-92b5e9e45a80", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/5103b7fb-ca4a-4717-9ecf-92b5e9e45a80"}, {"uuid": "ea8aa148-0521-4e9b-8746-617a98521e86", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/ea8aa148-0521-4e9b-8746-617a98521e86"}], "edge_evidence": []}], "name": "bt0066", "description": "1-Halo, 2-hydroxyaliphatic → 1,2-Epoxyaliphatic
1-Hydroxy, 2-haloaliphatic → 1,2-Epoxyaliphatic", "aliases": [], "simple_rules": [{"uuid": "cba098b2-aead-4ccf-acc8-81b8769069c4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/cba098b2-aead-4ccf-acc8-81b8769069c4"}, {"uuid": "e23238da-f08b-46b5-85d1-1cae38d873ae", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/e23238da-f08b-46b5-85d1-1cae38d873ae"}], "scenarios": []}, {"uuid": "57984a10-db28-4c1b-b536-03f09f1e498b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/57984a10-db28-4c1b-b536-03f09f1e498b", "enzymes": [{"uuid": "67616383-2b6c-4fc8-a36c-072a8ddc38e3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/57984a10-db28-4c1b-b536-03f09f1e498b/enzymelink/67616383-2b6c-4fc8-a36c-072a8ddc38e3", "ec_number": "1.5.99.14", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "7236f7b0-bf28-4fd7-b677-1225fc9531b3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/7236f7b0-bf28-4fd7-b677-1225fc9531b3"}], "edge_evidence": []}, {"uuid": "c0a36745-0dbb-42e5-8d83-a25a186f50c4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/57984a10-db28-4c1b-b536-03f09f1e498b/enzymelink/c0a36745-0dbb-42e5-8d83-a25a186f50c4", "ec_number": "1.17.3.3", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "a6725c3c-700f-4ea3-9c25-6c554639aea3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/57984a10-db28-4c1b-b536-03f09f1e498b/enzymelink/a6725c3c-700f-4ea3-9c25-6c554639aea3", "ec_number": "1.14.14.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "d56fd609-c8a0-4cc5-86cf-bce03e4e45e5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/d56fd609-c8a0-4cc5-86cf-bce03e4e45e5"}], "edge_evidence": []}, {"uuid": "29ecb740-5dd6-4b94-aea7-72480ec64fd2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/57984a10-db28-4c1b-b536-03f09f1e498b/enzymelink/29ecb740-5dd6-4b94-aea7-72480ec64fd2", "ec_number": "1.14.13.243", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "2607c77b-df4e-4253-bce5-d4f687855a77", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/57984a10-db28-4c1b-b536-03f09f1e498b/enzymelink/2607c77b-df4e-4253-bce5-d4f687855a77", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "c557919c-ef62-4c61-ab26-9b600d71584f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/c557919c-ef62-4c61-ab26-9b600d71584f"}], "edge_evidence": []}], "name": "bt0011", "description": "monosubstituted Benzenoid → Add o-OH
substituted Pyridine → Add o-OH", "aliases": [], "simple_rules": [{"uuid": "316251ba-dd4f-40a2-9e32-b732cfe70829", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/316251ba-dd4f-40a2-9e32-b732cfe70829"}, {"uuid": "ac9099fe-7f00-43cc-9bb2-55d6f3eeaa23", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/ac9099fe-7f00-43cc-9bb2-55d6f3eeaa23"}], "scenarios": []}, {"uuid": "37615e85-1b75-4462-8dc6-832d87267836", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/37615e85-1b75-4462-8dc6-832d87267836", "enzymes": [{"uuid": "2e80a09c-3ebb-486c-842a-d96dd8612274", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/37615e85-1b75-4462-8dc6-832d87267836/enzymelink/2e80a09c-3ebb-486c-842a-d96dd8612274", "ec_number": "1.3.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "658acc79-96c2-4128-bf41-ad4bbc24e57d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/658acc79-96c2-4128-bf41-ad4bbc24e57d"}], "edge_evidence": []}], "name": "bt0214", "description": "2,5-Cyclohexadiene-1,4-diol derivative → 1,4-Benzenediol derivative

Comments:
The 2,5-Cyclohexadiene-1,4-diol derivative at present can have any stereochemistry, since the stereochemistry of the enzyme reaction has not yet been determined.", "aliases": [], "simple_rules": [{"uuid": "0dd38c1a-5cd1-463e-a28b-a6a69db241f1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/0dd38c1a-5cd1-463e-a28b-a6a69db241f1"}], "scenarios": []}, {"uuid": "2251cba4-716d-4933-9c1b-bd8a6c94229e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/2251cba4-716d-4933-9c1b-bd8a6c94229e", "enzymes": [{"uuid": "27be3f7c-e8e8-4a27-8ba0-0ccc9054711d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/2251cba4-716d-4933-9c1b-bd8a6c94229e/enzymelink/27be3f7c-e8e8-4a27-8ba0-0ccc9054711d", "ec_number": "5.4.99.2", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "57a7f840-7767-4308-98c6-12ea8daf2395", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/57a7f840-7767-4308-98c6-12ea8daf2395"}], "edge_evidence": []}], "name": "bt0312", "description": "1-MethylenecarboxylCoA → 1-MethylcarboxylCoA

Comments:
Carbon chain rearrangement; the 2 carbon can have H, methyl or carboxylate substituents. Based on methylmalonyl-CoA mutase EC 5.4.99.2 and isobutyryl-CoA mutase EC 5.4.99.13 (see Figure 1 of Ratnatilleke et al., 1999). CoA ligation to the terminal carboxyl group occurs prior to the reaction but is bypassed in this rule for simplification.", "aliases": [], "simple_rules": [{"uuid": "4987140c-b3a9-484b-87ec-4bdbdfaa15ba", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/4987140c-b3a9-484b-87ec-4bdbdfaa15ba"}], "scenarios": []}, {"uuid": "353e0fa7-f57f-47a2-bb1f-febb11132d7d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/353e0fa7-f57f-47a2-bb1f-febb11132d7d", "enzymes": [{"uuid": "17f4347f-e503-489c-961f-314a9736f18c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/353e0fa7-f57f-47a2-bb1f-febb11132d7d/enzymelink/17f4347f-e503-489c-961f-314a9736f18c", "ec_number": "1.14.14.41", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "ba346fd7-7a8b-47c1-9da0-2ac916556457", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/353e0fa7-f57f-47a2-bb1f-febb11132d7d/enzymelink/ba346fd7-7a8b-47c1-9da0-2ac916556457", "ec_number": "1.14.14.37", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "b1416767-921b-4784-a548-a07ff7f2522e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/353e0fa7-f57f-47a2-bb1f-febb11132d7d/enzymelink/b1416767-921b-4784-a548-a07ff7f2522e", "ec_number": "4.99.1.7", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "65f5739b-b632-4907-aa03-404ef663ead8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/65f5739b-b632-4907-aa03-404ef663ead8"}], "edge_evidence": []}, {"uuid": "31fc7246-6171-4622-92f2-3816aa1b5bd7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/353e0fa7-f57f-47a2-bb1f-febb11132d7d/enzymelink/31fc7246-6171-4622-92f2-3816aa1b5bd7", "ec_number": "4.99.1.6", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0062", "description": "Aldoxime → Nitrile", "aliases": [], "simple_rules": [{"uuid": "a3057438-57ee-4c8c-a1d3-e8e64139a098", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/a3057438-57ee-4c8c-a1d3-e8e64139a098"}], "scenarios": []}, {"uuid": "7903627e-f58a-460f-a891-d148c93e37d1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/7903627e-f58a-460f-a891-d148c93e37d1", "enzymes": [{"uuid": "e6b34f36-e158-4d22-9f8b-7619a1a7f722", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/7903627e-f58a-460f-a891-d148c93e37d1/enzymelink/e6b34f36-e158-4d22-9f8b-7619a1a7f722", "ec_number": "1.3.8.7", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "0f6613e4-85c5-4f09-a920-3a3c218932c2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/7903627e-f58a-460f-a891-d148c93e37d1/enzymelink/0f6613e4-85c5-4f09-a920-3a3c218932c2", "ec_number": "1.3.8.4", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "6b2b0f0c-a2cc-416e-b2c6-c2414a4477ef", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/7903627e-f58a-460f-a891-d148c93e37d1/enzymelink/6b2b0f0c-a2cc-416e-b2c6-c2414a4477ef", "ec_number": "1.3.1.86", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "95e070a4-ac8e-48b3-8712-757879b58638", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/7903627e-f58a-460f-a891-d148c93e37d1/enzymelink/95e070a4-ac8e-48b3-8712-757879b58638", "ec_number": "1.3.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "8592db09-8e31-4d92-8d83-97da94524058", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/8592db09-8e31-4d92-8d83-97da94524058"}], "edge_evidence": []}, {"uuid": "01fd9e10-ae3a-4274-8c1f-1ab05872a569", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/7903627e-f58a-460f-a891-d148c93e37d1/enzymelink/01fd9e10-ae3a-4274-8c1f-1ab05872a569", "ec_number": "1.3.1.44", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "a0d3f309-af65-4857-877f-cdc529db9e9b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/7903627e-f58a-460f-a891-d148c93e37d1/enzymelink/a0d3f309-af65-4857-877f-cdc529db9e9b", "ec_number": "1.3.1.31", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0180", "description": "2-unsubstituted-3-Methyl-alkyl-CoA derivative → 2,3-Didehydroalkyl-CoA derivative

Comments:
This reaction is similar to the first step in the beta-oxidation process. CoA ligation to the terminal carboxyl group precedes oxidation to form the double bond but is bypassed in this rule for simplification.", "aliases": [], "simple_rules": [{"uuid": "6f4200dd-9e55-47fb-b2a0-c47f5bfe67b0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/6f4200dd-9e55-47fb-b2a0-c47f5bfe67b0"}], "scenarios": []}, {"uuid": "25d71e00-78b9-4f66-b404-5f4d3c1e5e14", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/25d71e00-78b9-4f66-b404-5f4d3c1e5e14", "enzymes": [], "name": "bt0340", "description": "1,2-Dihydroxypolyaromatic → 1-Hydroxy-2-carboxyaromatic
1,2-Dihydroxybenzothionoid → Benzothionate
Dihydroxyfluorene derivative → Carboxy-1-indanone derivative

Comments:
This rule handles the upper naphthalene pathway, and includes dioxygenation of selected polyaromatics to form a 2-hydroxy-2-carboxychromene derivative, isomerization to the trans-enoate, dioxygenation of benzothionoids and isomerization to the trans-enoate, combined dioxygenation and isomerization of other polyaromatics, aldolytic cleavage of the pyruvate group (not shown) leaving an aldehyde, and oxidation of the aldehyde to a carboxylate (bt0003). The rule does not handle intermediate metabolites in the upper naphthalene pathway.", "aliases": [], "simple_rules": [{"uuid": "10edf654-1726-47c6-86f8-498721505beb", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/10edf654-1726-47c6-86f8-498721505beb"}], "scenarios": []}, {"uuid": "9fa53a34-3e14-4a02-9dc3-15bfc872d60c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/9fa53a34-3e14-4a02-9dc3-15bfc872d60c", "enzymes": [{"uuid": "fe969bac-dd42-4f11-ab10-5a8a22de43bf", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/9fa53a34-3e14-4a02-9dc3-15bfc872d60c/enzymelink/fe969bac-dd42-4f11-ab10-5a8a22de43bf", "ec_number": "1.8.1.11", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "408cbb4b-c9df-43fa-adb1-4841885812ab", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/9fa53a34-3e14-4a02-9dc3-15bfc872d60c/enzymelink/408cbb4b-c9df-43fa-adb1-4841885812ab", "ec_number": "1.8.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "25c5b499-6c90-4b46-9f8a-201f2cc8e6c8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/25c5b499-6c90-4b46-9f8a-201f2cc8e6c8"}], "edge_evidence": []}], "name": "bt0260", "description": "disubstituted Disulfide → two Thiols

Comments:
Rule will produce cis products in rings with double bonds.", "aliases": [], "simple_rules": [{"uuid": "d14503d1-9b95-47cb-a634-3339f781456f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/d14503d1-9b95-47cb-a634-3339f781456f"}], "scenarios": []}, {"uuid": "c2ae056e-20a6-48fb-bf50-67b9a41dde07", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/c2ae056e-20a6-48fb-bf50-67b9a41dde07", "enzymes": [{"uuid": "d5c59d4a-29a8-4d43-ab81-6669b5c0fbda", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/c2ae056e-20a6-48fb-bf50-67b9a41dde07/enzymelink/d5c59d4a-29a8-4d43-ab81-6669b5c0fbda", "ec_number": "3.13.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "580ae86e-92bf-4438-8dd6-67f4e1811b03", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/580ae86e-92bf-4438-8dd6-67f4e1811b03"}], "edge_evidence": []}], "name": "bt0210", "description": "Sulfoaromatic → Aromatic alcohol", "aliases": [], "simple_rules": [{"uuid": "22c8f97a-3e6a-46b8-96fb-273779c10754", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/22c8f97a-3e6a-46b8-96fb-273779c10754"}], "scenarios": []}, {"uuid": "10967bcd-4301-4408-9770-e59a19bb88db", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/10967bcd-4301-4408-9770-e59a19bb88db", "enzymes": [{"uuid": "28e0f5eb-c5c9-4ff0-9b9b-4103834790f8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/10967bcd-4301-4408-9770-e59a19bb88db/enzymelink/28e0f5eb-c5c9-4ff0-9b9b-4103834790f8", "ec_number": "1.3.99.8", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "79d29e3a-23f9-450b-a249-8489c7f22770", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/79d29e3a-23f9-450b-a249-8489c7f22770"}], "edge_evidence": []}], "name": "bt0375", "description": "1-unsubstituted Furan derivative → 1-Hydroxyfuran derivative", "aliases": [], "simple_rules": [{"uuid": "e430f43f-a9b7-433f-a811-be82c10cdc2b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/e430f43f-a9b7-433f-a811-be82c10cdc2b"}], "scenarios": []}, {"uuid": "116e5635-f24c-4235-9cb9-540dbbe33e66", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/116e5635-f24c-4235-9cb9-540dbbe33e66", "enzymes": [{"uuid": "c7e12ae1-3ecc-44fd-879a-d35761fafd75", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/116e5635-f24c-4235-9cb9-540dbbe33e66/enzymelink/c7e12ae1-3ecc-44fd-879a-d35761fafd75", "ec_number": "5.5.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "c66c4b06-cea5-4b5e-b1ee-8c2a025e27cb", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/c66c4b06-cea5-4b5e-b1ee-8c2a025e27cb"}], "edge_evidence": []}], "name": "bt0306", "description": "Cyclopropanecarboxylate derivative → Crotonate derivative

Comments:
This rule handles cyclopropanecarboxylate ring opening. CoA ligation to the terminal carboxyl group occurs prior to ring opening but is bypassed in this rule for simplification.", "aliases": [], "simple_rules": [{"uuid": "ed70c823-fd01-4f8b-ae26-6a6f37e5b663", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/ed70c823-fd01-4f8b-ae26-6a6f37e5b663"}], "scenarios": []}, {"uuid": "723b2f60-13b2-4ea2-9bf0-77745f1b0272", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/723b2f60-13b2-4ea2-9bf0-77745f1b0272", "enzymes": [{"uuid": "e81884f9-5274-44ed-95fb-30991038cb97", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/723b2f60-13b2-4ea2-9bf0-77745f1b0272/enzymelink/e81884f9-5274-44ed-95fb-30991038cb97", "ec_number": "1.14.13.25", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "09225a8e-1684-4091-a105-1ef521b246ff", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/723b2f60-13b2-4ea2-9bf0-77745f1b0272/enzymelink/09225a8e-1684-4091-a105-1ef521b246ff", "ec_number": "1.14.13.181", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "99d1640e-7174-4e96-a0d3-276494286580", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/723b2f60-13b2-4ea2-9bf0-77745f1b0272/enzymelink/99d1640e-7174-4e96-a0d3-276494286580", "ec_number": "1.14.13.246", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "0b6a4c4f-cd93-41bf-a051-a770e5b8e011", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/723b2f60-13b2-4ea2-9bf0-77745f1b0272/enzymelink/0b6a4c4f-cd93-41bf-a051-a770e5b8e011", "ec_number": "1.14.14.52", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "02d63925-a4e5-4f0d-b8e9-24a38d261781", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/02d63925-a4e5-4f0d-b8e9-24a38d261781"}], "edge_evidence": []}, {"uuid": "981a8127-8f41-484b-84e0-80d723ac14fd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/723b2f60-13b2-4ea2-9bf0-77745f1b0272/enzymelink/981a8127-8f41-484b-84e0-80d723ac14fd", "ec_number": "1.14.15.3", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "a9cbbc3b-2500-4eb4-8459-1875ee4006b6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/a9cbbc3b-2500-4eb4-8459-1875ee4006b6"}], "edge_evidence": []}, {"uuid": "4edcc21d-0399-4885-87fb-8edbc8538e6f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/723b2f60-13b2-4ea2-9bf0-77745f1b0272/enzymelink/4edcc21d-0399-4885-87fb-8edbc8538e6f", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "6ed2b70f-47e8-4d55-979a-c02905eea0df", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/6ed2b70f-47e8-4d55-979a-c02905eea0df"}], "edge_evidence": []}, {"uuid": "b3279600-cb5f-4176-8a34-4b63e8270536", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/723b2f60-13b2-4ea2-9bf0-77745f1b0272/enzymelink/b3279600-cb5f-4176-8a34-4b63e8270536", "ec_number": "1.14.13.229", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "5654ae07-5136-418b-a22f-1be27ab6c5ae", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/723b2f60-13b2-4ea2-9bf0-77745f1b0272/enzymelink/5654ae07-5136-418b-a22f-1be27ab6c5ae", "ec_number": "1.14.13.25", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "f9fcecf3-8da8-4aef-8ab6-c8e39fbb20bb", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/f9fcecf3-8da8-4aef-8ab6-c8e39fbb20bb"}], "edge_evidence": []}], "name": "bt0332", "description": "aliphatic Methyl [H0] → primary Alcohol

Comments:
This rule handles aliphatic methyl groups where the alpha carbon has no hydrogen atoms attached to it.", "aliases": [], "simple_rules": [{"uuid": "9b7926da-a070-406d-803b-ab4e5616d2b9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/9b7926da-a070-406d-803b-ab4e5616d2b9"}], "scenarios": []}, {"uuid": "3108a1cd-540c-477d-b3a7-c9749cb688d5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/3108a1cd-540c-477d-b3a7-c9749cb688d5", "enzymes": [{"uuid": "67b14344-6af1-4255-839f-5332d5228396", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/3108a1cd-540c-477d-b3a7-c9749cb688d5/enzymelink/67b14344-6af1-4255-839f-5332d5228396", "ec_number": "1.13.11.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "82f35ba8-5064-489e-a326-c801cc67acfc", "url": 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Comments:
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Arylphosphodiester → Phenol derivative + Phosphoester
Arylphosphotriester → Phenol derivative + Phosphodiester

Comments:
This rule is also triggered by vinylphosphoesters. The enol product of vinyl phosphate substrates rapidly tautomerizes to the more stable keto form. This rule handles the enol-keto tautomerization.", "aliases": [], "simple_rules": [{"uuid": "e0842fb1-b3cb-4b2e-b897-97f20474548d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/e0842fb1-b3cb-4b2e-b897-97f20474548d"}, {"uuid": "e522d12a-678b-46d8-96c4-aee8ed9e1851", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/e522d12a-678b-46d8-96c4-aee8ed9e1851"}], "scenarios": []}, {"uuid": "f26c1052-2d79-41cd-aa28-e64d929019fa", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/f26c1052-2d79-41cd-aa28-e64d929019fa", "enzymes": [], "name": "bt0295", "description": "Ether with vicinal halogenated carbon [H1] → Ester
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Comments:
This rule handles aliphatic methyl groups where the alpha carbon has two hydrogen atoms attached to it.", "aliases": [], "simple_rules": [{"uuid": "e4bd5407-63c4-433d-a33d-3575e3bffc22", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/e4bd5407-63c4-433d-a33d-3575e3bffc22"}], "scenarios": []}, {"uuid": "a3f8dcda-b54c-40a4-b0b4-b9fc1b15dd02", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a3f8dcda-b54c-40a4-b0b4-b9fc1b15dd02", "enzymes": [{"uuid": "dccec50f-8a85-49c3-9ba7-b1674c50ad1f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a3f8dcda-b54c-40a4-b0b4-b9fc1b15dd02/enzymelink/dccec50f-8a85-49c3-9ba7-b1674c50ad1f", "ec_number": "1.14.12.14", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "bdb02b8f-51d4-4e86-8ed5-e36d6f7bb23f", "url": 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enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "bd529d5b-1d2c-4c8f-b04b-a863774238b5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a3f8dcda-b54c-40a4-b0b4-b9fc1b15dd02/enzymelink/bd529d5b-1d2c-4c8f-b04b-a863774238b5", "ec_number": "1.14.12.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "a95646dd-f96e-42e0-a11f-f9fc843651d6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/a95646dd-f96e-42e0-a11f-f9fc843651d6"}, {"uuid": "925a7fdb-683e-429f-b967-3f8ec628ee1e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/925a7fdb-683e-429f-b967-3f8ec628ee1e"}], "edge_evidence": []}, {"uuid": "40ec4a2f-7448-4c23-baf2-436f9ec9a91c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a3f8dcda-b54c-40a4-b0b4-b9fc1b15dd02/enzymelink/40ec4a2f-7448-4c23-baf2-436f9ec9a91c", "ec_number": "1.14.12.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "407a5f83-db46-4ccc-b86e-92888158f361", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/407a5f83-db46-4ccc-b86e-92888158f361"}], "edge_evidence": []}, {"uuid": "b0cf02bd-2429-4adc-8e7f-951df0c9d436", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a3f8dcda-b54c-40a4-b0b4-b9fc1b15dd02/enzymelink/b0cf02bd-2429-4adc-8e7f-951df0c9d436", "ec_number": "1.14.12.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "b55bff54-81ab-4b47-88ae-d7c4a1d1cafc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/b55bff54-81ab-4b47-88ae-d7c4a1d1cafc"}], "edge_evidence": []}, {"uuid": "568357c8-ee18-4d76-9d72-6811ca0246fc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a3f8dcda-b54c-40a4-b0b4-b9fc1b15dd02/enzymelink/568357c8-ee18-4d76-9d72-6811ca0246fc", "ec_number": "1.14.13.35", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "67e5e0c7-1158-498e-a138-84b9b66841f9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/67e5e0c7-1158-498e-a138-84b9b66841f9"}], "edge_evidence": []}, {"uuid": "b8a09a99-c577-49cc-b7a2-f4b357111cb1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a3f8dcda-b54c-40a4-b0b4-b9fc1b15dd02/enzymelink/b8a09a99-c577-49cc-b7a2-f4b357111cb1", "ec_number": "1.14.12.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "e4e6a66b-7dc5-4c82-9b9d-f3736f81a3ee", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/e4e6a66b-7dc5-4c82-9b9d-f3736f81a3ee"}], "edge_evidence": []}, {"uuid": "ad9ee663-8a7c-4a6d-b7a1-6634d12a5963", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a3f8dcda-b54c-40a4-b0b4-b9fc1b15dd02/enzymelink/ad9ee663-8a7c-4a6d-b7a1-6634d12a5963", "ec_number": "1.14.12.14", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "7216354d-6980-4a61-94b1-b95a2a45ae8d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a3f8dcda-b54c-40a4-b0b4-b9fc1b15dd02/enzymelink/7216354d-6980-4a61-94b1-b95a2a45ae8d", "ec_number": "1.14.12.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "687f31de-ce52-4151-9033-860b01fc83c7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/687f31de-ce52-4151-9033-860b01fc83c7"}], "edge_evidence": []}], "name": "bt0065", "description": "1-Amino-2-unsubstituted aromatic → vic-Dihydroxyaromatic + Amine
1-Amide-2-unsubstituted aromatic → vic-Dihydroxyaromatic + Amide

Comments:
Also handles fused rings. All fused aromatic ring products with hydroxyl at 2,3 position are excluded.", "aliases": [], "simple_rules": [{"uuid": "42add347-d29c-4ac9-9b35-89308c3b1bd6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/42add347-d29c-4ac9-9b35-89308c3b1bd6"}], "scenarios": []}, {"uuid": "6879b456-c54a-4ccd-8e35-00e9a8cd65ba", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/6879b456-c54a-4ccd-8e35-00e9a8cd65ba", "enzymes": [{"uuid": "f8adc173-014e-420e-a477-5840d282a27e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/6879b456-c54a-4ccd-8e35-00e9a8cd65ba/enzymelink/f8adc173-014e-420e-a477-5840d282a27e", "ec_number": "1.3.99.17", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "c45467e9-8a6b-45b2-9717-4db46848be66", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/c45467e9-8a6b-45b2-9717-4db46848be66"}], "edge_evidence": []}, {"uuid": "9877ff2e-8230-4d4b-91a4-b2bbbca47bd6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/6879b456-c54a-4ccd-8e35-00e9a8cd65ba/enzymelink/9877ff2e-8230-4d4b-91a4-b2bbbca47bd6", "ec_number": "1.3.99.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "8b134f86-85a2-4e2e-ba0e-ce6f869de101", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/8b134f86-85a2-4e2e-ba0e-ce6f869de101"}], "edge_evidence": []}], "name": "bt0166", "description": "2-unsubstituted Quinoline derivative → Hydroquinolin-2-one derivative
4-unsubstituted Quinoline derivative → Hydroquinolin-4-one derivative

Comments:
This rule oxygenates at the 2 position of the hetero-ring in 3-methyl, 4-methyl and unsubstituted quinolines. Oxygenation occurs at the 4 position for 2-methyl and unsubstituted quinolines.", "aliases": [], "simple_rules": [{"uuid": "cd67240d-9bfe-4e96-9d5f-8158e34b506e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/cd67240d-9bfe-4e96-9d5f-8158e34b506e"}, {"uuid": "1689357b-c428-48e3-94b5-cf1c47426985", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/1689357b-c428-48e3-94b5-cf1c47426985"}], "scenarios": []}, {"uuid": "971a2e6a-4b36-41f3-9b9a-988274b9f771", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/971a2e6a-4b36-41f3-9b9a-988274b9f771", "enzymes": [], "name": "bt0346", "description": "5-Hydroxyoxepan-2-one derivative → 5-(2-Hydroxyethyl)oxolan-2-one derivative

Comments:
Based on M. D. Mihovilovic (2006) Curr Org Chem 10:1265-1287.", "aliases": [], "simple_rules": [{"uuid": "3b6bbf3b-1e36-4198-b26e-3f4cea892c7f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/3b6bbf3b-1e36-4198-b26e-3f4cea892c7f"}], "scenarios": []}, {"uuid": "d5d9f0fa-bc75-47c1-a778-b9707c592672", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d5d9f0fa-bc75-47c1-a778-b9707c592672", "enzymes": [{"uuid": "b3da9a72-6037-4911-a61e-1dc131ad7fff", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d5d9f0fa-bc75-47c1-a778-b9707c592672/enzymelink/b3da9a72-6037-4911-a61e-1dc131ad7fff", "ec_number": "3.7.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "d2ce765e-26b2-4b4c-898d-5938bada7cf5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/d2ce765e-26b2-4b4c-898d-5938bada7cf5"}], "edge_evidence": []}, {"uuid": "eade2fff-4f6e-4299-a1fa-db1837968555", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d5d9f0fa-bc75-47c1-a778-b9707c592672/enzymelink/eade2fff-4f6e-4299-a1fa-db1837968555", "ec_number": "3.7.1.2", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "37c49e0a-e299-437e-b6bd-80a41312ba88", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/37c49e0a-e299-437e-b6bd-80a41312ba88"}], "edge_evidence": []}], "name": "bt0358", "description": "Maleylacetoacetate → Fumarate + Acetoacetate
Maleylpyruvate → Fumarate + Pyruvate

Comments:
This rule handles the lower hydroquinone pathway, and includes isomerization of the maleylpyruvate or maleylacetoacetate cis double bond (bt0290) and hydrolytic cleavage of the fumarylpyruvate or fumarylacetoacetate intermediate (bt0088 or bt0200) to produce fumarate and pyruvate or acetoacetate.", "aliases": [], "simple_rules": [{"uuid": "3cc8308c-6a99-437c-93b7-fe0b869e61e1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/3cc8308c-6a99-437c-93b7-fe0b869e61e1"}], "scenarios": []}, {"uuid": "c09d2fcf-23cf-4633-94a4-3a2b9f4989b8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/c09d2fcf-23cf-4633-94a4-3a2b9f4989b8", "enzymes": [{"uuid": "37edf671-d965-4618-869f-f5b128661fea", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/c09d2fcf-23cf-4633-94a4-3a2b9f4989b8/enzymelink/37edf671-d965-4618-869f-f5b128661fea", "ec_number": "1.3.8.3", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "a41fd82f-005d-4d84-b17b-953786e14478", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/a41fd82f-005d-4d84-b17b-953786e14478"}], "edge_evidence": []}, {"uuid": "0086ba9b-cf3e-406f-9340-146c6b00a97c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/c09d2fcf-23cf-4633-94a4-3a2b9f4989b8/enzymelink/0086ba9b-cf3e-406f-9340-146c6b00a97c", "ec_number": "1.3.99.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "ba859f54-3fcc-4b8f-a533-8dc972a63a3e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/ba859f54-3fcc-4b8f-a533-8dc972a63a3e"}], "edge_evidence": []}], "name": "bt0213", "description": "Benzylsuccinyl-CoA derivative → E-Phenylitaconyl-CoA derivative

Comments:
CoA ligation to the terminal carboxyl group occurs prior to double bond formation but is bypassed in this rule for simplification.", "aliases": [], "simple_rules": [{"uuid": "c455d93d-b220-442c-aca6-5e604c0a139f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/c455d93d-b220-442c-aca6-5e604c0a139f"}], "scenarios": []}, {"uuid": "7301dc1f-4a85-4511-8334-5d20810bba80", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/7301dc1f-4a85-4511-8334-5d20810bba80", "enzymes": [{"uuid": "3de7905c-1836-4476-9ad4-6711d7f9dcee", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/7301dc1f-4a85-4511-8334-5d20810bba80/enzymelink/3de7905c-1836-4476-9ad4-6711d7f9dcee", "ec_number": "3.11.1.2", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "bb6699c6-b44b-49e1-a81e-41a982a5e899", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/7301dc1f-4a85-4511-8334-5d20810bba80/enzymelink/bb6699c6-b44b-49e1-a81e-41a982a5e899", "ec_number": "4.99.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "c8470641-8003-4fb1-a1f4-a0063052cd39", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/c8470641-8003-4fb1-a1f4-a0063052cd39"}, {"uuid": "ba41fb79-ae84-4472-a255-b0d010595b7f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/ba41fb79-ae84-4472-a255-b0d010595b7f"}, {"uuid": "13a22fb2-183e-4bea-87a5-2d5113aff432", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/13a22fb2-183e-4bea-87a5-2d5113aff432"}], "edge_evidence": []}, {"uuid": "b0c362a2-19fb-45b3-a4ed-fec2df96764e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/7301dc1f-4a85-4511-8334-5d20810bba80/enzymelink/b0c362a2-19fb-45b3-a4ed-fec2df96764e", "ec_number": "3.11.1.1", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0147", "description": "Alkylphosphonate → R-CH3 + Phosphate
Dimethylphosphinate → Methylphosphonate

Comments:
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Comments:
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secondary Amine → Amine + Aldehyde or Ketone
tertiary Amine → secondary Amine + Aldehyde or Ketone
Methylammonium derivative → Trimethylamine + Aldehyde or Ketone

Comments:
Oxidative removal of an R group from an amine. An aldehyde is produced if the leaving R group is attached through a primary carbon. A ketone is produced if the leaving R group is attached through a secondary carbon. Rule will produce cis products in rings with double bonds.", "aliases": [], "simple_rules": [{"uuid": "580f46f2-b81d-4115-8b02-101ef6807b2c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/580f46f2-b81d-4115-8b02-101ef6807b2c"}, {"uuid": "edaada18-7db8-4a5a-a481-4188338bc87b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/edaada18-7db8-4a5a-a481-4188338bc87b"}], "scenarios": []}, {"uuid": "a5df0ccb-1d7f-476a-8bbc-3d4f678bece0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a5df0ccb-1d7f-476a-8bbc-3d4f678bece0", "enzymes": [{"uuid": "522e78ce-8000-42a3-b668-8eb39ad966bf", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a5df0ccb-1d7f-476a-8bbc-3d4f678bece0/enzymelink/522e78ce-8000-42a3-b668-8eb39ad966bf", "ec_number": "3.3.2.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "b74de9ed-5079-41ed-8b89-4e704f6ff195", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/b74de9ed-5079-41ed-8b89-4e704f6ff195"}], "edge_evidence": []}, {"uuid": "ffc3d1d8-5898-4fcf-89ca-47d910b121dd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a5df0ccb-1d7f-476a-8bbc-3d4f678bece0/enzymelink/ffc3d1d8-5898-4fcf-89ca-47d910b121dd", "ec_number": "3.3.2.12", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "4c556511-5dc7-410c-b7f8-8610db99532f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a5df0ccb-1d7f-476a-8bbc-3d4f678bece0/enzymelink/4c556511-5dc7-410c-b7f8-8610db99532f", "ec_number": "3.3.2.13", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "f98d81c1-2719-4fc1-a61b-1bb53a010736", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a5df0ccb-1d7f-476a-8bbc-3d4f678bece0/enzymelink/f98d81c1-2719-4fc1-a61b-1bb53a010736", "ec_number": "3.3.2.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "96f35679-6543-4d08-aca6-15c1d1ada2e1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/96f35679-6543-4d08-aca6-15c1d1ada2e1"}], "edge_evidence": []}, {"uuid": "6961ff07-dbd4-467e-adf5-80716be5e10a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a5df0ccb-1d7f-476a-8bbc-3d4f678bece0/enzymelink/6961ff07-dbd4-467e-adf5-80716be5e10a", "ec_number": "3.3.2.1", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "dbdc6800-ecd5-4d75-b424-d51bb18ed041", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a5df0ccb-1d7f-476a-8bbc-3d4f678bece0/enzymelink/dbdc6800-ecd5-4d75-b424-d51bb18ed041", "ec_number": "3.3.2.15", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0158", "description": "Enol ether → Keto + Alcohol
Aromatic ether → Aromatic alcohol + Alcohol

Comments:
Based on isochorismatase EC 3.3.2.1. Rule will produce cis products in rings with double bonds. If the substrate contains an enol ether, the reaction depicted by this rule produces an enol product. This spontaneously tautomerizes to the keto form, thus the keto form is shown in this rule.", "aliases": [], "simple_rules": [{"uuid": "a51377bf-cd68-460f-b57d-90b0c2d28211", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/a51377bf-cd68-460f-b57d-90b0c2d28211"}, {"uuid": "81f5a960-d378-40be-b38d-6ca18ac4440b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/81f5a960-d378-40be-b38d-6ca18ac4440b"}], "scenarios": []}, {"uuid": "e4cc0a0d-8a8f-48fa-a066-af23ac3a8d07", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e4cc0a0d-8a8f-48fa-a066-af23ac3a8d07", "enzymes": [{"uuid": "2bc8e283-12df-410c-b1df-621dc3cd9e66", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e4cc0a0d-8a8f-48fa-a066-af23ac3a8d07/enzymelink/2bc8e283-12df-410c-b1df-621dc3cd9e66", "ec_number": "3.1.6.17", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "8be397ab-2472-4e52-8d80-7dfd27811712", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e4cc0a0d-8a8f-48fa-a066-af23ac3a8d07/enzymelink/8be397ab-2472-4e52-8d80-7dfd27811712", "ec_number": "3.1.6.11", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "61d85d90-71ea-4348-9c25-84016efb708e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e4cc0a0d-8a8f-48fa-a066-af23ac3a8d07/enzymelink/61d85d90-71ea-4348-9c25-84016efb708e", "ec_number": "3.1.6.3", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "32c90ab0-710d-456b-9975-8e980beed37c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e4cc0a0d-8a8f-48fa-a066-af23ac3a8d07/enzymelink/32c90ab0-710d-456b-9975-8e980beed37c", "ec_number": "3.1.6.1", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "4345e3f6-6b23-4424-a529-67abf7db6250", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e4cc0a0d-8a8f-48fa-a066-af23ac3a8d07/enzymelink/4345e3f6-6b23-4424-a529-67abf7db6250", "ec_number": "3.1.6.6", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "2c05ad82-1e5c-4cb4-ad31-4d4783a00cb1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e4cc0a0d-8a8f-48fa-a066-af23ac3a8d07/enzymelink/2c05ad82-1e5c-4cb4-ad31-4d4783a00cb1", "ec_number": "3.1.6.10", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "bd10a16f-8779-4676-9fae-6ea83309594b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e4cc0a0d-8a8f-48fa-a066-af23ac3a8d07/enzymelink/bd10a16f-8779-4676-9fae-6ea83309594b", "ec_number": "3.1.6.2", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "4c8a4c57-6b95-4155-a0da-008d782543a8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e4cc0a0d-8a8f-48fa-a066-af23ac3a8d07/enzymelink/4c8a4c57-6b95-4155-a0da-008d782543a8", "ec_number": "3.1.6.9", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "244c0042-d79a-48df-aef9-14a9fe165af0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e4cc0a0d-8a8f-48fa-a066-af23ac3a8d07/enzymelink/244c0042-d79a-48df-aef9-14a9fe165af0", "ec_number": "3.1.6.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "a0f0a5c1-2478-441d-8525-8d23b5405228", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/a0f0a5c1-2478-441d-8525-8d23b5405228"}], "edge_evidence": []}, {"uuid": "73596f93-7fd9-4635-9179-5e9a3d68439c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e4cc0a0d-8a8f-48fa-a066-af23ac3a8d07/enzymelink/73596f93-7fd9-4635-9179-5e9a3d68439c", "ec_number": "3.1.6.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "2307cec8-c10e-414c-8077-8b6f82e13c4f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2307cec8-c10e-414c-8077-8b6f82e13c4f"}], "edge_evidence": []}], "name": "bt0143", "description": "Alkyl or aryl sulfate → Alkyl or aryl 1-ol

Comments:
Aryl sulfate hydrolysis based on EC 3.1.6.1.", "aliases": [], "simple_rules": [{"uuid": "2fb9a3b3-0f4d-457b-adcd-676313af4e2f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/2fb9a3b3-0f4d-457b-adcd-676313af4e2f"}], "scenarios": []}, {"uuid": "3b330efd-73bc-44b9-b745-75ec5b1e2768", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/3b330efd-73bc-44b9-b745-75ec5b1e2768", "enzymes": [{"uuid": "b26b0b3b-41af-4d15-9093-766f8cd41a50", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/3b330efd-73bc-44b9-b745-75ec5b1e2768/enzymelink/b26b0b3b-41af-4d15-9093-766f8cd41a50", "ec_number": "1.14.13.31", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "815d2a8f-7128-49b3-9a89-6b6c37088b0a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/815d2a8f-7128-49b3-9a89-6b6c37088b0a"}], "edge_evidence": []}, {"uuid": "840b0e13-218a-41a7-bb48-1ac77872b6bb", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/3b330efd-73bc-44b9-b745-75ec5b1e2768/enzymelink/840b0e13-218a-41a7-bb48-1ac77872b6bb", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "aed63c15-7f48-4fb6-a2f0-de1e5a1c2caf", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/aed63c15-7f48-4fb6-a2f0-de1e5a1c2caf"}], "edge_evidence": []}], "name": "bt0383", "description": "2-Nitrophenol derivative → Catechol derivative

Comments:
Based on EC 1.14.13.31 and data from Zeyer et al., 1986.", "aliases": [], "simple_rules": [{"uuid": "cde3c605-1c16-4a01-b5dc-147193b0459c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/cde3c605-1c16-4a01-b5dc-147193b0459c"}], "scenarios": []}, {"uuid": "a6224225-dea1-4fce-8956-ef2f454e5dc7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a6224225-dea1-4fce-8956-ef2f454e5dc7", "enzymes": [{"uuid": "47d93b10-d1f7-428c-a00b-00791b868682", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a6224225-dea1-4fce-8956-ef2f454e5dc7/enzymelink/47d93b10-d1f7-428c-a00b-00791b868682", "ec_number": "1.14.12.13", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "6d04345a-c135-4820-96db-869789bbd59d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a6224225-dea1-4fce-8956-ef2f454e5dc7/enzymelink/6d04345a-c135-4820-96db-869789bbd59d", "ec_number": "1.14.12.13", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "6dfc04f8-827b-43ee-9c34-b6c77d6a2a82", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/6dfc04f8-827b-43ee-9c34-b6c77d6a2a82"}], "edge_evidence": []}], "name": "bt0072", "description": "1-Carboxy-2-haloaromatic → 1,2-Dihydroxyaromatic

Comments:
Also handles fused rings. All fused aromatic ring products with hydroxyls at 2,3 position are excluded.", "aliases": [], "simple_rules": [{"uuid": "9dd6df6e-ca25-4bcf-ac02-6e7b0175549e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/9dd6df6e-ca25-4bcf-ac02-6e7b0175549e"}], "scenarios": []}, {"uuid": "cd6970df-6e24-4305-8e6e-3988cdf61de9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/cd6970df-6e24-4305-8e6e-3988cdf61de9", "enzymes": [{"uuid": "e372ad13-d10e-4eb5-94ec-2d414d120df0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/cd6970df-6e24-4305-8e6e-3988cdf61de9/enzymelink/e372ad13-d10e-4eb5-94ec-2d414d120df0", "ec_number": "1.1.3.8", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0044", "description": "Enol → Keto", "aliases": [], "simple_rules": [{"uuid": "e5c7f3b5-6ab0-4155-a2a1-3e5133e5b18e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/e5c7f3b5-6ab0-4155-a2a1-3e5133e5b18e"}], "scenarios": []}, {"uuid": "fd9b1692-6f7e-48d4-b51a-b5bc8ffaf8b3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/fd9b1692-6f7e-48d4-b51a-b5bc8ffaf8b3", "enzymes": [{"uuid": "5eee6f04-cb69-4fa9-aa06-e6f17e88041d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/fd9b1692-6f7e-48d4-b51a-b5bc8ffaf8b3/enzymelink/5eee6f04-cb69-4fa9-aa06-e6f17e88041d", "ec_number": "1.8.3.6", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "f33c8cdc-9166-4758-9a82-043ae36f0d7e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/fd9b1692-6f7e-48d4-b51a-b5bc8ffaf8b3/enzymelink/f33c8cdc-9166-4758-9a82-043ae36f0d7e", "ec_number": "1.1.1.306", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "d7b074a0-e912-4bb9-a5de-7d98a985c03b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/fd9b1692-6f7e-48d4-b51a-b5bc8ffaf8b3/enzymelink/d7b074a0-e912-4bb9-a5de-7d98a985c03b", "ec_number": "1.8.3.5", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "952f0bbf-a328-4e13-915c-827cdacb384c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/fd9b1692-6f7e-48d4-b51a-b5bc8ffaf8b3/enzymelink/952f0bbf-a328-4e13-915c-827cdacb384c", "ec_number": "1.14.13.131", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "c93a140a-1956-448a-910a-e6e227bc3865", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/fd9b1692-6f7e-48d4-b51a-b5bc8ffaf8b3/enzymelink/c93a140a-1956-448a-910a-e6e227bc3865", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "bea82459-e3ea-46d8-85a0-1c1b033ab841", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/bea82459-e3ea-46d8-85a0-1c1b033ab841"}], "edge_evidence": []}], "name": "bt0259", "description": "disubstituted Sulfide → Aldehyde + Sulfide
Monoalkylthiol → Aldehyde + H2S
Thiol alkene → Alcohol
Monoalkylthiophosphate → Aldehyde + Thiophosphate

Comments:
If there are two possible cleavage sites, will show products for both. Rule will produce cis products in rings with double bonds.", "aliases": [], "simple_rules": [{"uuid": "e41d9d65-6adf-417b-a36d-dcd56aa160a8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/e41d9d65-6adf-417b-a36d-dcd56aa160a8"}], "scenarios": []}, {"uuid": "82cf0eb4-310f-49cc-8682-dee6735f3fc2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/82cf0eb4-310f-49cc-8682-dee6735f3fc2", "enzymes": [{"uuid": "e52926b9-3cfc-4be5-a653-5d81193abc32", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/82cf0eb4-310f-49cc-8682-dee6735f3fc2/enzymelink/e52926b9-3cfc-4be5-a653-5d81193abc32", "ec_number": "1.14.13.64", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "4c8831b4-6f23-4d47-a38a-7bc88fcef3b8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/82cf0eb4-310f-49cc-8682-dee6735f3fc2/enzymelink/4c8831b4-6f23-4d47-a38a-7bc88fcef3b8", "ec_number": "1.14.13.27", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "3a1493b6-f9d2-41b9-9087-085689c04c8a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/82cf0eb4-310f-49cc-8682-dee6735f3fc2/enzymelink/3a1493b6-f9d2-41b9-9087-085689c04c8a", "ec_number": "1.14.13.27", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "696c0f5a-15b3-4f27-8b2b-629ab4230b3f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/696c0f5a-15b3-4f27-8b2b-629ab4230b3f"}], "edge_evidence": []}, {"uuid": "f95602c8-4b83-446b-9dc5-c8dcc42b334e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/82cf0eb4-310f-49cc-8682-dee6735f3fc2/enzymelink/f95602c8-4b83-446b-9dc5-c8dcc42b334e", "ec_number": "1.14.13.64", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "929e27f3-0e13-4ef6-a3bd-e36d232d2425", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/929e27f3-0e13-4ef6-a3bd-e36d232d2425"}], "edge_evidence": []}], "name": "bt0343", "description": "p-Hydroxybenzoate derivative → 1,4-Dihydroxybenzenoid
p-Aminobenzoate derivative → 1-Hydroxy-4-aminobenzenoid

Comments:
This rule acts on most para-hydroxy- or para-amino- benzoate derivatives. 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Comments:
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Lactam → Aminecarboxylate

Comments:
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Dihalomethyl derivative → 1-Halo-1-methylalcohol derivative

Comments:
Hydrolytic dehalogenation of aliphatic halomethyl and dihalomethyl derivatives.", "aliases": [], "simple_rules": [{"uuid": "d0b86488-563a-467d-b3af-30751e0bc6a2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/d0b86488-563a-467d-b3af-30751e0bc6a2"}], "scenarios": []}, {"uuid": "0c3a559d-5a8b-400b-a86f-7862fe82140a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/0c3a559d-5a8b-400b-a86f-7862fe82140a", "enzymes": [], "name": "bt0227", "description": "Acylsulfonate → Carboxylate + HSO3-", "aliases": [], "simple_rules": [{"uuid": "eaeb9e73-74d7-4b69-adf1-f67de85af2bc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/eaeb9e73-74d7-4b69-adf1-f67de85af2bc"}], "scenarios": []}, {"uuid": "fd284953-5c8f-4fdf-94af-736744ac5ea9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/fd284953-5c8f-4fdf-94af-736744ac5ea9", "enzymes": [{"uuid": "b22dabbb-f1ae-49b5-9e52-5b1958c71696", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/fd284953-5c8f-4fdf-94af-736744ac5ea9/enzymelink/b22dabbb-f1ae-49b5-9e52-5b1958c71696", "ec_number": "1.14.12.24", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "0b19a952-07c7-4ec2-bf6d-9819f43ccb4c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/fd284953-5c8f-4fdf-94af-736744ac5ea9/enzymelink/0b19a952-07c7-4ec2-bf6d-9819f43ccb4c", "ec_number": "1.14.12.23", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "5038bdf1-e78f-4b6c-9acf-969fbe08e746", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/fd284953-5c8f-4fdf-94af-736744ac5ea9/enzymelink/5038bdf1-e78f-4b6c-9acf-969fbe08e746", "ec_number": "1.14.12.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "0c5d1b22-a141-4bde-8a77-9ab38c5d0e83", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/0c5d1b22-a141-4bde-8a77-9ab38c5d0e83"}], "edge_evidence": []}, {"uuid": "5c92ace0-77c8-4b8f-bad7-8192cbd01799", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/fd284953-5c8f-4fdf-94af-736744ac5ea9/enzymelink/5c92ace0-77c8-4b8f-bad7-8192cbd01799", "ec_number": "1.14.12.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "0ed80ffd-c885-4ebc-ab56-d0471f41419b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/0ed80ffd-c885-4ebc-ab56-d0471f41419b"}], "edge_evidence": []}], "name": "bt0042", "description": "1-Nitro-2-unsubstituted aromatic → vic-Dihydroxyaromatic

Comments:
Also handles fused rings. All fused aromatic ring products with hydroxyl at 2,3 position are excluded.", "aliases": [], "simple_rules": [{"uuid": "cf2b98a3-7aba-403f-86d1-f1f827920c58", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/cf2b98a3-7aba-403f-86d1-f1f827920c58"}], "scenarios": []}, {"uuid": "557427b2-f8fc-46fd-93af-cb667ca28282", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/557427b2-f8fc-46fd-93af-cb667ca28282", "enzymes": [{"uuid": "ef50a78d-627f-4623-87d8-da233fa51cf8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/557427b2-f8fc-46fd-93af-cb667ca28282/enzymelink/ef50a78d-627f-4623-87d8-da233fa51cf8", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "833468ff-9560-45ba-af6d-7c123042d5b2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/833468ff-9560-45ba-af6d-7c123042d5b2"}], "edge_evidence": []}, {"uuid": "b9117c3c-5e4f-4a8c-aa36-e35e79d11094", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/557427b2-f8fc-46fd-93af-cb667ca28282/enzymelink/b9117c3c-5e4f-4a8c-aa36-e35e79d11094", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "b5988b4d-d08e-4092-b3cd-a2a93fd685a1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/b5988b4d-d08e-4092-b3cd-a2a93fd685a1"}], "edge_evidence": []}], "name": "bt0225", "description": "Bisphenol A derivative → 1,2-bis(4-Hydroxyphenyl)-2-propanol derivative", "aliases": [], "simple_rules": [{"uuid": "474002c8-dacd-4950-bd51-8f1c87312492", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/474002c8-dacd-4950-bd51-8f1c87312492"}], "scenarios": []}, {"uuid": "15e937b4-9236-4715-accd-12408ebddb91", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/15e937b4-9236-4715-accd-12408ebddb91", "enzymes": [{"uuid": "fa33b947-e85b-48fa-916b-230b06ee66ed", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/15e937b4-9236-4715-accd-12408ebddb91/enzymelink/fa33b947-e85b-48fa-916b-230b06ee66ed", "ec_number": "3.10.1.2", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "037257a5-3cd1-4af1-9739-b273967d08a5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/15e937b4-9236-4715-accd-12408ebddb91/enzymelink/037257a5-3cd1-4af1-9739-b273967d08a5", "ec_number": "3.10.1.2", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "f82b60bc-20f2-4d83-9b4e-d477e240b33a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/f82b60bc-20f2-4d83-9b4e-d477e240b33a"}], "edge_evidence": []}, {"uuid": "bdb7efb4-8616-4332-be10-3d6f89035a40", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/15e937b4-9236-4715-accd-12408ebddb91/enzymelink/bdb7efb4-8616-4332-be10-3d6f89035a40", "ec_number": "3.10.1.1", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "4055ef87-5568-40ee-9a65-dc4698b4b2b3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/15e937b4-9236-4715-accd-12408ebddb91/enzymelink/4055ef87-5568-40ee-9a65-dc4698b4b2b3", "ec_number": "3.10.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "76421dac-d9ac-4d53-ab22-18122ec0f758", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/76421dac-d9ac-4d53-ab22-18122ec0f758"}], "edge_evidence": []}], "name": "bt0144", "description": "Sulfamate → Amine
Sulfonamide → Amine + Sulfonate", "aliases": [], "simple_rules": [{"uuid": "ed642789-cfc1-4e94-b805-2b339fe54913", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/ed642789-cfc1-4e94-b805-2b339fe54913"}], "scenarios": []}, {"uuid": "25fc4c1b-c086-4ccc-a404-fe72af67ed6e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/25fc4c1b-c086-4ccc-a404-fe72af67ed6e", "enzymes": [{"uuid": "cf889536-43e8-4422-9ce7-1b3a499c5e5c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/25fc4c1b-c086-4ccc-a404-fe72af67ed6e/enzymelink/cf889536-43e8-4422-9ce7-1b3a499c5e5c", "ec_number": "1.14.13.242", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "b43bfda9-a0d9-4fdd-a27b-7a3526b49b52", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/25fc4c1b-c086-4ccc-a404-fe72af67ed6e/enzymelink/b43bfda9-a0d9-4fdd-a27b-7a3526b49b52", "ec_number": "1.14.13.242", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "0e1b7610-35e4-4907-9346-2aaeec0ed3e2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/0e1b7610-35e4-4907-9346-2aaeec0ed3e2"}], "edge_evidence": []}, {"uuid": "6776dca2-7e73-4ecf-a83d-37544bcca43e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/25fc4c1b-c086-4ccc-a404-fe72af67ed6e/enzymelink/6776dca2-7e73-4ecf-a83d-37544bcca43e", "ec_number": "1.14.13.241", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "43a769ef-c961-4ccf-a8c1-34e6c7c8c2bc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/43a769ef-c961-4ccf-a8c1-34e6c7c8c2bc"}], "edge_evidence": []}, {"uuid": "1e4f9294-3f0f-4786-9a93-a18c5995e754", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/25fc4c1b-c086-4ccc-a404-fe72af67ed6e/enzymelink/1e4f9294-3f0f-4786-9a93-a18c5995e754", "ec_number": "1.14.13.241", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0377", "description": "3-Hydroxy-2-methylpyridine-5-carboxylate derivative → 2-(Acetamidomethylene)succinate derivative

Comments:
Based on EC 1.14.12.4.", "aliases": [], "simple_rules": [{"uuid": "4761d039-1c2b-454a-9e0a-cee9187fc212", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/4761d039-1c2b-454a-9e0a-cee9187fc212"}], "scenarios": []}, {"uuid": "17ab026b-ac42-463a-b20e-d434faa9ae8c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/17ab026b-ac42-463a-b20e-d434faa9ae8c", "enzymes": [{"uuid": "d181a490-4035-4d61-956e-b0393d9472bd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/17ab026b-ac42-463a-b20e-d434faa9ae8c/enzymelink/d181a490-4035-4d61-956e-b0393d9472bd", "ec_number": "5.3.99.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "d5452f8f-f4eb-442d-9d3d-ae626c2fb1e1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/d5452f8f-f4eb-442d-9d3d-ae626c2fb1e1"}], "edge_evidence": []}, 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"http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/3a2d1855-bf74-4037-8330-d507248494d7/enzymelink/ce027a15-eb3b-4146-8fff-73ad611e478a", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "620f4a32-77e5-46cd-9a25-5c8153ba5286", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/620f4a32-77e5-46cd-9a25-5c8153ba5286"}], "edge_evidence": []}], "name": "bt0284", "description": "Benzothiophene-S,S-dioxide derivative → 2-Hydroxyphenyl-2-ethenesulfonate derivative

Comments:
Based on Ishii et al., 2005 and Furuya et al., 2002.", "aliases": [], "simple_rules": [{"uuid": "592ed53c-09ca-4b6c-a2a5-a5ce9859d6b8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/592ed53c-09ca-4b6c-a2a5-a5ce9859d6b8"}], "scenarios": []}, {"uuid": "021d3098-b5af-4083-ba0d-029d9c18a299", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/021d3098-b5af-4083-ba0d-029d9c18a299", "enzymes": [{"uuid": "4d1c7c44-8f79-48e3-9478-2e3b6a009e10", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/021d3098-b5af-4083-ba0d-029d9c18a299/enzymelink/4d1c7c44-8f79-48e3-9478-2e3b6a009e10", "ec_number": "3.5.4.43", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "ca07d10d-2932-48f2-adb9-db839999c919", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/021d3098-b5af-4083-ba0d-029d9c18a299/enzymelink/ca07d10d-2932-48f2-adb9-db839999c919", "ec_number": "3.5.4.42", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "12bbdbff-cbff-4d0b-84dc-3b0b3b8b5452", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/021d3098-b5af-4083-ba0d-029d9c18a299/enzymelink/12bbdbff-cbff-4d0b-84dc-3b0b3b8b5452", "ec_number": "3.5.4.42", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "134dc520-2d24-4b6f-83be-ae0747150706", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/134dc520-2d24-4b6f-83be-ae0747150706"}], "edge_evidence": []}, {"uuid": "ebb4b60b-6efe-4c7b-a4ad-a5fd19096501", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/021d3098-b5af-4083-ba0d-029d9c18a299/enzymelink/ebb4b60b-6efe-4c7b-a4ad-a5fd19096501", "ec_number": "3.5.4.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "6b93a42a-28d1-4ed4-84b7-5cb9a0a90d4c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/6b93a42a-28d1-4ed4-84b7-5cb9a0a90d4c"}], "edge_evidence": []}, {"uuid": "c68786d9-102f-4308-a279-5bc81394cd34", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/021d3098-b5af-4083-ba0d-029d9c18a299/enzymelink/c68786d9-102f-4308-a279-5bc81394cd34", "ec_number": "3.5.4.43", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "39f2b7be-20af-4fc8-b245-d95471319f76", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/39f2b7be-20af-4fc8-b245-d95471319f76"}], "edge_evidence": []}, {"uuid": "10880f28-cd2b-4f5a-bbcd-5542c8a41039", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/021d3098-b5af-4083-ba0d-029d9c18a299/enzymelink/10880f28-cd2b-4f5a-bbcd-5542c8a41039", "ec_number": "3.5.99.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "99a7d798-4411-4800-9e35-572087f81840", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/99a7d798-4411-4800-9e35-572087f81840"}], "edge_evidence": []}], "name": "bt0061", "description": "N-aliphatic-hydroxy-s-Triazine → hydroxy-s-Triazine", "aliases": [], "simple_rules": [{"uuid": "fca8ab1a-c0bd-4a96-833d-cc1c1eab8dd5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/fca8ab1a-c0bd-4a96-833d-cc1c1eab8dd5"}], "scenarios": []}, {"uuid": "929997e6-443c-42f0-b3d3-5faa0287f421", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/929997e6-443c-42f0-b3d3-5faa0287f421", "enzymes": [], "name": "bt0378", "description": "2,4,6-Trinitrophenol derivative → 2,4-Dinitrocyclohexanone derivative

Comments:
This rule is based on picric acid degradation and handles the di- and trinitrophenol pathway. It includes two initial hydride transferase reactions to form the DNP and TNP dihydride Meisenheimer complexes respectively (bt0304 and bt0311). The TNP dihydride complex undergoes elimination of nitrite (bt0307) and a third hydride transfer reaction to form the DNP dihydride complex (bt0305). Spontaneous protonation of this complex yields 2,4-Dinitrocyclohexanone. This rule DOES NOT handle intermediates in this pathway.", "aliases": [], "simple_rules": [{"uuid": "0ee829cd-8ef0-47fb-bdd0-22e7bb7986f9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/0ee829cd-8ef0-47fb-bdd0-22e7bb7986f9"}], "scenarios": []}, {"uuid": "f1bff44e-7777-4d6e-a6e5-01fca7af900a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/f1bff44e-7777-4d6e-a6e5-01fca7af900a", "enzymes": [{"uuid": "a4ee8bd4-e7ed-4fd9-aa52-a6721e841a24", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/f1bff44e-7777-4d6e-a6e5-01fca7af900a/enzymelink/a4ee8bd4-e7ed-4fd9-aa52-a6721e841a24", "ec_number": "3.7.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "d2ce765e-26b2-4b4c-898d-5938bada7cf5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/d2ce765e-26b2-4b4c-898d-5938bada7cf5"}], "edge_evidence": []}, {"uuid": "b08143bf-8da6-4f8b-928f-5512a1c19078", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/f1bff44e-7777-4d6e-a6e5-01fca7af900a/enzymelink/b08143bf-8da6-4f8b-928f-5512a1c19078", "ec_number": "3.7.1.5", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "37ef7b86-b98b-4855-8375-7b58a4aef5c4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/37ef7b86-b98b-4855-8375-7b58a4aef5c4"}], "edge_evidence": []}, {"uuid": "9ea5bff7-4273-41a9-bb0d-763533c7b48e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/f1bff44e-7777-4d6e-a6e5-01fca7af900a/enzymelink/9ea5bff7-4273-41a9-bb0d-763533c7b48e", "ec_number": "3.7.1.6", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "091619b8-cc9a-4a71-87e6-52f8081a8893", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/091619b8-cc9a-4a71-87e6-52f8081a8893"}], "edge_evidence": []}], "name": "bt0392", "description": "3-Formylpyruvate derivative → Pyruvate + Carboxylate

Comments:
Based on EC 3.7.1.5.", "aliases": [], "simple_rules": [{"uuid": "fb5a24fa-653a-48c8-9455-8d88369cd8b9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/fb5a24fa-653a-48c8-9455-8d88369cd8b9"}], "scenarios": []}, {"uuid": "2a1425cb-1ca4-4c81-8736-d2cb02c0110c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/2a1425cb-1ca4-4c81-8736-d2cb02c0110c", "enzymes": [{"uuid": "e82fc5fa-45f5-497d-96e8-e52e6a69fee0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/2a1425cb-1ca4-4c81-8736-d2cb02c0110c/enzymelink/e82fc5fa-45f5-497d-96e8-e52e6a69fee0", "ec_number": "4.2.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "ac370e35-6945-4f4c-a71c-a794c75da4c3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/ac370e35-6945-4f4c-a71c-a794c75da4c3"}], "edge_evidence": []}], "name": "bt0226", "description": "1,2-bis(4-Hydroxyphenyl)-2-propanol derivative → 4,4'-Dihydroxy-alpha-methylstilbene derivative", "aliases": [], "simple_rules": [{"uuid": "bef1d49d-3503-4255-a476-bbdaa0de7774", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/bef1d49d-3503-4255-a476-bbdaa0de7774"}], "scenarios": []}, {"uuid": "28e06e51-4e92-4061-8aa2-71625d5e3402", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/28e06e51-4e92-4061-8aa2-71625d5e3402", "enzymes": [{"uuid": "6dbda552-0b34-401f-ab43-0294e7b59bc3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/28e06e51-4e92-4061-8aa2-71625d5e3402/enzymelink/6dbda552-0b34-401f-ab43-0294e7b59bc3", "ec_number": "1.5.99.4", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "95f5dfd1-18fe-4d79-8732-8f4e6968b1e8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/95f5dfd1-18fe-4d79-8732-8f4e6968b1e8"}, {"uuid": "568a5a0e-e5b6-44e0-9061-615bd3d06c3c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/568a5a0e-e5b6-44e0-9061-615bd3d06c3c"}], "edge_evidence": []}, {"uuid": "d96d4d81-9b7d-47d1-8319-d0e8f19c4087", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/28e06e51-4e92-4061-8aa2-71625d5e3402/enzymelink/d96d4d81-9b7d-47d1-8319-d0e8f19c4087", "ec_number": "1.14.14.92", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "aa7280ca-07c5-4e10-b83c-84c5d4dcfbe6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/aa7280ca-07c5-4e10-b83c-84c5d4dcfbe6"}], "edge_evidence": []}, {"uuid": "30277c66-1030-4d9e-b425-279ec0b01591", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/28e06e51-4e92-4061-8aa2-71625d5e3402/enzymelink/30277c66-1030-4d9e-b425-279ec0b01591", "ec_number": "1.17.1.5", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "6f5252e7-1642-4f82-a087-0ee36fdee614", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/28e06e51-4e92-4061-8aa2-71625d5e3402/enzymelink/6f5252e7-1642-4f82-a087-0ee36fdee614", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "ebd26035-cca4-4e66-841c-c9757207197f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/ebd26035-cca4-4e66-841c-c9757207197f"}], "edge_evidence": []}, {"uuid": "2d6bd5af-049b-4469-994b-7df26ed0c520", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/28e06e51-4e92-4061-8aa2-71625d5e3402/enzymelink/2d6bd5af-049b-4469-994b-7df26ed0c520", "ec_number": "1.14.13.236", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0013", "description": "monosubstituted Benzenoid → Add p-OH
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Comments:
Ring alkenes need at least one free hydrogen.", "aliases": [], "simple_rules": [{"uuid": "c63ea43c-326e-4525-ad3d-e82bed4c0940", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/c63ea43c-326e-4525-ad3d-e82bed4c0940"}], "scenarios": []}, {"uuid": "f115a438-2f11-4029-9b39-9ebcec64afdd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/f115a438-2f11-4029-9b39-9ebcec64afdd", "enzymes": [], "name": "bt0280", "description": "N-carboxylate Amide → Amide + CO2

Comments:
The enamine form of the amide N-carboxylate first tautomerizes.", "aliases": [], "simple_rules": [{"uuid": "dc8e990f-743d-4dec-8e57-285b75c08d4b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/dc8e990f-743d-4dec-8e57-285b75c08d4b"}], "scenarios": []}, {"uuid": "5e466030-4312-48a5-bb56-a505dba93eaa", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5e466030-4312-48a5-bb56-a505dba93eaa", "enzymes": [{"uuid": "1d4f1f76-132a-44a6-bb48-0b446a01890e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5e466030-4312-48a5-bb56-a505dba93eaa/enzymelink/1d4f1f76-132a-44a6-bb48-0b446a01890e", "ec_number": "3.5.5.7", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "bef96a0c-079b-43a1-a8ef-1564acb1eb3a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5e466030-4312-48a5-bb56-a505dba93eaa/enzymelink/bef96a0c-079b-43a1-a8ef-1564acb1eb3a", "ec_number": "3.5.5.4", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "57233076-f264-4fe0-a9a9-71b90f2340d8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5e466030-4312-48a5-bb56-a505dba93eaa/enzymelink/57233076-f264-4fe0-a9a9-71b90f2340d8", "ec_number": "3.5.5.6", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "f211f5f3-601d-4571-8c76-55e3edc2d742", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/f211f5f3-601d-4571-8c76-55e3edc2d742"}], "edge_evidence": []}, {"uuid": "b86c7a8b-1748-40b3-a852-76ed0d42b4f5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5e466030-4312-48a5-bb56-a505dba93eaa/enzymelink/b86c7a8b-1748-40b3-a852-76ed0d42b4f5", "ec_number": "3.5.5.2", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "e605bc4d-f393-4b34-9d87-21990b75c978", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5e466030-4312-48a5-bb56-a505dba93eaa/enzymelink/e605bc4d-f393-4b34-9d87-21990b75c978", "ec_number": "3.5.5.6", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "a710aaa8-f916-4727-90b6-1763c23f4903", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5e466030-4312-48a5-bb56-a505dba93eaa/enzymelink/a710aaa8-f916-4727-90b6-1763c23f4903", "ec_number": "3.5.5.7", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "796511dc-aaac-4d0e-b926-09e02b3acd44", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/796511dc-aaac-4d0e-b926-09e02b3acd44"}], "edge_evidence": []}, {"uuid": "ab565bbd-7b6c-46e6-a66c-5bd29fffaff0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5e466030-4312-48a5-bb56-a505dba93eaa/enzymelink/ab565bbd-7b6c-46e6-a66c-5bd29fffaff0", "ec_number": "3.5.5.5", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "5a12a6c6-e039-4bc1-84f7-cf0fe222a9b4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5e466030-4312-48a5-bb56-a505dba93eaa/enzymelink/5a12a6c6-e039-4bc1-84f7-cf0fe222a9b4", "ec_number": "3.5.5.1", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "6d915ffb-aca6-4356-b2f2-7e9e228bf786", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5e466030-4312-48a5-bb56-a505dba93eaa/enzymelink/6d915ffb-aca6-4356-b2f2-7e9e228bf786", "ec_number": "3.5.5.1", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "6dd553bf-1240-4cff-a19c-097a02136875", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/6dd553bf-1240-4cff-a19c-097a02136875"}, {"uuid": "f5611bb1-6674-449f-a7c4-90ac8f23c588", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/f5611bb1-6674-449f-a7c4-90ac8f23c588"}], "edge_evidence": []}], "name": "bt0030", "description": "Nitrile → Carboxylate

Comments:
This rule handles the hydrolysis of a nitrile to a carboxylate. Some such biotransformations involve a primary amide intermediate, which is bypassed in this rule for simplification.", "aliases": [], "simple_rules": [{"uuid": "912abb86-535d-4d1c-a65e-09ba906d8023", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/912abb86-535d-4d1c-a65e-09ba906d8023"}], "scenarios": []}, {"uuid": "8e1eb251-3dd9-4ed6-834d-41cca45da438", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8e1eb251-3dd9-4ed6-834d-41cca45da438", "enzymes": [], "name": "bt0428", "description": "4-Amino-1,2,4-triazinone derivative → 1,2,4-Triazione

Comments:
Photolytic cleavage, based on Cox, L., Hermosin, M.C., Cornejo, J. and Mansour, M. (1996) Chemosphere 33:2057-2064, and Parlar, H. and Korte, F. 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mono-halo-substituted Benzenoid → 1-halo-2,3-dihydroxy Benzenoid
mono-pseudohalo-substituted Benzenoid → 1-pseudohalo-2,3-dihydroxy Benzenoid

Comments:
This rule handles the 2,3-dioxygenation of mono-substituted aromatics (bt0369) and subsequent oxidation to form the catechol derivative (bt0255). The substituents are based on \"Reactions of Toluene Dioxygenase\" and Hudlicky T, Gonzalez D, Gibson DT (1999) Aldrichimica Acta 32(2): 35-62. 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Lactone → Hydroxycarboxylate

Comments:
Rule will produce cis products in rings with double bonds.", "aliases": [], "simple_rules": [{"uuid": "57d978b5-f55f-462e-a9dc-c5908d165973", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/57d978b5-f55f-462e-a9dc-c5908d165973"}], "scenarios": []}, {"uuid": "bd17ffb6-782f-4715-ae78-39b70fff73e0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/bd17ffb6-782f-4715-ae78-39b70fff73e0", "enzymes": [{"uuid": "e379500b-fa79-423f-ae16-144a4d34023e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/bd17ffb6-782f-4715-ae78-39b70fff73e0/enzymelink/e379500b-fa79-423f-ae16-144a4d34023e", "ec_number": "1.3.1.25", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "6f3ff733-758c-4101-a3bd-c2ed46a79fbc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/6f3ff733-758c-4101-a3bd-c2ed46a79fbc"}, {"uuid": "5751b4c0-92b1-4f6f-b40e-910ef4422dd4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/5751b4c0-92b1-4f6f-b40e-910ef4422dd4"}, {"uuid": "37b7c78b-e89a-41d4-a150-c6667545dd2a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/37b7c78b-e89a-41d4-a150-c6667545dd2a"}, {"uuid": "995381e1-a1fc-4428-ac35-b8f938dbc265", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/995381e1-a1fc-4428-ac35-b8f938dbc265"}], "edge_evidence": []}, {"uuid": "14ba60ab-5193-4fae-85a7-630d89553d30", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/bd17ffb6-782f-4715-ae78-39b70fff73e0/enzymelink/14ba60ab-5193-4fae-85a7-630d89553d30", "ec_number": "1.3.1.25", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "e55844c4-3871-4e2a-8ddf-e14c9f90e0c7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/bd17ffb6-782f-4715-ae78-39b70fff73e0/enzymelink/e55844c4-3871-4e2a-8ddf-e14c9f90e0c7", "ec_number": "1.3.1.53", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "8086ff75-f7ca-4a58-9410-94e0d33df5c7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/bd17ffb6-782f-4715-ae78-39b70fff73e0/enzymelink/8086ff75-f7ca-4a58-9410-94e0d33df5c7", "ec_number": "1.3.1.53", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "c333a58a-ef39-4c32-9cb9-6859e33baa50", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/c333a58a-ef39-4c32-9cb9-6859e33baa50"}], "edge_evidence": []}, {"uuid": "d930f865-2c15-4dbb-ab4c-06bfd929a9af", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/bd17ffb6-782f-4715-ae78-39b70fff73e0/enzymelink/d930f865-2c15-4dbb-ab4c-06bfd929a9af", "ec_number": "1.3.1.68", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "59836b2d-59b9-4058-9c50-f7ee95efc98e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/59836b2d-59b9-4058-9c50-f7ee95efc98e"}], "edge_evidence": []}, {"uuid": "bb7bbca1-5bf7-4cf7-8c3c-132529971793", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/bd17ffb6-782f-4715-ae78-39b70fff73e0/enzymelink/bb7bbca1-5bf7-4cf7-8c3c-132529971793", "ec_number": "1.3.1.67", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "b1f87ee5-853e-4b55-bfbb-51b0694839f5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/b1f87ee5-853e-4b55-bfbb-51b0694839f5"}], "edge_evidence": []}, {"uuid": "427d119e-f691-4a68-a471-d613ac02774d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/bd17ffb6-782f-4715-ae78-39b70fff73e0/enzymelink/427d119e-f691-4a68-a471-d613ac02774d", "ec_number": "1.3.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "61aa540a-9fa1-4cd3-ace3-d7dcd0b6cecf", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/61aa540a-9fa1-4cd3-ace3-d7dcd0b6cecf"}], "edge_evidence": []}], "name": "bt0055", "description": "1-carboxy-2-unsubstituted Aromatic → Catechol derivative

Comments:
This rule handles the dioxygenation of 1-carboxyl-2-unsubstituted aromatics (bt0368) and subsequent oxidation to form the catechol derivative (bt0056).This rule is restricted from acting on phthalate, cumate and 1-naphthoate derivatives. All fused aromatic ring products with hydroxyls at 2,3 position are excluded. All pyridines with N para to carboxylate have been excluded. 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1-Amino-2-hydroxybenzenoid → 2-Amino-2,4-dienoate derivate + Carboxylate

Comments:
This rule handles extradiol (meta) ring cleavage for vic-dihydroxybenzenoids and 1-amino-2-hydroxybenzenoids, including, but not limited to, 2,3-dihydroxybiphenyl derivatives, many PCB congeners (Pieper, 2005), 3- and 4-substituted chlorocatechols, 2-aminophenol, 2,3-dihydroxy DDT and its derivatives, 3- and 4-substituted alkyl catechols, diphenylether derivatives, and aromatized intermediates of steroid degradation (e.g., testosterone). It includes extradiol ring cleavage of vic-dihydroxybenzenoids (bt0008) and distal ring cleavage of 1-amino-2-hydroxybenzenoids (bt0041) to form 2-hydroxymuconate semialdehyde and 2-aminomuconate semialdehyde derivatives, respectively. 2-Aminomuconate semialdehyde derivatives undergoes hydrolytic deamination (bt0032) to form the 2-hydroxymuconate semialdehyde product. 3-Carboxyl catechols, such as 2,3-dihydroxy-p-cumate, undergo decarboxylation of the 3-carboxy group following meta cleavage. Hydrolysis of the C5-C6 bond (bt0040), or oxidation of the aldehyde to a carboxylate (bt0003), followed by decarboxylation (bt0051), produces a 2-amino-2,4-dienoate derivative or an enol product, which quickly tautomerizes to a 2-oxopent-4-enoate derivative. 2,3-Dihydroxybiphenyl derivatives are only cleaved at the side closest to the second phenyl ring. Rings are not cleaved next to the halogenated carbon in 3-halocatechol substrates. If the catechol substrate is not symmetric and its cleavage site preference is unknown, the compound is cleaved on both sides of the vic-dihydroxyl group.", "aliases": [], "simple_rules": [{"uuid": "75215cab-628b-458c-a030-96106743fc73", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/75215cab-628b-458c-a030-96106743fc73"}, {"uuid": "4d77dc1f-f081-4068-b913-8ed120c7c124", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/4d77dc1f-f081-4068-b913-8ed120c7c124"}, {"uuid": "9a4f6f28-6474-439d-9a68-018d234131f4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/9a4f6f28-6474-439d-9a68-018d234131f4"}, {"uuid": "6b4cab58-7bd2-48cf-b706-06463a7f7f29", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/6b4cab58-7bd2-48cf-b706-06463a7f7f29"}, {"uuid": "b44b1686-16f9-4c58-bf80-d22d218d3bc1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/b44b1686-16f9-4c58-bf80-d22d218d3bc1"}, {"uuid": "4889250a-599e-446e-afd2-73d0aaace57c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/4889250a-599e-446e-afd2-73d0aaace57c"}], "scenarios": []}, {"uuid": "5e626f6b-50d7-4dd1-b2d8-006af682d2d2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5e626f6b-50d7-4dd1-b2d8-006af682d2d2", "enzymes": [], "name": "bt0288", "description": "5-Hydroxy-3,4,4-trimethyl-delta2-pimelyl-CoA-delta-lactone → delta2,5-3,4,4-Trimethylpimelyl-CoA derivative

Comments:
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"http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e103aa1c-42c9-475f-be5a-19ea80774441", "enzymes": [], "name": "bt0386", "description": "N-(dichloromethyl)sulfanylaniline derivative → Aminobenzene derivative + Dichloromethylsulfide derivative
N-(dichloro-fluoromethyl)sulfanylaniline derivative → Aminobenzene derivative + Dichloro-fluoromethylsulfide derivative

Comments:
Based on the degradation of dichlofluanid (T.R. Roberts, ed., Metabolic Pathways of Agrochemicals, vol. 2, Royal Society of Chemistry (Great Britain), pp. 1359-1362, 1999). 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"http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/19b6e2fe-7f7a-4e2c-87d9-eed39b9ce641"}], "edge_evidence": []}], "name": "bt0337", "description": "Fatty acid (n) → Fatty acid (n-2)
Fatty acid (n) w C2-C3 double bond → Fatty acid (n-2)
Fatty acid (n) w C3 -OH → Fatty acid (n-2)
Fatty acid (n) w C3 -keto → Fatty acid (n-2)

Comments:
This rule handles beta oxidation, and includes addition of CoA to the fatty acid derivate, formation of a double bond between C2 and C3 (bt0341), hydration of this double bond to add -OH on C3 (bt0335), oxidation of this -OH to a keto group (bt0336), thiolytic cleavage of the acetate group (bt0161 and bt0338), and release of the CoA moiety. The rule handles microbial variant beta oxidation with methyl on C2, and beta oxidation intermediates, such as appropriate compounds with a double bond at C2-C3, -OH on C3, or keto on C3. The rule also handles the variant beta-oxidation of a compound with a cis-C2-C3 double bond seen in the alpha-pinene pathway (Griffith et al., 1987) and the cyclic variant seen in the limonene pathway (van der Werf et al., 1999), but not other intermediates in these two variants. The rule will NOT handle compounds containing oxygen on C4.", "aliases": [], "simple_rules": [{"uuid": "f3fe4bf8-2868-4554-9313-de35ec9ed294", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/f3fe4bf8-2868-4554-9313-de35ec9ed294"}, {"uuid": "69daaa4c-eb1b-4cd2-bd9a-4d5bca790aab", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/69daaa4c-eb1b-4cd2-bd9a-4d5bca790aab"}, {"uuid": "9a77dfbe-95f9-4b3f-9cdb-725e944d3795", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/9a77dfbe-95f9-4b3f-9cdb-725e944d3795"}, {"uuid": "42cfea39-5c69-432a-9ef3-10b92361f782", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/42cfea39-5c69-432a-9ef3-10b92361f782"}, {"uuid": "6cc16f56-2810-4213-80d1-470e5bb833dd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/6cc16f56-2810-4213-80d1-470e5bb833dd"}, {"uuid": "028eb9ac-af57-411d-9b2d-dee988a6f1a8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/028eb9ac-af57-411d-9b2d-dee988a6f1a8"}], "scenarios": []}, {"uuid": "e5287f29-96a8-4cef-97f9-9e449358e225", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e5287f29-96a8-4cef-97f9-9e449358e225", "enzymes": [{"uuid": "a2b7e3ad-f382-4d34-b0fc-d48fffc41f2a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e5287f29-96a8-4cef-97f9-9e449358e225/enzymelink/a2b7e3ad-f382-4d34-b0fc-d48fffc41f2a", "ec_number": "4.2.1.112", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "b532c1c4-a707-4fac-8569-5899fde86553", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/b532c1c4-a707-4fac-8569-5899fde86553"}], "edge_evidence": []}], "name": "bt0020", "description": "terminal Alkyne → Aldehyde", "aliases": [], "simple_rules": [{"uuid": "ddedfa9e-0412-4bad-a619-b24e5a825d84", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/ddedfa9e-0412-4bad-a619-b24e5a825d84"}], "scenarios": []}, {"uuid": "844a5686-d690-4384-a017-b2be535d3fb9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/844a5686-d690-4384-a017-b2be535d3fb9", "enzymes": [{"uuid": "c341c1ad-993c-40c5-8f78-e2f77ede93e6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/844a5686-d690-4384-a017-b2be535d3fb9/enzymelink/c341c1ad-993c-40c5-8f78-e2f77ede93e6", "ec_number": "1.14.13.40", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "18ee3f45-310f-4b64-9991-372ecb2d0cda", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/18ee3f45-310f-4b64-9991-372ecb2d0cda"}], "edge_evidence": []}], "name": "bt0212", "description": "5-unsubstituted 2-Aminobenzoyl-CoA derivative → 2-Amino-5-oxo-cyclohex-1-enecarboxy-CoA derivative

Comments:
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Comments:
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2-Nitropropane → Acetone + Nitrite

Comments:
Oxidative cleavage of nitroalkanes based on EC 1.7.3.1.", "aliases": [], "simple_rules": [{"uuid": "3553f1d3-c4ec-4a5e-bf1b-d6464e852dde", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/3553f1d3-c4ec-4a5e-bf1b-d6464e852dde"}, {"uuid": "337ba1a3-091f-4fc5-ad8a-39311d509970", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/337ba1a3-091f-4fc5-ad8a-39311d509970"}], "scenarios": []}, {"uuid": "01c80247-fdef-4dd8-bc92-4ff9f4a906f2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/01c80247-fdef-4dd8-bc92-4ff9f4a906f2", "enzymes": [], "name": "bt0345", "description": "2-Oxo-3-enoate-4-Carboxyaromatic → 2-Carboxybenzaldehyde derivative", "aliases": [], "simple_rules": [{"uuid": "4377de6e-c875-4f92-8f09-b2397fe4184d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/4377de6e-c875-4f92-8f09-b2397fe4184d"}], "scenarios": []}, {"uuid": "e54c9849-15bf-46aa-baa8-3d51e40a3709", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e54c9849-15bf-46aa-baa8-3d51e40a3709", "enzymes": [{"uuid": "48253fa7-d564-4483-93e1-4173f358d92f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e54c9849-15bf-46aa-baa8-3d51e40a3709/enzymelink/48253fa7-d564-4483-93e1-4173f358d92f", "ec_number": "3.13.1.4", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "a05124f1-e1f9-4480-8f00-586d345ae497", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e54c9849-15bf-46aa-baa8-3d51e40a3709/enzymelink/a05124f1-e1f9-4480-8f00-586d345ae497", "ec_number": "3.13.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "e11f4a6a-41e3-42f5-aea4-b153be6df1ee", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/e11f4a6a-41e3-42f5-aea4-b153be6df1ee"}], "edge_evidence": []}, {"uuid": "c4ac24bd-066c-4cbf-804f-15884ea31a71", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e54c9849-15bf-46aa-baa8-3d51e40a3709/enzymelink/c4ac24bd-066c-4cbf-804f-15884ea31a71", "ec_number": "3.13.1.3", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "9c12e6b2-6e8c-435c-bfbc-2703fa63f4f4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/9c12e6b2-6e8c-435c-bfbc-2703fa63f4f4"}, {"uuid": "edd7ef13-194b-4595-ac7b-25d4f0f358d8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/edd7ef13-194b-4595-ac7b-25d4f0f358d8"}], "edge_evidence": []}, {"uuid": "8f6dc28b-6b12-45d7-a75d-b14c96d4c289", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e54c9849-15bf-46aa-baa8-3d51e40a3709/enzymelink/8f6dc28b-6b12-45d7-a75d-b14c96d4c289", "ec_number": "4.1.1.12", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "0bc4753d-ec1f-42e3-9fbe-a1ab93e329f0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e54c9849-15bf-46aa-baa8-3d51e40a3709/enzymelink/0bc4753d-ec1f-42e3-9fbe-a1ab93e329f0", "ec_number": "3.13.1.3", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0195", "description": "substituted Sulfinate → Sulfite + RH

Comments:
Rule excludes sulfonate and thioamide S,S-dioxide substrates.", "aliases": [], "simple_rules": [{"uuid": "a6421ac6-2fb0-43e8-93dd-044d78f34fdd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/a6421ac6-2fb0-43e8-93dd-044d78f34fdd"}], "scenarios": []}, {"uuid": "5d2d495c-b1d5-4d98-b633-363d13bd7f04", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5d2d495c-b1d5-4d98-b633-363d13bd7f04", "enzymes": [], "name": "bt0348", "description": "[mono-, di-, or tri-halo]cis,cis-Muconate derivative → Succinate
tetrahalo-cis,cis-Muconate → Malonate
[2-halo]Maleylacetate derivative → Succinate
3,5-Dichloro-2-methylmuconate → 2-Methyl-3-oxoadipate

Comments:
This rule handles the cis,cis-muconate (ortho) pathway for the unsubstituted compound, those with a 3-sulfo or 3-carboxy, and most halo derivatives. Most information is found for chloro derivatives; Br and I derivatives are predicted to be degraded in the same way as the Cl derivatives. It includes cycloisomerization of the muconate derivative to form a enelactone (bt0098) or a dienelactone (bt0181 or bt0206), possible isomerization of the enelactone, hydrolysis to form maleylacetate (bt0313), reduction of the double bond (bt0149), addition of CoA, cleavage of acetyl-CoA or haloacetyl-CoA (bt0205), and removal of CoA to form the succinate product. The halide in haloacetate is hydrolytically cleaved to form glycolate. The 2,3,5-trihalodienelactone is predicted to form a halosuccinate, the halide of which is predicted to be hydrolytically cleaved to leave malate, by analogy to chloroacetate. The 2,3,5-trihalomuconate forms the 2,5-dihalodienelactone; further metabolism of this lactone is predicted based on the known metabolism of the 2,3,4,5-tetrachloromuconate. The removal of halogen, carboxyl, and sulfur side groups occurs at different stages of the pathway depending on the substrate (see graphic). 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N, N-disubstituted Amide → N-substituted Amide + Aldehyde or Ketone
N-substituted Urea derivative → Urea derivative + Aldehyde or Ketone
N,N-disubstituted Urea derivative → N-substituted Urea derivative + Aldehyde or Ketone

Comments:
Oxidative removal of an aliphatic R group from a secondary or tertiary urea or amide nitrogen. An aldehyde is produced if the leaving R group is attached through a primary carbon. A ketone is produced if the leaving R group is attached through a secondary carbon. Oxidative cleavage of the C-N bond in amides and ureas are covered by a single rule, since there is no chemical reason to divide them. Cleavage of urea derivatives occurs between the N and the C with the most positive partial charge. Rule will produce cis products in rings with double bonds.", "aliases": [], "simple_rules": [{"uuid": "bf030393-4fc7-40f1-aa21-e3a853ba26c8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/bf030393-4fc7-40f1-aa21-e3a853ba26c8"}], "scenarios": []}, {"uuid": "9ff4213d-5e20-4a94-b22b-c91f1639d229", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/9ff4213d-5e20-4a94-b22b-c91f1639d229", "enzymes": [{"uuid": "a8394b3b-d42b-449b-b6f4-ecf95df20f23", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/9ff4213d-5e20-4a94-b22b-c91f1639d229/enzymelink/a8394b3b-d42b-449b-b6f4-ecf95df20f23", "ec_number": "1.14.12.9", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "19c2aac4-15eb-4e82-b492-991058789b93", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/9ff4213d-5e20-4a94-b22b-c91f1639d229/enzymelink/19c2aac4-15eb-4e82-b492-991058789b93", "ec_number": "1.14.12.9", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "5312350b-0e3e-4d8e-9952-ce7a854942a6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/5312350b-0e3e-4d8e-9952-ce7a854942a6"}], "edge_evidence": []}], "name": "bt0366", "description": "4-Halophenylacetate derivative → 3,4-Dihydroxyphenylacetate derivative
3-Chlorophenylacetate derivative → 3,4-Dihydroxyphenylacetate derivative", "aliases": [], "simple_rules": [{"uuid": "490fc319-ab75-47f5-83af-25bac0f51aea", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/490fc319-ab75-47f5-83af-25bac0f51aea"}, {"uuid": "780fead9-d87b-4f1f-aff4-3529b9a1ce38", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/780fead9-d87b-4f1f-aff4-3529b9a1ce38"}], "scenarios": []}, {"uuid": "22366f72-49b6-43f7-a3fd-f6951b6e7756", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/22366f72-49b6-43f7-a3fd-f6951b6e7756", "enzymes": [{"uuid": "0504c813-b430-4a46-af38-c5c88e69d741", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/22366f72-49b6-43f7-a3fd-f6951b6e7756/enzymelink/0504c813-b430-4a46-af38-c5c88e69d741", "ec_number": "4.1.3.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "9ef7b87d-c65f-4250-bab3-ed03ca29fa39", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/9ef7b87d-c65f-4250-bab3-ed03ca29fa39"}], "edge_evidence": []}, {"uuid": "f0bc9267-86e6-4947-87cc-2e7d49eaf829", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/22366f72-49b6-43f7-a3fd-f6951b6e7756/enzymelink/f0bc9267-86e6-4947-87cc-2e7d49eaf829", "ec_number": "3.7.1.6", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "091619b8-cc9a-4a71-87e6-52f8081a8893", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/091619b8-cc9a-4a71-87e6-52f8081a8893"}], "edge_evidence": []}, {"uuid": "33e22543-8d33-44c2-b2ba-1e3d99d14d5f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/22366f72-49b6-43f7-a3fd-f6951b6e7756/enzymelink/33e22543-8d33-44c2-b2ba-1e3d99d14d5f", "ec_number": "4.1.2.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "ba89a68e-5c80-4f21-8be5-0213f6edc8d8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/ba89a68e-5c80-4f21-8be5-0213f6edc8d8"}], "edge_evidence": []}, {"uuid": "5adc23ed-a6b2-4b36-ac73-388449494bfa", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/22366f72-49b6-43f7-a3fd-f6951b6e7756/enzymelink/5adc23ed-a6b2-4b36-ac73-388449494bfa", "ec_number": "4.1.3.39", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "dd4f9543-1ba5-4381-ba4e-9a50f1e9d6d3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/dd4f9543-1ba5-4381-ba4e-9a50f1e9d6d3"}, {"uuid": "9712c1c8-07ff-4a30-bf55-c8f4c1b1274c", "url": 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enviLink", "reaction_evidence": [{"uuid": "d2ce765e-26b2-4b4c-898d-5938bada7cf5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/d2ce765e-26b2-4b4c-898d-5938bada7cf5"}], "edge_evidence": []}, {"uuid": "13dee875-291c-4a2c-89de-afae13c48e40", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/22366f72-49b6-43f7-a3fd-f6951b6e7756/enzymelink/13dee875-291c-4a2c-89de-afae13c48e40", "ec_number": "4.1.3.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "9c203b2f-c5e2-4951-878c-3986a4dd33de", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/9c203b2f-c5e2-4951-878c-3986a4dd33de"}], "edge_evidence": []}, {"uuid": "9f232e03-6d04-4b99-b7da-6368a36da90b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/22366f72-49b6-43f7-a3fd-f6951b6e7756/enzymelink/9f232e03-6d04-4b99-b7da-6368a36da90b", "ec_number": "4.1.2.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "1453319c-487d-4f52-8b9d-68e20392211f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/1453319c-487d-4f52-8b9d-68e20392211f"}], "edge_evidence": []}], "name": "bt0352", "description": "2-Oxopent-4-enoate derivative → Pyruvate derivative + Acetaldehyde or Ketone
1-Methyl-2-oxo derivative → Acetate + RH

Comments:
This rule is a continuation of the extradiol (meta) ring cleavage pathway and handles all 2-oxopent-4-enoate derivatives produced by bt0351. It includes hydration of the C4-C5 double bond (bt0021) to form a 4-hydroxy-2-oxopentanoate derivative and subsequent aldolytic cleavage (bt0043) of the C3-C4 bond to yield, in the case where C4 is unsubstituted, pyruvate and acetate derivatives. If C4 does contain a functional group, pyruvate and ketone derivatives will be formed. 5-Chloro-2-oxopent-4-enoate follows this pathway and produces pyruvate and chloroacetate, which undergoes hydrolytic dehalogenation (bt0022) to yield glycolate. This rule also handles intermediates, such as appropriate compounds with -OH on C4.", "aliases": [], "simple_rules": [{"uuid": "ab0c5b13-6e3d-4faa-b781-fc117271ec5d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/ab0c5b13-6e3d-4faa-b781-fc117271ec5d"}, {"uuid": "d026f34e-feb4-4037-9eca-0770ba585781", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/d026f34e-feb4-4037-9eca-0770ba585781"}, {"uuid": "e4bfe962-cfa8-47cb-beb9-d0c38efec095", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/e4bfe962-cfa8-47cb-beb9-d0c38efec095"}, {"uuid": "dcc910e8-df40-4a1b-8d34-ee3be620ae40", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/dcc910e8-df40-4a1b-8d34-ee3be620ae40"}, {"uuid": "87b0b664-d57f-45ee-8a3a-8caef8e6cd72", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/87b0b664-d57f-45ee-8a3a-8caef8e6cd72"}, {"uuid": "78cd18fe-e246-47b1-9e74-fe057bbb63cc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/78cd18fe-e246-47b1-9e74-fe057bbb63cc"}], "scenarios": []}, {"uuid": "f7116e10-308b-4b69-b11b-ee3374191d1f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/f7116e10-308b-4b69-b11b-ee3374191d1f", "enzymes": [{"uuid": "589d7b7c-fe87-4d86-b57f-9d300482f6ef", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/f7116e10-308b-4b69-b11b-ee3374191d1f/enzymelink/589d7b7c-fe87-4d86-b57f-9d300482f6ef", "ec_number": "1.14.12.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "237c3d37-0e1b-485b-ad25-635f4b17084f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/237c3d37-0e1b-485b-ad25-635f4b17084f"}], "edge_evidence": []}], "name": "bt0425", "description": "Saccharin → Catechol

Comments:
This rule handles dioxygenation and subsequent oxidation of saccharin resulting in the formation of catechol with release of sulfate, ammonium, and carbon dioxide (Schleheck and Cook, 2003).", "aliases": [], "simple_rules": [{"uuid": "71b025f4-51e4-4101-b69b-c71562b32509", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/71b025f4-51e4-4101-b69b-c71562b32509"}], "scenarios": []}, {"uuid": "af745278-4d2a-44bf-b74d-91e4716c8ce1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/af745278-4d2a-44bf-b74d-91e4716c8ce1", "enzymes": [{"uuid": "5f5184d2-4189-4e23-a2e4-f2207b44ae83", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/af745278-4d2a-44bf-b74d-91e4716c8ce1/enzymelink/5f5184d2-4189-4e23-a2e4-f2207b44ae83", "ec_number": "3.5.4.45", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": 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"ec_number": "3.5.4.42", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "553ad3f0-95ce-480c-9b05-db4b82afba2a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/553ad3f0-95ce-480c-9b05-db4b82afba2a"}], "edge_evidence": []}], "name": "bt0330", "description": "1-halo or 1-pseudohalo-s-Triazine → 1-hydroxy-s-Triazine

Comments:
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N,N-disubstituted Urea derivative → N-substituted Carbamate + primary Amine

Comments:
Rule will only act on linear urea derivatives and will cleave between the carbonyl and the nitrogen with the most positive partial charge.", "aliases": [], "simple_rules": [{"uuid": "6fc88bdf-db6e-40d3-874d-c47b5f823703", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/6fc88bdf-db6e-40d3-874d-c47b5f823703"}], "scenarios": []}, {"uuid": "b419db19-9005-462d-b99e-03fbdec17aab", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b419db19-9005-462d-b99e-03fbdec17aab", "enzymes": [{"uuid": "306e3632-e8cc-4bf9-8c94-00fbeed63791", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b419db19-9005-462d-b99e-03fbdec17aab/enzymelink/306e3632-e8cc-4bf9-8c94-00fbeed63791", "ec_number": "6.4.1.5", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "4bef8562-b95f-4bd2-918f-655ec0334014", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/4bef8562-b95f-4bd2-918f-655ec0334014"}], "edge_evidence": []}, {"uuid": "bf2f8b39-5620-420d-add9-51bbb8684b84", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b419db19-9005-462d-b99e-03fbdec17aab/enzymelink/bf2f8b39-5620-420d-add9-51bbb8684b84", "ec_number": "6.4.1.5", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0322", "description": "cis-2-ene-CoA thioester → Isohexenyl-glutaconyl-CoA

Comments:
CoA ligation to the terminal carboxyl group occurs prior to carboxylation but is bypassed in this rule for simplification.", "aliases": [], "simple_rules": [{"uuid": "bd417ab5-e08c-48d1-8df0-0b56d39df1f2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/bd417ab5-e08c-48d1-8df0-0b56d39df1f2"}], "scenarios": []}, {"uuid": "756c98ba-f2ff-4e72-9527-0d8574b3c25c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/756c98ba-f2ff-4e72-9527-0d8574b3c25c", "enzymes": [{"uuid": "cb170dd7-77ce-4488-b2ca-0b1d870b0d19", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/756c98ba-f2ff-4e72-9527-0d8574b3c25c/enzymelink/cb170dd7-77ce-4488-b2ca-0b1d870b0d19", "ec_number": "1.3.1.57", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "a01ebf2e-75dc-401b-ab64-18fc890efd23", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/a01ebf2e-75dc-401b-ab64-18fc890efd23"}], "edge_evidence": []}], "name": "bt0190", "description": "Phloroglucinol derivative → Dihydrophloroglucinol derivative", "aliases": [], "simple_rules": [{"uuid": "7b83f09b-5f36-4b0a-9b44-4bb99532d297", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/7b83f09b-5f36-4b0a-9b44-4bb99532d297"}], "scenarios": []}, {"uuid": "b21ce29b-20de-4d0c-ae1f-303da9087b4d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b21ce29b-20de-4d0c-ae1f-303da9087b4d", "enzymes": [{"uuid": "fd3737b3-cf79-4d1e-b2c8-4b31c97a42a3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b21ce29b-20de-4d0c-ae1f-303da9087b4d/enzymelink/fd3737b3-cf79-4d1e-b2c8-4b31c97a42a3", "ec_number": "1.14.13.43", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0418", "description": "Anthrone derivative → 2-[(2-Hydroxyphenyl)methyl]benzoate derivative
Anthrone derivative → 2-Hydroxybenzoylacrylate derivative

Comments:
This rule handles Baeyer-Villiger oxidation (bt0071) of anthrone derivatives and subsequent hydrolysis of the cyclic ester (bt0024). This rule is needed because the partial aromatic nature of the BV oxidation product does not permit its hydrolysis by bt0024. The oxidation and cleavage occurs between the carbonyl carbon and neighboring carbon with the biggest sigma charge.", "aliases": [], "simple_rules": [{"uuid": "1aac16e1-1943-4dd2-b9d6-a035b802c121", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/1aac16e1-1943-4dd2-b9d6-a035b802c121"}, {"uuid": "69f03ac6-5348-4261-a0d9-4637f86245c0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/69f03ac6-5348-4261-a0d9-4637f86245c0"}], "scenarios": []}, {"uuid": "dec2f6b4-8ee6-40ba-be39-a4367b0619bc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/dec2f6b4-8ee6-40ba-be39-a4367b0619bc", "enzymes": [], "name": "bt0435", "description": "Thiol → RH + H2S

Comments:
Reductive desulfurization of an HS-C group based on Miller et al. (1992) and Hebting et al. 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"description": "aliphatic Phosphoester → Alcohol
aliphatic Phosphodiester → Alcohol + aliphatic Phosphoester
aliphatic Phosphotriester → Alcohol + aliphatic Phosphodiester
aliphatic Thiophosphoester → Alcohol + aliphatic Thiophospate

Comments:
Hydrolysis of phosphate esters. Depending on compound and environment, some of these may be spontaneous. Others are catalyzed by microbial phosphatases, such as alkaline phosphatase (EC 3.1.3.1), acid phosphatase (EC 3.1.3.2), and organophosphate hydrolase (EC 3.1.8.1) This rule also handles thiophosphoester derivatives.", "aliases": [], "simple_rules": [{"uuid": "6cc072c7-22a5-4206-a0d3-c72d93fbf8ff", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/6cc072c7-22a5-4206-a0d3-c72d93fbf8ff"}], "scenarios": []}, {"uuid": "b330946e-f8a9-4860-86c5-1953f230c837", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b330946e-f8a9-4860-86c5-1953f230c837", "enzymes": [{"uuid": "1f611528-0d5d-47ca-9c41-b16703c98f60", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b330946e-f8a9-4860-86c5-1953f230c837/enzymelink/1f611528-0d5d-47ca-9c41-b16703c98f60", "ec_number": "1.14.15.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "260abeec-26f7-470c-9bfc-6602edf4d653", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/260abeec-26f7-470c-9bfc-6602edf4d653"}, {"uuid": "26695429-ca3e-4308-98a9-95f72619b63d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/26695429-ca3e-4308-98a9-95f72619b63d"}], "edge_evidence": []}, {"uuid": "a9b1ac5d-fbe5-4404-9592-325d88cf806c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b330946e-f8a9-4860-86c5-1953f230c837/enzymelink/a9b1ac5d-fbe5-4404-9592-325d88cf806c", "ec_number": "1.14.15.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "d33a6604-f8b1-41e1-aafc-638091af8cd7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/d33a6604-f8b1-41e1-aafc-638091af8cd7"}], "edge_evidence": []}], "name": "bt0339", "description": "N-aliphatic-s-triazine → Amino-s-triazine", "aliases": [], "simple_rules": [{"uuid": "2dce8433-b77e-4094-bb5b-8f030c954381", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/2dce8433-b77e-4094-bb5b-8f030c954381"}], "scenarios": []}, {"uuid": "8c7e68a3-ba32-4cd6-98e4-784d5e9dd3fd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8c7e68a3-ba32-4cd6-98e4-784d5e9dd3fd", "enzymes": [{"uuid": "3b82c519-d6c6-41c4-bbb8-557151a55580", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8c7e68a3-ba32-4cd6-98e4-784d5e9dd3fd/enzymelink/3b82c519-d6c6-41c4-bbb8-557151a55580", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "15da0ed5-7988-4629-8b33-67eb2f525c90", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/15da0ed5-7988-4629-8b33-67eb2f525c90"}], "edge_evidence": []}, {"uuid": "bd5ddc30-5fc1-4981-b433-725ecf28f504", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8c7e68a3-ba32-4cd6-98e4-784d5e9dd3fd/enzymelink/bd5ddc30-5fc1-4981-b433-725ecf28f504", "ec_number": "1.8.1.3", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "71cad392-32bc-43dc-bc79-8b58aab06e26", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8c7e68a3-ba32-4cd6-98e4-784d5e9dd3fd/enzymelink/71cad392-32bc-43dc-bc79-8b58aab06e26", "ec_number": "1.8.1.17", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "e024e842-cc76-4446-9aac-cd456763f4be", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8c7e68a3-ba32-4cd6-98e4-784d5e9dd3fd/enzymelink/e024e842-cc76-4446-9aac-cd456763f4be", "ec_number": "1.14.14.1", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "7ca24759-b08e-4931-b10d-e7b8b61fee88", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/7ca24759-b08e-4931-b10d-e7b8b61fee88"}], "edge_evidence": []}, {"uuid": "9f5399a9-824a-463f-bebc-ea74e2b199f9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8c7e68a3-ba32-4cd6-98e4-784d5e9dd3fd/enzymelink/9f5399a9-824a-463f-bebc-ea74e2b199f9", "ec_number": "1.14.13.245", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0193", "description": "di-[C,O]-substituted Sulfoxide → di-[C,O]-substituted Sulfone

Comments:
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Comments:
Based on Grogan (2005), Straganz et al. 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"http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5f07518c-501f-4e70-bb0a-1bca4f34ebb1/enzymelink/e85b8ba6-e883-4e16-81c1-4b7863479915", "ec_number": "1.13.11.35", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0254", "description": "vic-Dihydroxyaromatic → intradiol ring cleavage
vic-Dihydroxypyridine → intradiol ring cleavage

Comments:
This rule does not handle 2,3-dihydroxy linear polyaromatics such as 2,3-dihydroxynaphthalene, 3-methylcatechol, 3-sulfocatechol, 3-fluorocatechol, 4-C-substituted catechol, 3,4-dihydroxyphenylacetate or 2,3,5-trihydroxytoluene derivatives. Though certain compounds are predicted as being cleaved exclusively by an intradiol or by an extradiol pathway, this does not mean that they can never be cleaved by the other pathway in certain environments or by certain organisms.", "aliases": [], "simple_rules": [{"uuid": "dc32ffa4-bb0b-4649-b9f0-828768ab2804", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/dc32ffa4-bb0b-4649-b9f0-828768ab2804"}, {"uuid": "b78d1fba-9140-4af6-885f-8c3c4edfe1e7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/b78d1fba-9140-4af6-885f-8c3c4edfe1e7"}], "scenarios": []}, {"uuid": "5d21a92d-9298-4af5-8a1b-aebd66424c26", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5d21a92d-9298-4af5-8a1b-aebd66424c26", "enzymes": [{"uuid": "ef9a75cc-ea11-4f5d-97f7-7d4431cda63e", "url": 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"http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8536cec5-c0ed-47ee-b68b-e347d01d8991/enzymelink/8ff9a367-b57b-4b81-a28c-68953e77d40f", "ec_number": "1.13.11.86", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0184", "description": "2-Hydroxy-5-aminobenzoate derivate → 4-Amino-6-oxohepta-2,4-dienedioate derivative
2-Hydroxy-5-nitrobenzoate derivative → 4-Nitro-6-oxohepta-2,4-dienedioate derivative
Hydroxy-2-naphthoate → 6-Carboxy-2,4-dien-2-oxoproponate benzyl derivative", "aliases": [], "simple_rules": [{"uuid": "f631e909-ddf7-4043-92e3-3db4c7d6517b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/f631e909-ddf7-4043-92e3-3db4c7d6517b"}, {"uuid": "f6a47b2f-ac19-4cff-bfef-d0faeac7fcfd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/f6a47b2f-ac19-4cff-bfef-d0faeac7fcfd"}], "scenarios": []}, {"uuid": "8d196920-1ab2-419d-baee-bcc9cb0b9bd9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8d196920-1ab2-419d-baee-bcc9cb0b9bd9", "enzymes": [{"uuid": "b0ba505f-930e-46cf-9b25-837fd29385a6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8d196920-1ab2-419d-baee-bcc9cb0b9bd9/enzymelink/b0ba505f-930e-46cf-9b25-837fd29385a6", "ec_number": "3.1.8.2", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "ab76dc03-f53a-4b12-8ec1-af19bfce841d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8d196920-1ab2-419d-baee-bcc9cb0b9bd9/enzymelink/ab76dc03-f53a-4b12-8ec1-af19bfce841d", "ec_number": "3.1.8.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "4a0e81df-9603-4765-a9e9-799eb08ca30e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/4a0e81df-9603-4765-a9e9-799eb08ca30e"}], "edge_evidence": []}, {"uuid": "6eed35eb-d387-414d-8662-6e40adf03118", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8d196920-1ab2-419d-baee-bcc9cb0b9bd9/enzymelink/6eed35eb-d387-414d-8662-6e40adf03118", "ec_number": "3.1.8.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "8a3a7181-0c2f-4563-883d-49b791093678", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/8a3a7181-0c2f-4563-883d-49b791093678"}], "edge_evidence": []}, {"uuid": "9b39ee36-5139-446a-b103-8fffd2368659", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8d196920-1ab2-419d-baee-bcc9cb0b9bd9/enzymelink/9b39ee36-5139-446a-b103-8fffd2368659", "ec_number": "3.1.8.1", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "f01c7058-732f-4366-8c53-1666ae5f10fc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/f01c7058-732f-4366-8c53-1666ae5f10fc"}], "edge_evidence": []}], "name": "bt0432", "description": "Phosphonofluoridate derivative → Phosphonate derivative
Phosphorofluoridate derivative → Phosphate derivative
Thiophosphate derivative → Phosphate derivative + Thiol
Cyanophosphate derivative → Phosphate derivative + cyanide

Comments:
Based on Singh & Walker, 2006 and Lai et al., 1995.", "aliases": [], "simple_rules": [{"uuid": "6b035440-129a-4423-ad9e-8a72101b3bea", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/6b035440-129a-4423-ad9e-8a72101b3bea"}], "scenarios": []}, {"uuid": "99bef257-71ca-4804-8cfb-12f120bb7cd1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/99bef257-71ca-4804-8cfb-12f120bb7cd1", "enzymes": [{"uuid": "ebc0a318-d29d-408c-a50b-f1509763121d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/99bef257-71ca-4804-8cfb-12f120bb7cd1/enzymelink/ebc0a318-d29d-408c-a50b-f1509763121d", "ec_number": "3.9.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "5d7033cf-895b-4014-8ce7-18484802ae9b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/5d7033cf-895b-4014-8ce7-18484802ae9b"}], "edge_evidence": []}, {"uuid": "d8a5fc4b-0138-4a3f-84bb-83274281e0b6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/99bef257-71ca-4804-8cfb-12f120bb7cd1/enzymelink/d8a5fc4b-0138-4a3f-84bb-83274281e0b6", "ec_number": "3.9.1.1", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0440", "description": "Phosphoramidate derivative → Phosphate + Amine", "aliases": [], "simple_rules": [{"uuid": "fe8f3f49-b487-44f0-8c88-3b61b770f630", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/fe8f3f49-b487-44f0-8c88-3b61b770f630"}], "scenarios": []}, {"uuid": "ef91bf96-59f2-479b-ae6f-d88f2935b09a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/ef91bf96-59f2-479b-ae6f-d88f2935b09a", "enzymes": [{"uuid": "9bd76d16-7976-442a-947f-6519251a75cb", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/ef91bf96-59f2-479b-ae6f-d88f2935b09a/enzymelink/9bd76d16-7976-442a-947f-6519251a75cb", "ec_number": "3.8.1.7", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "3d565108-13cf-4c2b-817a-a95b1b849c52", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/ef91bf96-59f2-479b-ae6f-d88f2935b09a/enzymelink/3d565108-13cf-4c2b-817a-a95b1b849c52", "ec_number": "3.8.1.7", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "44b6f3bc-e3f6-4707-af2c-17d5f2527e0d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/44b6f3bc-e3f6-4707-af2c-17d5f2527e0d"}, {"uuid": "a153d091-e9ea-4009-97ae-d4327ed596dd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/a153d091-e9ea-4009-97ae-d4327ed596dd"}], "edge_evidence": []}, {"uuid": "ad9cfc54-0e71-4676-bd92-e90904a226ad", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/ef91bf96-59f2-479b-ae6f-d88f2935b09a/enzymelink/ad9cfc54-0e71-4676-bd92-e90904a226ad", "ec_number": "1.14.13.50", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "f0920a31-29b2-4dad-8621-3817b3c572b8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/f0920a31-29b2-4dad-8621-3817b3c572b8"}], "edge_evidence": []}, {"uuid": "36ae0f46-efa9-45e2-9cdf-da2ceeb7f003", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/ef91bf96-59f2-479b-ae6f-d88f2935b09a/enzymelink/36ae0f46-efa9-45e2-9cdf-da2ceeb7f003", "ec_number": "3.8.1.6", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "12bddd0b-0457-4d20-8fe0-ca4f3dc96f39", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/ef91bf96-59f2-479b-ae6f-d88f2935b09a/enzymelink/12bddd0b-0457-4d20-8fe0-ca4f3dc96f39", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "fbe3306b-8324-40a5-8fc5-58d96b072fb7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/fbe3306b-8324-40a5-8fc5-58d96b072fb7"}, {"uuid": "6ec8156b-0187-4881-9588-d4255d631739", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/6ec8156b-0187-4881-9588-d4255d631739"}], "edge_evidence": []}], "name": "bt0359", "description": "4-Halophenol derivative → Hydroquinone derivative
4-Halobenzoate derivative → 4-Hydroxybenzoate derivative

Comments:
This rule handles hydrolytic dehalogenation of 4-halogenated benzoates and oxidative dehalogenation of 4-halogenated phenols. Halobenzoate derivatives add CoA to form the thioester before dehalogenation but this step is bypassed for simplification.", "aliases": [], "simple_rules": [{"uuid": "10b20b9f-e9b0-41ba-94d4-d422247a0ac5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/10b20b9f-e9b0-41ba-94d4-d422247a0ac5"}], "scenarios": []}, {"uuid": "d48a18f0-2f8f-43af-b741-2984903eb4d7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d48a18f0-2f8f-43af-b741-2984903eb4d7", "enzymes": [{"uuid": "e94f1231-0cc2-4254-ab88-27193a99d6a6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d48a18f0-2f8f-43af-b741-2984903eb4d7/enzymelink/e94f1231-0cc2-4254-ab88-27193a99d6a6", "ec_number": "3.5.1.116", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "c311b5fd-3e78-48f0-8c7f-652286a40f2c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d48a18f0-2f8f-43af-b741-2984903eb4d7/enzymelink/c311b5fd-3e78-48f0-8c7f-652286a40f2c", "ec_number": "4.3.2.3", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0219", "description": "Hemiaminal → Amine + Aldehyde
Hydroxyaminal → Amine + Amide", "aliases": [], "simple_rules": [{"uuid": "9c2b6ebf-25e8-4b71-ae3d-614653059c01", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/9c2b6ebf-25e8-4b71-ae3d-614653059c01"}], "scenarios": []}, {"uuid": "6af75e9a-3cfc-42ef-9415-dd03a39c0666", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/6af75e9a-3cfc-42ef-9415-dd03a39c0666", "enzymes": [{"uuid": "d428b2cf-84bf-4b86-bf05-8ee584cded14", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/6af75e9a-3cfc-42ef-9415-dd03a39c0666/enzymelink/d428b2cf-84bf-4b86-bf05-8ee584cded14", "ec_number": "3.5.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "e9dadd3d-a7f6-4355-82ee-a63361dda41c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/e9dadd3d-a7f6-4355-82ee-a63361dda41c"}], "edge_evidence": []}], "name": "bt0404", "description": "1,2,4-Triazinone derivative → Hydrazonoethanoate derivative

Comments:
This rule handles the hydrolysis of a 1,2,4-triazinone derivative to the corresponding hydrazone. A second hydrolysis step eliminates the amine or hydrazine at the 4 position to yield the hydrazonoethanoate derivative.", "aliases": [], "simple_rules": [{"uuid": "db1e2cbc-d8da-46d4-bf5b-9403f5e744b3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/db1e2cbc-d8da-46d4-bf5b-9403f5e744b3"}], "scenarios": []}, {"uuid": "a6d72e1c-5352-4b6c-b3bb-98c119855c5d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a6d72e1c-5352-4b6c-b3bb-98c119855c5d", "enzymes": [{"uuid": "203d748e-3be1-4216-80c2-c7d1ff210bc1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a6d72e1c-5352-4b6c-b3bb-98c119855c5d/enzymelink/203d748e-3be1-4216-80c2-c7d1ff210bc1", "ec_number": "1.14.13.10", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "f98c59e0-8ceb-4747-a3ed-132c9992ee52", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/f98c59e0-8ceb-4747-a3ed-132c9992ee52"}], "edge_evidence": []}, {"uuid": "88fa06cb-b5a7-4246-b960-e1ad89828e4a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a6d72e1c-5352-4b6c-b3bb-98c119855c5d/enzymelink/88fa06cb-b5a7-4246-b960-e1ad89828e4a", "ec_number": "1.14.13.10", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0372", "description": "2,6-Dihydroxypyridine derivative → 2,3,6-Trihydroxypyridine derivative", "aliases": [], "simple_rules": [{"uuid": "55eda6c4-ef6c-4c21-ad44-ac5f07e76288", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/55eda6c4-ef6c-4c21-ad44-ac5f07e76288"}], "scenarios": []}, {"uuid": "b85cbb98-7cd1-45c0-be20-ffa3e9e292e8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b85cbb98-7cd1-45c0-be20-ffa3e9e292e8", "enzymes": [{"uuid": "b16471c5-ba0e-4557-bb56-f3cb5aa26f72", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b85cbb98-7cd1-45c0-be20-ffa3e9e292e8/enzymelink/b16471c5-ba0e-4557-bb56-f3cb5aa26f72", "ec_number": "3.5.99.8", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "58494dd8-b697-4359-bff8-879b074ee42f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b85cbb98-7cd1-45c0-be20-ffa3e9e292e8/enzymelink/58494dd8-b697-4359-bff8-879b074ee42f", "ec_number": "1.10.3.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "c17be7df-8293-46a9-9494-53d13fbfaa84", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/c17be7df-8293-46a9-9494-53d13fbfaa84"}], "edge_evidence": []}, {"uuid": "d6c6e425-5c9b-45d6-bea8-fcbf02e5129c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b85cbb98-7cd1-45c0-be20-ffa3e9e292e8/enzymelink/d6c6e425-5c9b-45d6-bea8-fcbf02e5129c", "ec_number": "3.5.99.8", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "83680653-34cc-4dbd-91c1-7316535c9925", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/83680653-34cc-4dbd-91c1-7316535c9925"}], "edge_evidence": []}, {"uuid": "b518ffe7-cd61-48a5-95c4-2de94cbcef91", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b85cbb98-7cd1-45c0-be20-ffa3e9e292e8/enzymelink/b518ffe7-cd61-48a5-95c4-2de94cbcef91", "ec_number": "1.10.3.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "a4e0aae1-4351-4ea6-a6cc-f84154db9965", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/a4e0aae1-4351-4ea6-a6cc-f84154db9965"}], "edge_evidence": []}], "name": "bt0388", "description": "4-Aminophenol derivative → 1,4-Dihydroxybenzenoid
4-Nitroaniline derivative → 4-Nitrophenol derivative
2-Aminophenol derivative → vic-Dihydroxybenzenoid
3-Aminophenol derivative → 1,3-Dihydroxybenzenoid
o-Benzoquinone derivative → vic-Dihydroxybenzenoid

Comments:
This rule handles the aminophenol pathway. It includes initial oxidation followed by rapid hydrolysis of an o-, m- or p-aminophenol derivative to form an o-, m- or p-benzoquinone, respectively (bt0105). The p-benzoquinone intermediate is quickly reduced to a 1,4-dihydroxybenzenoid (bt0107), while the o-benzoquinone intermediate is similarly reduced to a vic-dihydroxybenzenoid. This rule handles the known benzoquinone intermediates in this pathway, based on Zhao et al., 2000 and Kutty et al., 2000. This rule also handles the 5-nitroanthranilate amidohydrolase reaction, which might include a transient benzoquinone intermediate, based on Qu and Spain (2010).", "aliases": [], "simple_rules": [{"uuid": "bae44e51-7985-4f38-9abb-84410a0723c3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/bae44e51-7985-4f38-9abb-84410a0723c3"}, {"uuid": "10425859-003d-4a3a-9fcb-f3a2cc56c7d0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/10425859-003d-4a3a-9fcb-f3a2cc56c7d0"}, {"uuid": "3eca53ce-9199-492c-bbad-7f10a76443f6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/3eca53ce-9199-492c-bbad-7f10a76443f6"}], "scenarios": []}, {"uuid": "9194577d-2653-483b-a596-c81610941598", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/9194577d-2653-483b-a596-c81610941598", "enzymes": [{"uuid": "76122f78-23c0-4430-88fc-28eac10ac499", 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Comments:
Baeyer-Villiger oxidation of saturated rings. Based on M. D. 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"bt0064", "description": "1-Hydroxy-4-unsubstituted benzenoid → 1,4-Dihydroxybenzenoid derivative

Comments:
This rule is excluded from acting on catechols, polynuclear aromatics and mono-substituted phenols with R= -CH2CH2CH3 or -OCH2CH4.", "aliases": [], "simple_rules": [{"uuid": "f2d84038-66a1-44cb-a73e-946a9d7c9115", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/f2d84038-66a1-44cb-a73e-946a9d7c9115"}], "scenarios": []}, {"uuid": "172b09d2-03b1-4dbb-bfd4-19436b012052", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/172b09d2-03b1-4dbb-bfd4-19436b012052", "enzymes": [], "name": "bt0103", "description": "Thiophosphate diester → Phosphate diester
Thiophosphate triester → Phosphate triester
Dithiophosphate diester → Thiophosphate diester", "aliases": [], "simple_rules": [{"uuid": "47c6247e-14e5-41bb-8a32-a36e9d0ad1ae", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/47c6247e-14e5-41bb-8a32-a36e9d0ad1ae"}, {"uuid": "a1698922-cc9a-4bf5-9e9f-003a93af1b80", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/a1698922-cc9a-4bf5-9e9f-003a93af1b80"}], "scenarios": []}, {"uuid": "36eb565f-51c9-47fb-842e-3956e8a3dc0f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/36eb565f-51c9-47fb-842e-3956e8a3dc0f", "enzymes": [{"uuid": "b1050eaf-a39f-40e3-812d-48e593a9b557", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/36eb565f-51c9-47fb-842e-3956e8a3dc0f/enzymelink/b1050eaf-a39f-40e3-812d-48e593a9b557", "ec_number": "1.14.13.58", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0012", "description": "monosubstituted Benzenoid → Add m-OH
substituted Pyridine → Add m-OH", "aliases": [], "simple_rules": [{"uuid": "91ab65c9-55ec-4503-a1b9-c6ce3d08a752", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/91ab65c9-55ec-4503-a1b9-c6ce3d08a752"}, {"uuid": "5dad6444-3366-417d-8360-31ca020597ef", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/5dad6444-3366-417d-8360-31ca020597ef"}], "scenarios": []}, {"uuid": "b3fdcd55-2508-48b1-9f95-9b1d846b6531", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b3fdcd55-2508-48b1-9f95-9b1d846b6531", "enzymes": [{"uuid": "92dd0783-dbd1-40f1-afb5-85372affb7e3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b3fdcd55-2508-48b1-9f95-9b1d846b6531/enzymelink/92dd0783-dbd1-40f1-afb5-85372affb7e3", "ec_number": "1.3.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "2adaa9d4-2531-4bef-8493-4268aebe0100", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2adaa9d4-2531-4bef-8493-4268aebe0100"}], "edge_evidence": []}], "name": "bt0320", "description": "substituted Cyclohexanone → substituted Cyclohexenone", "aliases": [], "simple_rules": [{"uuid": "153c207c-6b68-405f-833e-cd25f0ec0913", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/153c207c-6b68-405f-833e-cd25f0ec0913"}], "scenarios": []}, {"uuid": "123171e1-c100-4ada-a0b2-db1d2abe1d76", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/123171e1-c100-4ada-a0b2-db1d2abe1d76", "enzymes": [], "name": "bt0391", "description": "primary Imine → Aldehyde
cyclic Imine → Ketone + Amine

Comments:
This rule acts on all primary and cyclic imine groups not part of an aromatic system. 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Comments:
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Comments:
Based on Bruland et al., 2009. 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Comments:
This rule handles the dioxygenation of vic-unsubstituted aromatics (bt0367) and subsequent oxidation to form the catechol derivative (bt0255).When there is more than one potential site of dioxygenation, all possible positions are given. All fused aromatic ring products with hydroxyl at 2,3 position are excluded. The aromatic hydrocarbon dioxygenases produce an activated dioxygen species that is thought to be sufficiently reactive to potentially functionalize most, if not all, aromatic ring carbon atoms (Lipscomb and Hoffman, 2005). Commonly, the position of dioxygenation will be determined by the orientation of the ring(s) in the enzyme's active site, which cannot be predicted. This rule does not act on heterocyclic aromatic rings except for some pyridines, and does not act on many aromatic carboxylates.", "aliases": [], "simple_rules": [{"uuid": "bffc454d-c2a0-4726-9cbd-45a801526b39", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/bffc454d-c2a0-4726-9cbd-45a801526b39"}, {"uuid": "333e9050-8a30-4af0-9f64-881ab5bd4598", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/333e9050-8a30-4af0-9f64-881ab5bd4598"}], "scenarios": []}, {"uuid": "9e3e8600-124c-4533-ab67-f2fe91c2692a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/9e3e8600-124c-4533-ab67-f2fe91c2692a", "enzymes": [{"uuid": "04b0fad9-3b2c-43f3-80ef-4d794f2cc475", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/9e3e8600-124c-4533-ab67-f2fe91c2692a/enzymelink/04b0fad9-3b2c-43f3-80ef-4d794f2cc475", "ec_number": "1.14.12.12", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "cb98c6a4-6f79-49b2-a06e-a646fe2080f6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/cb98c6a4-6f79-49b2-a06e-a646fe2080f6"}], "edge_evidence": []}], "name": "bt0416", "description": "vic-Dihydronaphthalene derivative → vic-Dihydroxytetrahydronaphthalene derivative

Comments:
This rule also produces vic-dihydrodiols for the substrates benzothiophene, benzofuran, indene, and indole. 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Comments:
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"reaction_evidence": [{"uuid": "e42bf9ad-b03e-45bf-813c-9cce5c8d7dbb", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/e42bf9ad-b03e-45bf-813c-9cce5c8d7dbb"}], "edge_evidence": []}], "name": "bt0023", "description": "dialiphatic Ether → Alcohol + Aldehyde
aromatic-aliphatic Ether → Phenol derivative + Aldehyde

Comments:
Does NOT handle ethers when the vincinal carbons are halogenated. When given an aromatic-aliphatic ether, Ar-O-R1, it will produce ArOH + R1CHO. When given a dialiphatic ether, R1-O-R2, it will produce both R1-OH + R2CHO, and R2-OH + R1-CHO. This rule will only act on ring ethers containing tertiary or quartiary carbon atoms neighboring the oxygen. It will not act on a diaromatic ether, Ar1-O-Ar2. Rule is blocked from acting on CoA.", "aliases": [], "simple_rules": [{"uuid": "cf2bc731-6b0c-4f1d-b192-8e859d9505aa", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/cf2bc731-6b0c-4f1d-b192-8e859d9505aa"}, {"uuid": "9ddddabb-4277-4324-a095-6ac834976dcd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/9ddddabb-4277-4324-a095-6ac834976dcd"}], "scenarios": []}, {"uuid": "059117ad-2172-4490-bcb9-8a4c1996f96c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/059117ad-2172-4490-bcb9-8a4c1996f96c", "enzymes": [{"uuid": "37040011-0007-4d5c-8e84-434e9fac13e9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/059117ad-2172-4490-bcb9-8a4c1996f96c/enzymelink/37040011-0007-4d5c-8e84-434e9fac13e9", "ec_number": "1.7.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "dcbb08f1-8ddf-4d0a-9c7e-f38d6f5811e4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/dcbb08f1-8ddf-4d0a-9c7e-f38d6f5811e4"}], "edge_evidence": []}, {"uuid": "c7ab9c8c-0c50-4cc2-a101-c28540477c82", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/059117ad-2172-4490-bcb9-8a4c1996f96c/enzymelink/c7ab9c8c-0c50-4cc2-a101-c28540477c82", "ec_number": "1.7.1.6", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "bf13fd76-65da-4420-ae6d-16ae39e15c04", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/bf13fd76-65da-4420-ae6d-16ae39e15c04"}], "edge_evidence": []}], "name": "bt0146", "description": "Diazene → RNH2 + R'NH2", "aliases": [], "simple_rules": [{"uuid": "4ee6f515-41dc-492e-843e-f593b0fb8223", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/4ee6f515-41dc-492e-843e-f593b0fb8223"}], "scenarios": []}, {"uuid": "58092f0b-fc7e-40fe-bc0a-b2644dac5f14", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/58092f0b-fc7e-40fe-bc0a-b2644dac5f14", "enzymes": [], "name": "bt0379", "description": "vic-Dihalogenated cyclohexane derivative → Cyclohexene derivative

Comments:
This rule handles the reductive elimination of two halogens to form a double bond on halogenated derivatives of cyclohexane, cyclohexene and cyclohexadiene.", "aliases": [], "simple_rules": [{"uuid": "1dca2441-6dbf-4b0e-a130-bd84c965d724", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/1dca2441-6dbf-4b0e-a130-bd84c965d724"}], "scenarios": []}, {"uuid": "ae6729d5-16f0-43be-9585-850b00127c81", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/ae6729d5-16f0-43be-9585-850b00127c81", "enzymes": [], "name": "bt0286", "description": "Alkylsulfonic acid derivative → Aldehyde + Sulfurous acid", "aliases": [], "simple_rules": [{"uuid": "74762408-0e93-4162-9bce-ab52e72815a1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/74762408-0e93-4162-9bce-ab52e72815a1"}], "scenarios": []}, {"uuid": "502bbc55-c591-44cb-a7af-473bc1c1228a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/502bbc55-c591-44cb-a7af-473bc1c1228a", "enzymes": [], "name": "bt0333", "description": "aliphatic Methyl [H1] → primary Alcohol

Comments:
This rule handles aliphatic methyl groups where the alpha carbon has one hydrogen atom attached to it.", "aliases": [], "simple_rules": [{"uuid": "adba3e70-1098-4a85-8fb5-ae0eb2125e62", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/adba3e70-1098-4a85-8fb5-ae0eb2125e62"}], "scenarios": []}, {"uuid": "c4acf729-9d0d-445e-b67b-544de58f9354", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/c4acf729-9d0d-445e-b67b-544de58f9354", "enzymes": [{"uuid": "c1e3c23f-4363-4371-8b98-d7fd75ec07b8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/c4acf729-9d0d-445e-b67b-544de58f9354/enzymelink/c1e3c23f-4363-4371-8b98-d7fd75ec07b8", "ec_number": "1.14.13.18", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "1b4c0cba-3714-4ce8-bb7b-8ab838158194", "url": 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enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "aa99fb1d-95bf-4c26-85e7-12d354809ba2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/183b4d3c-f894-4010-8a54-479c38a195db/enzymelink/aa99fb1d-95bf-4c26-85e7-12d354809ba2", "ec_number": "1.14.13.1", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "3f560ee2-ccb9-4d3a-b037-fd6158bbbf2e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/183b4d3c-f894-4010-8a54-479c38a195db/enzymelink/3f560ee2-ccb9-4d3a-b037-fd6158bbbf2e", "ec_number": "1.14.12.1", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "faa3f9c5-32c5-437f-8ed9-934217f5ec5e", "url": 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vic-Aminocarboxyaromatic → Catechol derivative", "aliases": [], "simple_rules": [{"uuid": "620525f2-3dfe-461f-b2b5-56e4fb4ffd88", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/620525f2-3dfe-461f-b2b5-56e4fb4ffd88"}], "scenarios": []}, {"uuid": "d346f588-647e-4207-82f6-249a0633808a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d346f588-647e-4207-82f6-249a0633808a", "enzymes": [{"uuid": "1a92e258-2fe5-4334-8e79-0be246e6659b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d346f588-647e-4207-82f6-249a0633808a/enzymelink/1a92e258-2fe5-4334-8e79-0be246e6659b", "ec_number": "4.2.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "f3413d29-0002-4571-8d0e-9aac53c73fd5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/f3413d29-0002-4571-8d0e-9aac53c73fd5"}], "edge_evidence": []}], "name": "bt0282", "description": "3-Methyl-5-hydroxy-6-(3-carboxy-3-oxopropenyl)-1H-2-pyridon derivative → 2,5,6-Trihydroxy-3-methylpyridine derivative", "aliases": [], "simple_rules": [{"uuid": "2cd0663f-f9fd-4e44-ab9a-abd33ac53e63", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/2cd0663f-f9fd-4e44-ab9a-abd33ac53e63"}], "scenarios": []}, {"uuid": "66d5b8da-a61a-43f1-b49f-3da124c0095a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/66d5b8da-a61a-43f1-b49f-3da124c0095a", "enzymes": [{"uuid": "e41786d6-139f-4f46-9f53-a08ac40d7d6f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/66d5b8da-a61a-43f1-b49f-3da124c0095a/enzymelink/e41786d6-139f-4f46-9f53-a08ac40d7d6f", "ec_number": "3.5.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "caed5eb4-e4c3-4cee-9ca4-076d99b80867", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/caed5eb4-e4c3-4cee-9ca4-076d99b80867"}], "edge_evidence": []}, {"uuid": "64e88036-aa5c-4aa0-9623-a9946e100ad5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/66d5b8da-a61a-43f1-b49f-3da124c0095a/enzymelink/64e88036-aa5c-4aa0-9623-a9946e100ad5", "ec_number": "3.5.3.21", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "eede184b-7fa6-4a7c-858a-b4f90f8055fa", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/66d5b8da-a61a-43f1-b49f-3da124c0095a/enzymelink/eede184b-7fa6-4a7c-858a-b4f90f8055fa", "ec_number": "3.5.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "ac381546-596e-4d9b-bd01-11e389fa5276", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/ac381546-596e-4d9b-bd01-11e389fa5276"}], "edge_evidence": []}, {"uuid": "cadd4cab-c768-4177-a362-efd9d449a920", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/66d5b8da-a61a-43f1-b49f-3da124c0095a/enzymelink/cadd4cab-c768-4177-a362-efd9d449a920", "ec_number": "3.5.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "e09dc13c-52c4-4816-9531-973ab65d0351", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/e09dc13c-52c4-4816-9531-973ab65d0351"}], "edge_evidence": []}], "name": "bt0318", "description": "Carbamyl → Amine + Carbonate
Carbamate → Amine

Comments:
This rule is based on De Schrijver and De Mot, 1999 and Balba et al., 1979.", "aliases": [], "simple_rules": [{"uuid": "113151e6-83ec-43fd-ace5-9a0aed3d90b8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/113151e6-83ec-43fd-ace5-9a0aed3d90b8"}, {"uuid": "4c5ac780-11ca-4718-9b4c-e104214f4e33", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/4c5ac780-11ca-4718-9b4c-e104214f4e33"}], "scenarios": []}, {"uuid": "1181b5fc-b384-437d-9f37-cccaa351d632", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/1181b5fc-b384-437d-9f37-cccaa351d632", "enzymes": [], "name": "bt0431", "description": "Tricarballylate → cis-Aconitate

Comments:
The type of oxidation is based on Lewis A and Escalante-Semerena, 2007.", "aliases": [], "simple_rules": [{"uuid": "6c083942-0fec-421d-94d7-39f7d1837bfa", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/6c083942-0fec-421d-94d7-39f7d1837bfa"}], "scenarios": []}, {"uuid": "c21ae7fe-4c81-4a3b-891a-4f89a28d20d7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/c21ae7fe-4c81-4a3b-891a-4f89a28d20d7", "enzymes": [{"uuid": "9b34270b-fb3c-4dee-8349-39f2e0b5b4c9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/c21ae7fe-4c81-4a3b-891a-4f89a28d20d7/enzymelink/9b34270b-fb3c-4dee-8349-39f2e0b5b4c9", "ec_number": "3.5.1.106", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "cb1be86e-e642-46f3-b24e-bdcf8c9b2935", "url": 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enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "421018ee-bcd8-4f4b-b624-88efe96ce7b6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/c21ae7fe-4c81-4a3b-891a-4f89a28d20d7/enzymelink/421018ee-bcd8-4f4b-b624-88efe96ce7b6", "ec_number": "3.5.1.106", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "24028c04-996e-4a7e-b517-c791a45b4f7f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/24028c04-996e-4a7e-b517-c791a45b4f7f"}], "edge_evidence": []}, {"uuid": "f5880ff6-ae64-4aad-92d3-d6bb48e41c8e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/c21ae7fe-4c81-4a3b-891a-4f89a28d20d7/enzymelink/f5880ff6-ae64-4aad-92d3-d6bb48e41c8e", "ec_number": "3.5.1.9", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": 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enviLink", "reaction_evidence": [{"uuid": "4852d8b0-6a1a-4b21-b7a1-caf808c317f9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/4852d8b0-6a1a-4b21-b7a1-caf808c317f9"}], "edge_evidence": []}, {"uuid": "5355409c-af01-4f13-8902-b453de0b78ee", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/c21ae7fe-4c81-4a3b-891a-4f89a28d20d7/enzymelink/5355409c-af01-4f13-8902-b453de0b78ee", "ec_number": "3.5.1.91", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "4af8677d-1fa4-4a2a-8bd0-f1b147c66991", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/c21ae7fe-4c81-4a3b-891a-4f89a28d20d7/enzymelink/4af8677d-1fa4-4a2a-8bd0-f1b147c66991", "ec_number": "3.5.1.31", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0421", "description": "Formamide → Amine + Formate", "aliases": [], "simple_rules": [{"uuid": "626b62b8-a3ce-4a71-a6df-1ed2f365ab12", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/626b62b8-a3ce-4a71-a6df-1ed2f365ab12"}], "scenarios": []}, {"uuid": "4d105a61-b9e8-4b67-9994-57c8dce36a2f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/4d105a61-b9e8-4b67-9994-57c8dce36a2f", "enzymes": [], "name": "bt0417", "description": "3-Methyl-cis,cis-muconate → 4-Methyl-3-oxoadipate

Comments:
This rule handles the 3-methyl-cis,cis-muconate pathway including lactonization, methyl isomerization, and hydrolysis of the lactone ring to form 4-methyl-3-oxoadipate. Based on Erb et al. (1998).", "aliases": [], "simple_rules": [{"uuid": "27d09225-e10d-4b32-bd9b-6b2d04748a92", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/27d09225-e10d-4b32-bd9b-6b2d04748a92"}], "scenarios": []}, {"uuid": "8ae1cca7-9c9d-4ce5-97a3-863196991f51", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8ae1cca7-9c9d-4ce5-97a3-863196991f51", "enzymes": [{"uuid": "81084a9b-c10b-429f-bbd5-a8f09bc4e538", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8ae1cca7-9c9d-4ce5-97a3-863196991f51/enzymelink/81084a9b-c10b-429f-bbd5-a8f09bc4e538", "ec_number": "1.14.12.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "c30bf5bb-21ad-4704-980c-15d6248efec3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/c30bf5bb-21ad-4704-980c-15d6248efec3"}, {"uuid": "e35a8c16-f9bf-44b7-8fec-6e840b89f8f1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/e35a8c16-f9bf-44b7-8fec-6e840b89f8f1"}], "edge_evidence": []}, {"uuid": "79f7a1d7-ecc6-4372-8b2e-3fa97865483d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8ae1cca7-9c9d-4ce5-97a3-863196991f51/enzymelink/79f7a1d7-ecc6-4372-8b2e-3fa97865483d", "ec_number": "1.14.12.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "12b00765-8ce6-4e18-84a3-52d79189a39c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/12b00765-8ce6-4e18-84a3-52d79189a39c"}], "edge_evidence": []}, {"uuid": "b6b18f7e-1835-4791-9199-c3c8d9d83154", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8ae1cca7-9c9d-4ce5-97a3-863196991f51/enzymelink/b6b18f7e-1835-4791-9199-c3c8d9d83154", "ec_number": "1.14.12.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "04116817-1eb6-4cab-863a-bbec78202def", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/04116817-1eb6-4cab-863a-bbec78202def"}, {"uuid": "76620386-6790-44e8-b669-b8dbea1db0f0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/76620386-6790-44e8-b669-b8dbea1db0f0"}], "edge_evidence": []}, {"uuid": "69b6222a-d445-4899-b374-bb3a03386109", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8ae1cca7-9c9d-4ce5-97a3-863196991f51/enzymelink/69b6222a-d445-4899-b374-bb3a03386109", "ec_number": "1.14.12.22", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "8a0d8030-1238-41a9-ba22-84dd05b0340e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8ae1cca7-9c9d-4ce5-97a3-863196991f51/enzymelink/8a0d8030-1238-41a9-ba22-84dd05b0340e", "ec_number": "1.14.12.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "e5ea4431-c222-4f61-8bf4-2dc33af2e2ec", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/e5ea4431-c222-4f61-8bf4-2dc33af2e2ec"}, {"uuid": "cee19d44-a33d-4d77-bfe5-1555a66d5db0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/cee19d44-a33d-4d77-bfe5-1555a66d5db0"}], "edge_evidence": []}, {"uuid": "7a88978f-50ae-425d-9a33-8b23a7291739", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8ae1cca7-9c9d-4ce5-97a3-863196991f51/enzymelink/7a88978f-50ae-425d-9a33-8b23a7291739", "ec_number": "1.14.12.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "5692ef17-e826-45c6-a85c-98458f3aaf65", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/5692ef17-e826-45c6-a85c-98458f3aaf65"}], "edge_evidence": []}, {"uuid": "ce611192-944c-4b7b-bd47-480c8aa11dad", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8ae1cca7-9c9d-4ce5-97a3-863196991f51/enzymelink/ce611192-944c-4b7b-bd47-480c8aa11dad", "ec_number": "1.14.12.22", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "24915d44-3adc-4aea-ba01-ac56d97939c4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/24915d44-3adc-4aea-ba01-ac56d97939c4"}], "edge_evidence": []}], "name": "bt0374", "description": "polynuclear Aromatic system → 1,2-dioxygenation and cleavage at connecting atom

Comments:
This rule handles the polynuclear aromatic system pathway and includes angular 1,2-dioxygenation of aromatic rings connected by an ether (Schmidt et al., 1992), amine or carbonyl, with an unsubstituted or halogenated ring carbon adjacent to the connecting atom to form a hemiacetal-like polynuclear aromatic system, and its cleavage. Hemiacetal-like connections formed from an ether or amine are spontaneously cleaved. If a carbonyl formed the original connection, the cleavage is an enzymatic reaction (Nojiri et al., 2001). The rule does not handle intermediate metabolites in the polynuclear aromatic system pathway.", "aliases": [], "simple_rules": [{"uuid": "a1663755-a8ef-414d-8ae5-174db21f3911", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/a1663755-a8ef-414d-8ae5-174db21f3911"}, {"uuid": "d863ae24-eb3c-411f-ac3b-fa4cf05f785b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/d863ae24-eb3c-411f-ac3b-fa4cf05f785b"}, {"uuid": "e4ffbfda-9b43-4bd1-87e6-2c7eda6fe262", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/e4ffbfda-9b43-4bd1-87e6-2c7eda6fe262"}], "scenarios": []}, {"uuid": "dc2ac02d-0dad-490d-9f47-3d86f35da7fb", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/dc2ac02d-0dad-490d-9f47-3d86f35da7fb", "enzymes": [], "name": "bt0420", "description": "Nitroguanidine derivative → Urea derivative

Comments:
This rule handles the 'magic nitro' pathway and includes reduction of nitroguanidine to the corresponding aminoguanidine derivative, cleavage of the amine to form a guanidine metabolite, and hydrolysis to yield the urea derivative (Pandey et al., 2009).", "aliases": [], "simple_rules": [{"uuid": "53647c10-4607-4a38-8196-d7d817ac50a3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/53647c10-4607-4a38-8196-d7d817ac50a3"}, {"uuid": "edfed4b3-fcc7-4f53-afbc-a2309d9cc20a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/edfed4b3-fcc7-4f53-afbc-a2309d9cc20a"}], "scenarios": []}, {"uuid": "b4a01d3f-07cc-4201-ac4c-fc84fe59f651", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b4a01d3f-07cc-4201-ac4c-fc84fe59f651", "enzymes": [{"uuid": "d65118c7-b22f-48e0-b231-f687c7051de6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b4a01d3f-07cc-4201-ac4c-fc84fe59f651/enzymelink/d65118c7-b22f-48e0-b231-f687c7051de6", "ec_number": "1.11.1.26", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "90ead771-acae-4e93-a9e4-c0d5c987dc40", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/90ead771-acae-4e93-a9e4-c0d5c987dc40"}], "edge_evidence": []}], "name": "bt0077", "description": "Peroxide → primary Alcohol", "aliases": [], "simple_rules": [{"uuid": "adf3fed5-bd13-4d19-b3f8-5f3f5cdd2594", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/adf3fed5-bd13-4d19-b3f8-5f3f5cdd2594"}], "scenarios": []}, {"uuid": "854d943a-3008-4b4c-8f2a-2d3b561b78b7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/854d943a-3008-4b4c-8f2a-2d3b561b78b7", "enzymes": [{"uuid": "da250433-38c7-420a-b086-1157b7e863d0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/854d943a-3008-4b4c-8f2a-2d3b561b78b7/enzymelink/da250433-38c7-420a-b086-1157b7e863d0", "ec_number": "1.7.2.3", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "3cb37765-2226-48f0-b2e8-b4f5924ff7de", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/3cb37765-2226-48f0-b2e8-b4f5924ff7de"}], "edge_evidence": []}], "name": "bt0408", "description": "tri-substituted Amine N-oxide → tertiary Amine

Comments:
Based on EC 1.6.6.9.", "aliases": [], "simple_rules": [{"uuid": "4985c45b-0df5-4897-bb92-fe1e85ae8f75", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/4985c45b-0df5-4897-bb92-fe1e85ae8f75"}], "scenarios": []}, {"uuid": "b7d77873-65b8-4164-9349-b8e7da31dcd6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b7d77873-65b8-4164-9349-b8e7da31dcd6", "enzymes": [{"uuid": "9358981b-aa17-44cc-aeab-b4f6e3ca4127", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b7d77873-65b8-4164-9349-b8e7da31dcd6/enzymelink/9358981b-aa17-44cc-aeab-b4f6e3ca4127", "ec_number": "1.14.13.69", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "7edcea43-9edd-4757-961d-e034db28625d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b7d77873-65b8-4164-9349-b8e7da31dcd6/enzymelink/7edcea43-9edd-4757-961d-e034db28625d", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "7ecd3eac-7eab-478c-bd06-37fd0870e535", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/7ecd3eac-7eab-478c-bd06-37fd0870e535"}], "edge_evidence": []}, {"uuid": "36486868-6224-44ca-9d94-ea449ec569db", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b7d77873-65b8-4164-9349-b8e7da31dcd6/enzymelink/36486868-6224-44ca-9d94-ea449ec569db", "ec_number": "1.14.14.11", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "477c4803-bba6-4383-99fe-e77cb3924891", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/b7d77873-65b8-4164-9349-b8e7da31dcd6/enzymelink/477c4803-bba6-4383-99fe-e77cb3924891", "ec_number": "1.14.13.69", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "b4655d3d-dcd1-41d8-8c8b-541cf4733dcc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/b4655d3d-dcd1-41d8-8c8b-541cf4733dcc"}, {"uuid": "4df5d1ed-f34e-433c-a01e-104036321cd7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/4df5d1ed-f34e-433c-a01e-104036321cd7"}, {"uuid": "3563c1c9-8d70-4c14-a493-4580adccbd9f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/3563c1c9-8d70-4c14-a493-4580adccbd9f"}], "edge_evidence": []}], "name": "bt0049", "description": "1,2-Alkene → 1,2-Epoxide

Comments:
Acts on any terminal 1,2-alkene. Rule is excluded from acting on any reactant that already contains an epoxide.", "aliases": [], "simple_rules": [{"uuid": "3c969632-d3db-4bc9-9f9b-1b41755d4253", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/3c969632-d3db-4bc9-9f9b-1b41755d4253"}], "scenarios": []}, {"uuid": "0e5e568c-5c5f-4fa5-8426-ca434d86e8cd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/0e5e568c-5c5f-4fa5-8426-ca434d86e8cd", "enzymes": [], "name": "bt0257", "description": "Cyclic 1,2-epoxide → 1-Hydroxyaromatic", "aliases": [], "simple_rules": [{"uuid": "a93f4451-8108-46f2-b79c-0ecbfb9290c7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/a93f4451-8108-46f2-b79c-0ecbfb9290c7"}, {"uuid": "abdaf876-b53f-452a-aac4-a51e9df3eba4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/abdaf876-b53f-452a-aac4-a51e9df3eba4"}, {"uuid": "084ee4f2-bdd5-4c72-8312-e45cd7fbb328", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/084ee4f2-bdd5-4c72-8312-e45cd7fbb328"}, {"uuid": "e76125cf-14a7-4e79-9481-133cedfcf708", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/e76125cf-14a7-4e79-9481-133cedfcf708"}], "scenarios": []}, {"uuid": "754e9b69-7e26-4027-9f1b-36f0f810481b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/754e9b69-7e26-4027-9f1b-36f0f810481b", "enzymes": [{"uuid": "768aa971-a72e-4c36-ad14-4c90106cfa70", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/754e9b69-7e26-4027-9f1b-36f0f810481b/enzymelink/768aa971-a72e-4c36-ad14-4c90106cfa70", "ec_number": "1.14.99.35", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "e6a95111-2d7f-4ab3-9dc6-10cdfc0c3da8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/e6a95111-2d7f-4ab3-9dc6-10cdfc0c3da8"}], "edge_evidence": []}], "name": "bt0324", "description": "Thiophene-2-carboxyl-CoA → 5-Oxo-4,5-dihydrothiophene-2-carboxyl-CoA

Comments:
The starting product for this rule appears aromatic. However, the enzyme probably stabilizes a double bond between C4 and C5. C5 is then hydroxylated to form an enol, which spontaneously tautomerizes to the keto form seen in the ending product. 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Comments:
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Comments:
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Comments:
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4-Hydroxypyridine derivative → 3,4-Dihydroxypyridine derivative

Comments:
When two ring positions are possible for the hydroxylation, both products are produced. Enzymes will produce only one of these two products, but it is not possible to predict which one that is. Hydroxylation of 4-hydroxypyridine is based on Watson et al., 1974. Rule is excluded from acting on vic-dihydroxyaromatic substrates.", "aliases": [], "simple_rules": [{"uuid": "d2c05443-dde1-4fe3-96e4-0e99517a00ed", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/d2c05443-dde1-4fe3-96e4-0e99517a00ed"}], "scenarios": []}, {"uuid": "e67775a5-9e73-449f-be5b-4429b2aa43cd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e67775a5-9e73-449f-be5b-4429b2aa43cd", "enzymes": [], "name": "bt0237", "description": "2-Hydroxyethanone derivative → Aldehyde derivative(s)

Comments:
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Comments:
Carbon chain rearrangement; the 2 carbon can have H, methyl or carboxylate substituents. Based on methylmalonyl-CoA mutase EC 5.4.99.2 and isobutyryl-CoA mutase EC 5.4.99.13 (see Figure 1 of Ratnatilleke et al., 1999). 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"reaction_evidence": [{"uuid": "645ee442-80b6-4b75-bcac-ac9f8f9ff208", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/645ee442-80b6-4b75-bcac-ac9f8f9ff208"}], "edge_evidence": []}, {"uuid": "272e424f-4e22-449b-b10c-9ed6cb70dff3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/3220779a-88c8-4096-9d4d-9ede4b896248/enzymelink/272e424f-4e22-449b-b10c-9ed6cb70dff3", "ec_number": "1.13.11.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "2b18848a-204b-4576-bf4b-857d05fdd620", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2b18848a-204b-4576-bf4b-857d05fdd620"}], "edge_evidence": []}, {"uuid": "4e5b14c6-871c-4cfa-9f64-1042a4bdb09d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/3220779a-88c8-4096-9d4d-9ede4b896248/enzymelink/4e5b14c6-871c-4cfa-9f64-1042a4bdb09d", "ec_number": "1.13.11.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "48a22333-dbae-4688-84f2-2bbd63b3b2b3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/48a22333-dbae-4688-84f2-2bbd63b3b2b3"}], "edge_evidence": []}], "name": "bt0342", "description": "1,2-Dihydroxybenzenoid w fused aliphatic ring → 2-Oxo-3-butenoate aliphatic ring", "aliases": [], "simple_rules": [{"uuid": "00eadd1b-3aa7-4b95-b075-21525140afab", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/00eadd1b-3aa7-4b95-b075-21525140afab"}, {"uuid": "09b3147e-f101-448d-b3d9-37ea46158a0c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/09b3147e-f101-448d-b3d9-37ea46158a0c"}], "scenarios": []}, {"uuid": "23a1b5ea-9033-4b2f-9401-90191f6948f7", "url": 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"http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/23a1b5ea-9033-4b2f-9401-90191f6948f7/enzymelink/aa43e393-6bd6-4288-a924-2cc4b812e868", "ec_number": "1.17.1.4", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "d1bb4f1d-755f-4d4d-ac0b-9ab4a11d9c5f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/23a1b5ea-9033-4b2f-9401-90191f6948f7/enzymelink/d1bb4f1d-755f-4d4d-ac0b-9ab4a11d9c5f", "ec_number": "1.17.5.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "8e252152-5f45-43f2-9f60-dcd2d50decc8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/8e252152-5f45-43f2-9f60-dcd2d50decc8"}], "edge_evidence": []}, {"uuid": "751676b9-a87d-4e62-9b2a-db8e0f12da13", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/23a1b5ea-9033-4b2f-9401-90191f6948f7/enzymelink/751676b9-a87d-4e62-9b2a-db8e0f12da13", "ec_number": "1.17.3.2", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0316", "description": "Xanthine derivative → Uric acid derivative", "aliases": [], "simple_rules": [{"uuid": "195f1ec3-c7fd-4c07-b9a5-50560713a2ce", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/195f1ec3-c7fd-4c07-b9a5-50560713a2ce"}], "scenarios": []}, {"uuid": "343a1f23-a680-4921-97fb-e3b975a8c443", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/343a1f23-a680-4921-97fb-e3b975a8c443", "enzymes": [{"uuid": "143af018-5301-4787-a069-696fc4da31bb", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/343a1f23-a680-4921-97fb-e3b975a8c443/enzymelink/143af018-5301-4787-a069-696fc4da31bb", "ec_number": "3.5.99.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "0f1c3ecb-444d-4919-a867-967016165e27", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/0f1c3ecb-444d-4919-a867-967016165e27"}], "edge_evidence": []}], "name": "bt0390", "description": "N-Methylideneformamide derivative → Methanimine derivative", "aliases": [], "simple_rules": [{"uuid": "3f81ec9d-a29e-455e-bfc6-1ce697994ee2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/3f81ec9d-a29e-455e-bfc6-1ce697994ee2"}], "scenarios": []}, {"uuid": "95d435fa-5bb7-41a3-b9a7-027be46ac2a5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/95d435fa-5bb7-41a3-b9a7-027be46ac2a5", "enzymes": [{"uuid": "3b00136c-6e56-49cd-adcd-0cbfb7dfeeac", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/95d435fa-5bb7-41a3-b9a7-027be46ac2a5/enzymelink/3b00136c-6e56-49cd-adcd-0cbfb7dfeeac", "ec_number": "4.1.1.61", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "471c984a-3504-4b3b-b15f-6a3e9dfaf78d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/471c984a-3504-4b3b-b15f-6a3e9dfaf78d"}], "edge_evidence": []}], "name": "bt0209", "description": "4-unsubstituted Phenol derivative → 4-Hydroxybenzoate derivative", "aliases": [], "simple_rules": [{"uuid": "7144d0b0-7b86-446a-b0ca-6b44e95e524c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/7144d0b0-7b86-446a-b0ca-6b44e95e524c"}], "scenarios": []}, {"uuid": "723f7b18-9e80-4cea-a2ea-9682d56c8bb5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/723f7b18-9e80-4cea-a2ea-9682d56c8bb5", "enzymes": [{"uuid": "89ba2807-646b-4607-9c73-67894441473e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/723f7b18-9e80-4cea-a2ea-9682d56c8bb5/enzymelink/89ba2807-646b-4607-9c73-67894441473e", "ec_number": "1.3.7.8", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "3409e288-b5d4-40b5-915a-706021b136e0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/3409e288-b5d4-40b5-915a-706021b136e0"}], "edge_evidence": []}], "name": "bt0192", "description": "Benzoyl-CoA derivative → Cyclohex-1,5-diene-1-carboxy-CoA derivative

Comments:
CoA ligation to the carboxy group occurs prior to aromatic ring reduction but is bypassed in this rule for simplification.", "aliases": [], "simple_rules": [{"uuid": "dfe40f0f-ad1d-4c5d-9928-5101d88a64aa", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/dfe40f0f-ad1d-4c5d-9928-5101d88a64aa"}], "scenarios": []}, {"uuid": "5ea405f6-8be6-47b4-b1e2-f081ca001087", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5ea405f6-8be6-47b4-b1e2-f081ca001087", "enzymes": [{"uuid": "ec44100e-b055-400d-ba21-81b04b7d5cbe", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5ea405f6-8be6-47b4-b1e2-f081ca001087/enzymelink/ec44100e-b055-400d-ba21-81b04b7d5cbe", "ec_number": "3.5.4.44", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0350", "description": "Formamidine → Amide + Methyl or Amine derivative

Comments:
This rule is blocked from acting on CoA and will not act on atoms in a ring. Based on Lenicek et al., 2006.", "aliases": [], "simple_rules": [{"uuid": "2e1b307c-e57e-46ab-8894-2704f658582f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/2e1b307c-e57e-46ab-8894-2704f658582f"}, {"uuid": "55da1538-25d0-4a46-b04d-15c8f2e33e8f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/55da1538-25d0-4a46-b04d-15c8f2e33e8f"}], "scenarios": []}, {"uuid": "3dea9481-c6f9-49ee-9d3c-7e7a9737972d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/3dea9481-c6f9-49ee-9d3c-7e7a9737972d", "enzymes": [], "name": "bt0110", "description": "Isocyanate → Carbamate

Comments:
Based on half-life data for phenyl isocyanate (Ekberg and Nilsson, 1976), n-butyl isocyanate (Brown and Wold, 1971) and methyl isocyanate (P. H. Howard, et al. (1991) Handbook of Environmental Degradation Rates p614-615.)", "aliases": [], "simple_rules": [{"uuid": "90ce8644-9092-4d3c-affd-ba0fa1bc4045", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/90ce8644-9092-4d3c-affd-ba0fa1bc4045"}], "scenarios": []}, {"uuid": "d86f86d1-a9f5-4536-b607-6bcf6284e25d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d86f86d1-a9f5-4536-b607-6bcf6284e25d", "enzymes": [{"uuid": "e0af6194-c066-4f74-ae7f-56c025431b9e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d86f86d1-a9f5-4536-b607-6bcf6284e25d/enzymelink/e0af6194-c066-4f74-ae7f-56c025431b9e", "ec_number": "1.6.99.1", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "c3582844-0f15-402f-8fb1-eb6052871c3d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/c3582844-0f15-402f-8fb1-eb6052871c3d"}, {"uuid": "23e9f6a3-b8ec-4c77-9b65-d6935a064e57", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/23e9f6a3-b8ec-4c77-9b65-d6935a064e57"}, {"uuid": "b1efdae0-9037-47a7-89d7-4f6a6cc889c7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/b1efdae0-9037-47a7-89d7-4f6a6cc889c7"}], "edge_evidence": []}], "name": "bt0033", "description": "Nitro → Nitroso", "aliases": [], "simple_rules": [{"uuid": "fc3b2418-cf37-4348-9f1e-002f277eced2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/fc3b2418-cf37-4348-9f1e-002f277eced2"}], "scenarios": []}, {"uuid": "8cb2a4e3-efcb-4471-a5d5-2049c6bd82b7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/8cb2a4e3-efcb-4471-a5d5-2049c6bd82b7", "enzymes": [], "name": "bt0108", "description": "1-Nitro-4-hydroxybenzenoid → 1,4-Dihydroxybenzenoid

Comments:
This rule handles the para-nitrophenol pathway and includes oxidative elimination of the nitro group to form a benzoquinone intermediate (bt0400) which is quickly reduced to the 1,4-dihydroxybenzenoid product (bt0107).", "aliases": [], "simple_rules": [{"uuid": "70e0953c-92e7-46f2-b077-82478ed8521a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/70e0953c-92e7-46f2-b077-82478ed8521a"}], "scenarios": []}, {"uuid": "3152f3ae-4461-4ee9-a86e-9a5907598fd2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/3152f3ae-4461-4ee9-a86e-9a5907598fd2", "enzymes": [{"uuid": "e6b0ee29-3c86-402f-8115-93452d3e0b99", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/3152f3ae-4461-4ee9-a86e-9a5907598fd2/enzymelink/e6b0ee29-3c86-402f-8115-93452d3e0b99", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "2ada7e02-b938-48c6-b490-a185f23c2e21", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/2ada7e02-b938-48c6-b490-a185f23c2e21"}], "edge_evidence": []}], "name": "bt0073", "description": "2-unsubstituted Cyclic ether → 2-Hydroxy cyclic ether

Comments:
If both carbon atoms adjacent to the ether oxygen are unsubstituted, hydroxylation will occur on the carbon with the most positive charge. 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Comments:
This rule handles the 2-phenylacyl dioxygenation pathway and includes CoA ligation to the acyl (acetyl or 2-propanyl) substituent, 1,2-dioxygenation, elimination of acyl-CoA, and formation of the catechol derivative, based on Murdoch and Hay (2005) and a review by Kagle et al. 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"classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "2d9eb61b-f5a2-495f-b74b-9eedcef0970b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/94452d99-9963-4ac1-8c11-c83c95d41576/enzymelink/2d9eb61b-f5a2-495f-b74b-9eedcef0970b", "ec_number": "3.5.1.86", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "f5891760-2202-42ef-b746-525f0cb819c7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/94452d99-9963-4ac1-8c11-c83c95d41576/enzymelink/f5891760-2202-42ef-b746-525f0cb819c7", "ec_number": "3.5.1.73", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "c77d5cbc-27b9-4e04-8cdf-15612d4613e6", "url": 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"linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "99f59197-983f-467a-882e-650bf5dd65ac", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a4a41b34-2d4d-4ecf-8127-13d34ed67905/enzymelink/99f59197-983f-467a-882e-650bf5dd65ac", "ec_number": "4.5.1.1", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "5d1851fc-787a-43ce-b613-f1192595e0a5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/5d1851fc-787a-43ce-b613-f1192595e0a5"}], "edge_evidence": []}, {"uuid": "6102b793-bb52-4ac0-bb50-a25a0153ff9c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/a4a41b34-2d4d-4ecf-8127-13d34ed67905/enzymelink/6102b793-bb52-4ac0-bb50-a25a0153ff9c", "ec_number": "4.5.1.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": 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Comments:
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Comments:
CoA ligation to the carboxyl group occurs prior to reductive elimination of the ring hydroxyl group but is bypassed in this rule for simplification.", "aliases": [], "simple_rules": [{"uuid": "9778e01a-5af7-4070-b64e-dbfa93345c00", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/9778e01a-5af7-4070-b64e-dbfa93345c00"}], "scenarios": []}, {"uuid": "7e94dd67-22d4-4d4d-be15-49442afd72aa", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/7e94dd67-22d4-4d4d-be15-49442afd72aa", "enzymes": [{"uuid": "837b12e2-22f6-4bc0-b573-911698896fcd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/7e94dd67-22d4-4d4d-be15-49442afd72aa/enzymelink/837b12e2-22f6-4bc0-b573-911698896fcd", "ec_number": "4.3.3.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "f86f958c-10f4-4c0e-81f1-dbc2246f212b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/f86f958c-10f4-4c0e-81f1-dbc2246f212b"}, {"uuid": "4091c5d9-cf81-4ab9-a583-a3c2905fc1b6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/4091c5d9-cf81-4ab9-a583-a3c2905fc1b6"}], "edge_evidence": []}], "name": "bt0444", "description": "Iminodisuccinate derivative → Aspartate derivative + Fumarate derivative", "aliases": [], "simple_rules": [{"uuid": "6566de10-ded5-4b9c-95f0-7193fa4459c3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/6566de10-ded5-4b9c-95f0-7193fa4459c3"}], "scenarios": []}, {"uuid": "281ec867-da03-4100-968d-38c0bfaca470", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/281ec867-da03-4100-968d-38c0bfaca470", "enzymes": [{"uuid": "9d4371cc-8d34-4243-9e00-a9d5f8f9398c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/281ec867-da03-4100-968d-38c0bfaca470/enzymelink/9d4371cc-8d34-4243-9e00-a9d5f8f9398c", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "201c50ba-a67d-4298-a1d3-d41becb4388c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/201c50ba-a67d-4298-a1d3-d41becb4388c"}], "edge_evidence": []}, {"uuid": "93bfd6b2-ea4d-464d-a1b8-df2d4f8a048c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/281ec867-da03-4100-968d-38c0bfaca470/enzymelink/93bfd6b2-ea4d-464d-a1b8-df2d4f8a048c", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "e408659a-6d21-46ab-827c-f44b4065cf94", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/e408659a-6d21-46ab-827c-f44b4065cf94"}], "edge_evidence": []}, {"uuid": "dc681ae9-33c5-431f-93ca-11bc47a6f524", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/281ec867-da03-4100-968d-38c0bfaca470/enzymelink/dc681ae9-33c5-431f-93ca-11bc47a6f524", "ec_number": "1.14.13.84", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0423", "description": "Acetophenone derivative → Acetylphenol derivative
methyl Ketone → Alkyl acetate

Comments:
This rule acts on unsubstituted or para-substituted aromatic ketones with either electron-donating (OH, CH3, NH2, OCH3) or electron-withdrawing (Cl, F, NO2, SO3-) groups, and linear methyl ketones, based on Park et al., 2009.", "aliases": [], "simple_rules": [{"uuid": "36eb9d8a-a8e3-488c-a9c3-f07fd82e4af7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/36eb9d8a-a8e3-488c-a9c3-f07fd82e4af7"}, {"uuid": "96f07d1e-51cf-4bb7-922c-9d81c22b26b7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/96f07d1e-51cf-4bb7-922c-9d81c22b26b7"}], "scenarios": []}, {"uuid": "3570cef4-e58e-4c5e-b4f6-6ef5a9e98944", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/3570cef4-e58e-4c5e-b4f6-6ef5a9e98944", "enzymes": [{"uuid": "d36ebd80-33d9-4090-ba6d-4eeba697d936", "url": 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1-unsubstituted-2-Sulfoaromatic → vic-Dihydroxyaromatic + Sulfonite

Comments:
Also handles fused rings; all fused aromatic ring products with hydroxyl at 2,3 position are excluded.", "aliases": [], "simple_rules": [{"uuid": "3f669b82-c713-4116-b8a2-3ade10c6a9cf", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/3f669b82-c713-4116-b8a2-3ade10c6a9cf"}], "scenarios": []}, {"uuid": "314a71ae-53ca-4fba-8380-14c08f7425d1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/314a71ae-53ca-4fba-8380-14c08f7425d1", "enzymes": [], "name": "bt0385", "description": "disubstituted Carbonate → Aryl/alkyl 1-ol + Aryl/alkyl 1-ol

Comments:
Based on Andreoni et al., 1990.", "aliases": [], "simple_rules": [{"uuid": "e8b1f897-1482-4a36-ad8e-c0dcdd99924f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/e8b1f897-1482-4a36-ad8e-c0dcdd99924f"}], "scenarios": []}, {"uuid": "0c79d13c-dca5-42a7-bb4e-3e2201f27042", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/0c79d13c-dca5-42a7-bb4e-3e2201f27042", "enzymes": [{"uuid": "024c89c4-244b-48e4-b10f-6de8c24d0da5", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/0c79d13c-dca5-42a7-bb4e-3e2201f27042/enzymelink/024c89c4-244b-48e4-b10f-6de8c24d0da5", "ec_number": "1.13.11.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "bf43b1ef-d399-4e9c-914b-666f8ff48fdd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/bf43b1ef-d399-4e9c-914b-666f8ff48fdd"}, {"uuid": "bd6295a0-9704-4310-b8b8-ef51e9fd5d82", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/bd6295a0-9704-4310-b8b8-ef51e9fd5d82"}], "edge_evidence": []}], "name": "bt0357", "description": "1,4-Dihydroxybenzenoid → Maleylacetate derivative

Comments:
This rule handles the upper hydroquinone pathway, and includes extradiol-type cleavage of hydroquinone derivatives (bt0297), gentisate and homogentisate (bt0174) and 2,6-dihalohydroquinones (bt0069). The initial ring cleavage reaction is catalyzed by an extradiol or an extradiol-type enzyme (Vaillancourt et al., 2006) producing a ketone product or an aldehyde intermediate, which is oxidized to form the carboxylate product (bt0003).", "aliases": [], "simple_rules": [{"uuid": "f6a56c0f-a4a0-4ee3-b006-d765b4767cf6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/f6a56c0f-a4a0-4ee3-b006-d765b4767cf6"}], "scenarios": []}, {"uuid": "56b64343-2fb4-44a0-b98f-545c96d0c9b2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/56b64343-2fb4-44a0-b98f-545c96d0c9b2", "enzymes": [], "name": "bt0429", "description": "Methoxyacetamide derivative → Primary Amide + Alcohol

Comments:
Reductive cleavage of an N-O bond contiguous to an amide, based on Tomco et al. (2010) and Klier et al. Tetrahedron Letters 28: 2677-2680 (1987).", "aliases": [], "simple_rules": [{"uuid": "f3d3535f-5e02-4dd5-bc43-78a1b93936a9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/f3d3535f-5e02-4dd5-bc43-78a1b93936a9"}], "scenarios": []}, {"uuid": "394a4797-0dbd-4be7-b100-ae58d018734c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/394a4797-0dbd-4be7-b100-ae58d018734c", "enzymes": [{"uuid": "acd6b724-24a4-4c1b-8a98-8ed55c6aedb6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/394a4797-0dbd-4be7-b100-ae58d018734c/enzymelink/acd6b724-24a4-4c1b-8a98-8ed55c6aedb6", "ec_number": "1.2.1.52", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "3938c214-60d7-45fb-b7d5-106029ef6529", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/394a4797-0dbd-4be7-b100-ae58d018734c/enzymelink/3938c214-60d7-45fb-b7d5-106029ef6529", "ec_number": "1.2.1.58", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "0924a9c2-eeb3-4bb2-8eae-e17aa497304e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/394a4797-0dbd-4be7-b100-ae58d018734c/enzymelink/0924a9c2-eeb3-4bb2-8eae-e17aa497304e", "ec_number": "1.14.13.168", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "c35d7f80-8f1d-485b-b860-c1d24883efef", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/394a4797-0dbd-4be7-b100-ae58d018734c/enzymelink/c35d7f80-8f1d-485b-b860-c1d24883efef", "ec_number": "1.2.7.1", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "0ea9e93a-5df6-4174-b881-9ceb7441ceba", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/0ea9e93a-5df6-4174-b881-9ceb7441ceba"}], "edge_evidence": []}, {"uuid": "2e250a96-26cb-433b-9a0e-133989be9113", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/394a4797-0dbd-4be7-b100-ae58d018734c/enzymelink/2e250a96-26cb-433b-9a0e-133989be9113", "ec_number": "2.3.1.54", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "bba11d9d-3ab7-4f48-885f-1425a7641361", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/394a4797-0dbd-4be7-b100-ae58d018734c/enzymelink/bba11d9d-3ab7-4f48-885f-1425a7641361", "ec_number": "1.2.1.25", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "2248b35d-4676-427f-a6d0-601310fe9161", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/394a4797-0dbd-4be7-b100-ae58d018734c/enzymelink/2248b35d-4676-427f-a6d0-601310fe9161", "ec_number": "1.2.3.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "1ed5290d-bf21-45af-bdb9-e04d7be77a58", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/1ed5290d-bf21-45af-bdb9-e04d7be77a58"}], "edge_evidence": []}, {"uuid": "f67f38f4-8df9-4c44-b30b-ce83550e9b39", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/394a4797-0dbd-4be7-b100-ae58d018734c/enzymelink/f67f38f4-8df9-4c44-b30b-ce83550e9b39", "ec_number": "1.2.3.13", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "9c2bb08a-38ca-4ed2-ab7a-613328dcb220", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/9c2bb08a-38ca-4ed2-ab7a-613328dcb220"}], "edge_evidence": []}], "name": "bt0082", "description": "2-Ketocarboxylate → Carboxylate + CO2

Comments:
After decarboxylation, some 2-ketocarboxylates transiently form an aldehyde, but this is quickly oxidized to the carboxylate. Others directly form the carboxylate, and the carboxylate is shown here. The rule does not decarboxylate 2-oxoacids that are cleaved to remove pyruvate or similar compounds rather than CO2, such as 2-oxo-3-ene, 2-oxo-4-imine, and 2,4-dioxo acids.", "aliases": [], "simple_rules": [{"uuid": "d14fcfbb-45a6-4039-be4c-9cd9000ee72c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/d14fcfbb-45a6-4039-be4c-9cd9000ee72c"}], "scenarios": []}, {"uuid": "f7a7a163-10a0-409a-a9fe-027af25aa325", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/f7a7a163-10a0-409a-a9fe-027af25aa325", "enzymes": [], "name": "bt0436", "description": "4-substituted Phenol → Hydroquinone + primary Alcohol

Comments:
The phenol is substituted only in the 4 position. 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"classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "1f98f5a9-45ea-4903-a8b5-640bbcefe2dc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/4a1f948d-d154-4b7f-a576-a861068aa5e8/enzymelink/1f98f5a9-45ea-4903-a8b5-640bbcefe2dc", "ec_number": "4.1.3.35", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0427", "description": "3-Hydroxy-3-alkylcarboxylate → Acetate + Ketone
3-Hydroxy-3-alkylketone → 2 Ketones

Comments:
Some compounds that trigger this rule are CoA adducts. CoA has been removed for simplification.", "aliases": [], "simple_rules": [{"uuid": "40aff953-1f49-4863-881a-b05141f028e8", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/40aff953-1f49-4863-881a-b05141f028e8"}], "scenarios": []}, {"uuid": "062bf2f5-1b06-4206-9b3f-7ca4ba559c5e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/062bf2f5-1b06-4206-9b3f-7ca4ba559c5e", "enzymes": [], "name": "bt0364", "description": "Pyridine → 5-Iminopentanoate

Comments:
This rule handles the unsubstituted pyridine ring cleavage pathway. An initial reduction step breaks aromaticity of the ring, forming a 1,4-dihydropyridine intermediate which is predicted to undergo hydrolytic cleavage to produce 5-iminopentaldehyde (Watson and Cain, 1975). The aldehyde is quickly oxidized to form 5-iminopentanoate (bt0003). The iminoaldehyde is postulated to transition between the linear form and a cyclic tautomer (see graphic). This rule does not handle the tautomerization.", "aliases": [], "simple_rules": [{"uuid": "a2ee00ce-28db-4476-997d-13913bf2c180", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/a2ee00ce-28db-4476-997d-13913bf2c180"}], "scenarios": []}, {"uuid": "09eec854-b68d-4064-9ca0-011da18bfa99", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/09eec854-b68d-4064-9ca0-011da18bfa99", "enzymes": [{"uuid": "20a31145-6ed4-401d-bb4f-48a021d68a07", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/09eec854-b68d-4064-9ca0-011da18bfa99/enzymelink/20a31145-6ed4-401d-bb4f-48a021d68a07", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "63eb4bd6-9c76-4dd1-b0b0-a03e321bac0c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/63eb4bd6-9c76-4dd1-b0b0-a03e321bac0c"}], "edge_evidence": []}, {"uuid": "362ab8ba-ee9e-4db1-b124-c7a442d161c3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/09eec854-b68d-4064-9ca0-011da18bfa99/enzymelink/362ab8ba-ee9e-4db1-b124-c7a442d161c3", "ec_number": "1.14.13.245", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "b7e6a992-6c7f-4d4e-b578-bfbf7d816dbc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/09eec854-b68d-4064-9ca0-011da18bfa99/enzymelink/b7e6a992-6c7f-4d4e-b578-bfbf7d816dbc", "ec_number": "1.14.13.32", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "92661b6b-08b9-414b-aa81-892bd0aa2510", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/09eec854-b68d-4064-9ca0-011da18bfa99/enzymelink/92661b6b-08b9-414b-aa81-892bd0aa2510", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "27c64345-70d5-4992-8905-9a78dfdac543", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/27c64345-70d5-4992-8905-9a78dfdac543"}], "edge_evidence": []}, {"uuid": "ec36d9ed-1536-461e-9b1a-81009aa5c691", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/09eec854-b68d-4064-9ca0-011da18bfa99/enzymelink/ec36d9ed-1536-461e-9b1a-81009aa5c691", "ec_number": "1.14.13.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "ed774412-e4f5-4341-a884-c6ddfecf9da6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/ed774412-e4f5-4341-a884-c6ddfecf9da6"}], "edge_evidence": []}, {"uuid": "20f3ee97-b5c3-4e6c-9c20-43a99232f9a4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/09eec854-b68d-4064-9ca0-011da18bfa99/enzymelink/20f3ee97-b5c3-4e6c-9c20-43a99232f9a4", "ec_number": "1.10.3.2", "classification_level": 4, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "ade491b1-f754-43c3-967b-5bdff3bb9f71", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/ade491b1-f754-43c3-967b-5bdff3bb9f71"}], "edge_evidence": []}], "name": "bt0162", "description": "disubstituted Sulfide → disubstituted Sulfoxide

Comments:
This rule is restricted to disubstituted sulfide and thioamide derivatives. Will handle aromatic compounds such as dibenzthiophene.", "aliases": [], "simple_rules": [{"uuid": "fe9bb9f7-f1ef-4f9e-8eaa-0f7b84c2ff6b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/fe9bb9f7-f1ef-4f9e-8eaa-0f7b84c2ff6b"}], "scenarios": []}, {"uuid": "d1d235fc-2053-4991-a5c7-6cdee36af45d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d1d235fc-2053-4991-a5c7-6cdee36af45d", "enzymes": [{"uuid": "d9164ce5-cf89-4529-a3ed-2df0964e6fad", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d1d235fc-2053-4991-a5c7-6cdee36af45d/enzymelink/d9164ce5-cf89-4529-a3ed-2df0964e6fad", "ec_number": "4.1.3.4", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "7cd6f3fe-b600-4e3a-a10d-f6453584eb79", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d1d235fc-2053-4991-a5c7-6cdee36af45d/enzymelink/7cd6f3fe-b600-4e3a-a10d-f6453584eb79", "ec_number": "4.1.3.26", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}, {"uuid": "aba81ef8-e62b-4aa1-93ad-96f669deea40", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/d1d235fc-2053-4991-a5c7-6cdee36af45d/enzymelink/aba81ef8-e62b-4aa1-93ad-96f669deea40", "ec_number": "4.1.99.-", "classification_level": 3, "linking_method": "EAWAG-BBD 2020-10-21 enviLink", "reaction_evidence": [{"uuid": "85a6fe03-0c66-49d8-b2b7-0fd8aaa5aa9a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/85a6fe03-0c66-49d8-b2b7-0fd8aaa5aa9a"}], "edge_evidence": []}], "name": "bt0323", "description": "3-Hydroxy-3-isohexenylglutaconyl-CoA → 7-Methyl-3-oxo-6-octenoyl-CoA + Acetate

Comments:
CoA ligation to the terminal carboxyl group occurs prior to the elimination of acetate but is bypassed in this rule for simplification.", "aliases": [], "simple_rules": [{"uuid": "cea3d416-e5b8-41da-93ae-42bbb7ff1954", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/cea3d416-e5b8-41da-93ae-42bbb7ff1954"}], "scenarios": []}, {"uuid": "5da90e6c-c59d-401a-9ee0-f67df673eef6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/5da90e6c-c59d-401a-9ee0-f67df673eef6", "enzymes": [], "name": "bt0438", "description": "Phenylacetate → 2-Oxepin-2(3H)-ylideneacetate

Comments:
This rule handles the aerobic phenylacetate pathway and includes ligation with CoA, epoxidation of the phenyl ring followed by isomerization to form the oxepin ring. CoA is removed to simplify the rule. Based on Teufel et al. (2010).", "aliases": [], "simple_rules": [{"uuid": "5382dfe9-5647-436c-b49c-b6aa07a4413f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/5382dfe9-5647-436c-b49c-b6aa07a4413f"}], "scenarios": []}, {"uuid": "e1692c2a-6379-476a-a6ce-e57d041bd78b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e1692c2a-6379-476a-a6ce-e57d041bd78b", "enzymes": [{"uuid": "027639d1-476f-4c01-a2c6-90933520eba6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/e1692c2a-6379-476a-a6ce-e57d041bd78b/enzymelink/027639d1-476f-4c01-a2c6-90933520eba6", "ec_number": "1.14.13.114", "classification_level": 4, "linking_method": "KEGG 2020-10-21 enviLink", "reaction_evidence": [], "edge_evidence": []}], "name": "bt0362", "description": "2- or 3-Hydroxypyridine → 2,5-Dihydroxypyridine
2- or 3-Carboxypyridine → 2,5-Dihydroxypyridine

Comments:
This rule handles the upper substituted pyridine pathway for 2- or 3-hydroxypyridine, 2-carboxypyridine (2-picolinate), 3-carboxypyridine (nicotinate) and intermediates of nicotine degradation (Gherna et al., 1965). These compounds, and possibly others, have been found to degrade to the common metabolite, 2,5-dihydroxypyridine (Kaiser et al., 1996). 2- or 3-Hydroxypyridine and 3-carboxypyridine undergo an initial para hydroxylation to form 2,5-dihydroxypyridine and 2-hydroxy-5-carboxypyridine respectively. The latter product is subject to oxidative decarboxylation to form the 2,5-dihydroxy product. This rule also handles intermediates in this pathway.", "aliases": [], "simple_rules": [{"uuid": "90aa8a3f-3043-47b6-b663-6ea46f189cf0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/90aa8a3f-3043-47b6-b663-6ea46f189cf0"}, {"uuid": "95f9a756-05db-4640-a6ba-6cad48084f56", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/95f9a756-05db-4640-a6ba-6cad48084f56"}, {"uuid": "0cb9d7fc-c983-4385-bfed-2bc2e6a04451", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/0cb9d7fc-c983-4385-bfed-2bc2e6a04451"}], "scenarios": []}, {"uuid": "4b1072e1-90bc-4ac9-909f-60908b3e2c89", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/parallel-rule/4b1072e1-90bc-4ac9-909f-60908b3e2c89", "enzymes": [], "name": "bt0173", "description": "Stilbene derivative → Aldo/Keto derivative + Aldo/Keto derivative", "aliases": [], "simple_rules": [{"uuid": "bff24fe1-b1d1-4807-a9e0-bc5c626f4633", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/simple-ambit-rule/bff24fe1-b1d1-4807-a9e0-bc5c626f4633"}], "scenarios": []}], "pathways": [{"uuid": "202640d3-990d-4688-8965-1a653477bbc7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/202640d3-990d-4688-8965-1a653477bbc7", "name": "Methamidophos", "description": "Methamidophos (O,S-dimethyl phosphoramidothioate) is a widely used organophosphorus insecticide. Because of its persistence and toxicity, its use has been prohibited or restricted in several countries. Thus its biodegradation is of interest ([http://www.ncbi.nlm.nih.gov/pubmed/19960233|Wang et al., 2010]). Hyphomicrobium sp. MAP-1 can utilize methamidophos as its sole carbon, nitrogen, and phosphorous source for growth. The first step in the pathway is cleavage of the P-N bond to form O,S-dimethyl hydrogen thiophosphate. This is hydrolyzed at either the P-O bond to form S-methyl dihydrogen thiophosphate, or the P-S bond to form methyl dihydrogen phosphate. It is proposed that these last two compounds are further hydrolyzed to phosphate ([http://www.ncbi.nlm.nih.gov/pubmed/19960233|Wang et al., 2010]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "c8795a8a-bfd0-403a-94f4-230b097d1958", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/202640d3-990d-4688-8965-1a653477bbc7/node/c8795a8a-bfd0-403a-94f4-230b097d1958", "name": "Phosphate", "description": "no description", "aliases": [], "default_node_label": {"uuid": "1b5cf519-07ea-4315-a016-804cf762d6dd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c581b2ce-6238-45de-abc0-60ca8d47ed04/structure/1b5cf519-07ea-4315-a016-804cf762d6dd"}, "node_labels": [{"uuid": "1b5cf519-07ea-4315-a016-804cf762d6dd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c581b2ce-6238-45de-abc0-60ca8d47ed04/structure/1b5cf519-07ea-4315-a016-804cf762d6dd"}], "depth": 3, "stereo_removed": false, 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dihydrogen phosphorothioate", "description": "no description", "aliases": [], "default_node_label": {"uuid": "d17d300b-6aca-4c26-a2ff-539d8fbb96bd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/71a624f2-855d-453c-b3f9-81dd4e62cdaa/structure/d17d300b-6aca-4c26-a2ff-539d8fbb96bd"}, "node_labels": [{"uuid": "d17d300b-6aca-4c26-a2ff-539d8fbb96bd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/71a624f2-855d-453c-b3f9-81dd4e62cdaa/structure/d17d300b-6aca-4c26-a2ff-539d8fbb96bd"}], "depth": 2, "stereo_removed": false, "scenarios": []}, {"uuid": "e09af2ea-f2f7-46c6-ac42-94a131885c89", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/202640d3-990d-4688-8965-1a653477bbc7/node/e09af2ea-f2f7-46c6-ac42-94a131885c89", "name": "O,S-Dimethyl hydrogen phosphorothioate", "description": "no description", "aliases": [], "default_node_label": {"uuid": "581c30cd-cb45-4e11-8d49-56bac26b7d1f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c0b27113-1035-4f9d-a932-cbffe7c6895e/structure/581c30cd-cb45-4e11-8d49-56bac26b7d1f"}, "node_labels": [{"uuid": "581c30cd-cb45-4e11-8d49-56bac26b7d1f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c0b27113-1035-4f9d-a932-cbffe7c6895e/structure/581c30cd-cb45-4e11-8d49-56bac26b7d1f"}], "depth": 1, "stereo_removed": false, "scenarios": []}, {"uuid": "8cf8a69d-5aeb-48b9-9da5-2928ae1f277d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/202640d3-990d-4688-8965-1a653477bbc7/node/8cf8a69d-5aeb-48b9-9da5-2928ae1f277d", "name": "Methylphosphate", "description": "no description", "aliases": [], "default_node_label": {"uuid": "1b3e27fa-fa91-4128-9980-b72ad8c00212", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/1f9f1cb3-0efa-412c-9911-7ebe3f275319/structure/1b3e27fa-fa91-4128-9980-b72ad8c00212"}, "node_labels": 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Because it has been extensively applied directly to fields, it can be detected a considerable distance away from the original site of application. Contamination of drinking water and food, as well as detrimental effects to wildlife are important concerns ([http://www.ncbi.nlm.nih.gov/pubmed/12549541|Siddique et al., 2003)]. The EPA allows endosulfan to be present in food no more than 0.1 to 2 ppm. i The FDA prohibits levels above 24 ppm in dry tea. High doses of endosulfan in humans primarily affect the central nervous system, resulting in respiratory depression, dry mouth, convulsions, and possibly death. Low doses have been shown to compromise the immune system, liver, kidneys and reproductive system in animals. This compound has been shown to be highly toxic with oral LD50 values ranging from 18 to 160 mg/kg in rats. For dermal exposure, LD50 values in rats ranged from 78 to 359 mg/kg (EXTOXNET). Commercially available endosulfan exists as two diastereoisomers, alpha and beta, in a ratio of 7:3. The former is more volatile and thought to be more toxic ([http://www.ncbi.nlm.nih.gov/pubmed/12549541|Siddique et al., 2003] and [http://www.ncbi.nlm.nih.gov/pubmed/17090129|Lee et al., 2006]). Thus, it is important to note that some microbial enzymes are specific to one isomer, or catalyze at different rates for each isomer ([http://www.ncbi.nlm.nih.gov/pubmed/15700124|Kwon et al., 2005]). For example, a Mycobacterium tuberculosis ESD enzyme degrades beta-endosulfan to the monoaldehyde and hydroxyether (depending on the reducing equivalent stoichiometry), but transforms alpha-endosulfan to the more toxic endosulfan sulfate ([http://www.ncbi.nlm.nih.gov/pubmed/12450848|Sutherland et al., 2002a]). However, oxidation of endosulfan or endosulfan sulfate by the monooxygenase encoded by ese in Arthrobacter sp. KW yields endosulfan monoalcohol ([http://www.ncbi.nlm.nih.gov/pubmed/16672499|Weir et al., 2006]). Both ese and esd proteins are part of the unique Two Component Flavin Dependent Monooxygenase Family, which require reduced flavin. They are conditionally expressed when no or very little sulfate or sulfite is available, and endosulfan is available to provide sulfur in these starved conditions ([http://www.ncbi.nlm.nih.gov/pubmed/12174035|Sutherland et al., 2002b]). The references include more details about isomer specificity and rates. Alternatively, hydrolysis of endosulfan in some bacteria (Pseudomonas aeruginosa, Burkholderia cepaeia) yields the less toxic metabolite endosulfan diol ([http://www.ncbi.nlm.nih.gov/pubmed/17289112|Kumar et al., 2006]). Endosulfan can spontanteously hydrolyze to the diol in alkaline conditions, so it is difficult to separate bacterial from abiotic hydrolysis ([http://www.ncbi.nlm.nih.gov/pubmed/12450848|Sutherland et al., 2002a]). The diol can be converted to endosulfan ether ([http://www.ncbi.nlm.nih.gov/pubmed/17252313|Hussein et al., 2007)] or endosulfan hydroxyether ([http://www.ncbi.nlm.nih.gov/pubmed/12590478|Lee et al., 2003]) and then endosulfan lactone ([http://www.ncbi.nlm.nih.gov/pubmed/12883876|Awasthi et al., 2003]). Hydrolysis of endosulfan lactone yields endosulfan hydroxycarboxylate ([http://www.ncbi.nlm.nih.gov/pubmed/12833978|Walse et al., 2003]). 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Uranyl ion can be precipitated as cell-bound hydrogen uranyl phosphate without change in oxidation state of the uranium, as shown in the right-most pathway branch. This reaction is facilitated by acid phosphatase N from Citrobacter sp. 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Hundreds of thousands of kilograms of 2-aminobenzenesulfonic acid are produced for use in the U.S. annually. It is used in organic synthesis and in the manufacture of various dyes and medicines. The initial step in the degradation of 2-aminobenzenesulfonate involves the transport of the compound across the outer membrane of the cell. Alcaligenes sp. O-1 has a selective permeability barrier, allowing three aromatic sulfonates (benzene sulfonate, toluene-4-sulfonate, and 2-aminobenzenesulfonate) to pass through, as described by [http://www.ncbi.nlm.nih.gov/pubmed/8075807|Junker et al. (1994)]. Cell extracts of this species were shown to be capable of degrading at least seven substrates. Deamination of the aromatic ring in strain O-1 has been shown by [http://www.ncbi.nlm.nih.gov/pubmed/8002948|Junker et al. (1994)] to precede desulfurization. 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It is one of the most abundant environmental pollutants of groundwater in the United States. In some groundwater, TCE undergoes reductive dechlorination catalyzed by anaerobic bacteria that yields vinyl chloride, a potent human carcinogen. TCE removal by dumping or air stripping is now largely disallowed and this has focused efforts on biological methods of TCE remediation in soil and water. The enzyme that starts one branch of this pathway, toluene 1,2-dioxygenase, has many other catalytic abilities, which are documented in a table of the Reactions of Toluene 1,2-Dioxygenase. The spontaneous degradation of trichloroethylene epoxide can produce as many as four products: dichloroacetate, carbon monoxide, glyoxylate, and formate. 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Nearly everyone knows that it causes the addictive nature of cigarettes, cigars and snuff - some still experience this first hand. Less known is that nicotine, under the names Nico-Fume, Black Leaf 40 (a 40% solution of nicotine), Tendust and others, can be used as an insecticide. This practice is rare within the United States yet much is still sold outside the US for this purpose. In Arthrobacter nicotinovorans ([http://www.ncbi.nlm.nih.gov/pubmed/7815950|Grether-Beck et al., 1994]) and Arthrobacter oxydans ([http://www.ncbi.nlm.nih.gov/pubmed/5835946|Gherna et al., 1965]), nicotine is converted to both (S)-6-Hydroxynicotine and (R)-6-Hydroxynicotine by nicotine dehydrogenase. Stereospecific enzymes (S)-6-hydroxynicotine oxygenase and (R)-6-hydroxynicotine oxygenase catalyze the formation of 6-hydroxypseudooxynicotine which is degraded through 2,6-dihydroxypyridine ([http://www.ncbi.nlm.nih.gov/pubmed/7815950|Grether-Beck et al., 1994]). Pseudomonas sp. strains P-34 and JTS-006 convert 6-hydroxypseudooxynicotine to 6-hydroxy-3-succinoylpyridine, which forms 2,5- (rather than 2,6-) dihydroxypyridine ([http://www.ncbi.nlm.nih.gov/pubmed/5835946|Gherna et al., 1965]). Pseudomonas putida biotype A strain S16 uses a varient of this pathway. It delays 6-hydroxylation of the aromatic ring until the formation of 3-succinoylpyridine. This is hydroxylated to form 6-hydroxy-3-succinoylpyridine, and the remaining pathway for that is as shown here ([http://www.ncbi.nlm.nih.gov/pubmed/17464070|Wang et al., 2007]). The three end products of this degradation as shown here are Maleamate, 4-Aminobutyrate, and 2,6-Dihydroxy-N-methylmyosmine. The metabolism of Maleamate and 4-Aminobutyrate continue through regular microbial channels. 2,6-Dihydroxy-N-methylmyosmine formed spontaneously from 2,6-Dihydroxypseudooxynicotine is reported as metabolically inactive in this species. Organisms which can initiate the pathway are given, but other organisms may also carry out later steps. 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When ingested by humans, caffeine stimulates the central nervous system, elevates blood pressure, increases metabolic rate, and acts as a diuretic ([http://www.ncbi.nlm.nih.gov/pubmed/16507475|Higdon and Frei, 2006]). Caffeine consumption may reduce the risk of Parkinson`s disease. However, adverse reactions to caffeine consumption can include anxiety, insomnia, heart palpitations, abdominal pain, and nausea, and high caffeine intake has been linked with increased risk of osteoporosis and complications in pregnancy ([http://www.ncbi.nlm.nih.gov/pubmed/17009088|Dash and Gummadi, 2006]). Caffeine is also mildly addictive. Withdrawal symptoms can include headache, fatigue, depressed mood, difficulty concentrating, irritability, nausea, and muscle pain ([http://www.ncbi.nlm.nih.gov/pubmed/16507475|Higdon and Frei, 2006]). Coffee pulp, a waste product produced during coffee processing, is a major pollutant in water bodies near coffee plants. Despite the fact that it is high in nutrients, it cannot be used as animal feed due to the high levels of caffeine and other unwanted compounds ([http://www.ncbi.nlm.nih.gov/pubmed/10959086|Pandey et al., 2000]). Solvents commonly used to produce caffeine-free products are either very expensive to use or toxic ([http://www.ncbi.nlm.nih.gov/pubmed/17009088|Dash and Gummadi, 2006]). However, a number of bacterial and fungal strains capable of degrading caffeine have been identified ([http://www.ncbi.nlm.nih.gov/pubmed/14977550|Mazzafera, 2004]). There are multiple possible pathways depending on the genus, species and strain of organism degrading the caffeine. In the bacteria Psuedomonas putida and Serratia marcescens, the major pathway is through theobromine to 7-methylxanthine to xanthine ([http://www.ncbi.nlm.nih.gov/pubmed/14977550|Mazzafera, 2004]). Minor branches produce methyluric acids; it has been proposed that these degrade to uric acid ([http://www.ncbi.nlm.nih.gov/pubmed/17009088|Dash and Gummadi, 2006]), but this has not been confirmed. Another bacterial pathway, found in Rhodococcus and Klebsiella spp., requires oxidation to yield 1,3,7-trimethyluric acid ([http://www.ncbi.nlm.nih.gov/pubmed/9705852|Madyastha and Sridhar, 1998]). 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Humans exposed to 2,4-Dichloroaniline for relatively short periods of time are subject to slight skin and eye irritation, blue skin, blue lips or finger nails, dizziness, nausea, shortness of breath, confusion, convulsions. Unconsciousness, or abdominal pain. However, humans subjected to prolonged exposure are prone to the formation of methaemoglobin in their blood supply, which effectively reduces the oxygen carrying capacity of the bloodstream and could rapidly result in death. The substance is particularly toxic to aquatic organisms, which is due to the impediment of the 2,4-Dichloroaniline on the oxygen carrying capacity of the blood supply, thus effectively suffocating the aquatic organism. 2,4-Dichloroaniline present in soil biodegrades relatively slowly. However, 2,4-Dichloroaniline (2,4-DCA) does not sorb onto soil particles very well and as a result may leach into the groundwater. The first step of the biodegradation of 2,4-DCA is the dechlorination of 2,4-DCA with a reductive dehalogenase that remove chlorine from the ortho position to form a monochlorinated aniline that can be readily degraded ([http://www.ncbi.nlm.nih.gov/pubmed/2604394|Struijs & Rogers, 1989]). The second step is an oxidative deamination of chloroaniline to chlorocatechol via a modified ortho-cleavage pathway ([http://www.ncbi.nlm.nih.gov/pubmed/4051488|Zeyer et al., 1985]). With chlorinated anilines, a meta cleavage pathway forms dead end products or suicide (highly reactive) products. 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As an initial step, Pseudomonas putida F1 degrades p-cymene by oxidizing the benzylic methyl group to yield p-cumic alcohol ([http://www.ncbi.nlm.nih.gov/pubmed/9150211|Eaton, 1997]). The p-cumic alcohol can then be further catabolised to isobutyrate, pyruvate, and acetyl-CoA by Pseudomonas putida PL ([http://www.ncbi.nlm.nih.gov/pubmed/8631713|Eaton, 1996]). Similar methyl group oxidations are found in other methyl substituted aromatic compounds including toluene, xylenes, methylnaphthalene and p-cresol. 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"Oxygenated adamantanes such as hydroxylated adamantanone have recently shown to possess promising immunomodulating and other useful properties. Adamantanone is hydroxylated by purified cytochrome P-450CAM, the camphor hydroxylating component of soluble camphor monooxygenase from Pseudomonas putida ATCC 17453. After growth in media with camphor as sole carbon and energy source, washed cells were capable of transforming adamantanone into number of metabolites. Microbial metabolism of adamantanone (tricyclo[3.3.13,7]decan-2-one) is documented by [http://www.ncbi.nlm.nih.gov/pubmed/1510672| Selifonov (1992).] The potential of such organisms in the biotransformation and production of specialty chemicals however has not yet been fully explored. Hydroxylated and non-hydroxylated adamantane lactones, compounds of potential pharmaceutical and synthetic interest, can be easily obtained using the same biocatalyst, cells of the P.putida, in a \"one pot synthesis\" in essentially quantitative yield. Biotransformation pathways for adamantanone in P.putida strain PpG1 (ATCC 17453) can be proposed as shown in the pathway map. Two divergent reactions of adamantanone oxidation are apparently provided by enzymes responsible for the initial steps of camphor catabolism: camphor 5-monooxygenase(P-450CAM) and camphor 1,2-monooxygenase, a NADH-dependent two-component cycloalkanone monooxygenase, leading to formation of 5-hydroxyadamantan-2-one and 4-oxahomoadamantan-5-one, respectively. Cytochrome P-450CAM in cell-free experiments has been shown to catalyze the formation of 5-hydroxyadamantan-2-one from adamantanone. However, camphor 1,2-monooxygenase appears to be the first enzyme shown to perform biological Baeyer-Villiger reaction with adamantanone. Further conversion of compounds to hydroxylactone are evidently mediated by camphor 1,2-monooxygenase and camphor 5-monooxygenase both recognizing these adamantane derivatives as substrate analogs of camphor. 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Both aromatic sulfonic acids and azo groups are rare among natural products and thus confer a xenobiotic character to sulfonated azo dyes. In conventional sewage plants, certain aromatic compounds carrying sulfonic acid groups as substituents resist biodegradation or are incompletely degraded. [http://www.ncbi.nlm.nih.gov/pubmed/1781678|Haug et al. (1991)] found that Pseudomonas sp. BN6 mineralised Mordant Yellow 3 to produce stoichiometric amounts of 6-Amino-2-naphthalenesulfonic acid (6A2NS) and 5-Aminosalicylate(5AS) that were excreted into the growth media (under anoxic growth conditions). The enzyme catalysing this reduction is a highly non-specific azo reductase. Products of this step in turn become substrates for further degradation via the aerobic 6-Amino-2-naphthalene sulfonic acid pathway, initiated by naphthalene 1,2-dioxygenase. This versatile enzyme has many other catalytic abilities, which are documented in a table of the Reactions of Naphthalene 1,2-Dioxygenase. Various biological systems have also been known to posess the capability to cleave the azo bond reductively under anaerobic conditions. In mammalian tissues, azo reductase activity is primarily found in the liver. Consequently intestinal flora have also been found to reduce azo bonds, namely Streptococcus faecalis. The degradative process for 6-Amino-2-Naphthalene sulfonic acid as well as 5 Aminosalicylate are both aerobic processes that are performed by two strains in conjunction namely Pseudomonas sp. BN6 and Pseudomonas sp. BN9. Strain BN6 under aerobic conditions catalyses the conversion of 6A2NS to 5AS with the release of pyruvate as an energy source. 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In recent reports, strains of Pseudomonas aeruginosa capable of utilizing Caprolactam as the sole source of carbon and nitrogen were readily isolated following enrichment of pond water, or activated sludge ([http://www.ncbi.nlm.nih.gov/pubmed/7487018|Steffensen and Alexander, 1995]; [http://www.ncbi.nlm.nih.gov/pubmed/9688819|Kulkarni and Kanekar, 1998]). Furthermore, there are numerous reports showing the removal of Caprolactam with normal waste water treatment. 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"description": "Polycyclic aromatic hydrocarbons (PAHs), such as phenanthrene are commonly found as pollutants in soils, estuarine waters and sediments, and other terrestrial and aquatic sites. Phenanthrene has been shown to be toxic to marine diatoms, gastropods, mussels, crustaceans, and fish. Phenanthrene has a fused-ring structure resembling higher molecular weight carcinogenic PAHs, and has received interest as a useful model PAH for mammalian and fungal studies. In general, bacteria that utilize phenanthrene as the sole source of carbon and energy oxidize it via a dioxygenase primarily in the \"bay-region\" to form a phenanthrene cis-dihydrodiol. In contrast to these bacteria, Streptomyces flavovirens and the marine cyanobacterium Agmenellum quadruplicatum metabolize phenanthrene in the \"K-region\", mainly to phenanthrene trans-9,10- dihydrodiol with a 9S,10S absolute configuration similar to that produced by mammalian enzymes. Besides the bacterial metabolic pathways of phenanthrene , fungi are also able to biotransform phenanthrene. Unlike bacteria, fungi do not utilize phenanthrene as the sole source of carbon and energy but, instead cometabolize the PAH to hydroxylated products. Many nonligninolytic fungi metabolize phenanthrene in a highly redio- and stereoselective manner, via cytochrome P-450 monooxygenase and epoxide hydrolase, to form phenanthrene trans-1,2-, trans-3,4, and trans-9,10-dihydrodiol; 1-, 2-, 3-, 4-, and 9-phenanthrols; and sulfate, glucoside, and glucuronide conjugates of primary metabolites. The fungi are known to biotransform phenanthrene to trans-dihydrodiol metabolites that are generally the mirror images of the corresponding trans-dihydrodiols obtained from rat liver microsomes. Although the 1,2-, 3,4-position (\"bay-region\") of phenanthrene is the main site of enzymatic attack, fungi are also able to transform phenanthrene at the 9,10-position ( \"K-region\"), which is a major site of mammalian enzymatic attack. The metabolic pathways and biochemical reaction mechanisms for the biotransformation of phenanthrene by these fungi closely resemble phase I (oxidation) and subsequent phase II (conjugation) metabolic pathways documented for terrestrial and aquatic animals. Cytochrome P-450, epoxide hydrolase, UDP-glucuronyltransferase, glycosyltransferase, and aryl-sulfotransferase activities have been demonstrated to be involved in the oxidation and subsequent conjugation of phenanthrene. 1-phenanthryl-beta-D-glucopyranoside and a novel phenanthrene glucoside conjugate, 2-hydroxy-1-phenanthrylbeta- D-glucopyranoside were produced by C. elegans ATCC 9245. The possible mechanism could involve two intermediates: trans-1,2-dihydrodiol and its dehydrogenated product 1,2-dihydroxyphenanthrene. 1-methoxyphenanthrene was identified only in A. niger van Tieghem (strain b52, DSM 11167) via methylation ([http://www.ncbi.nlm.nih.gov/pubmed/9212437|Thomas et al., 1997]). The five phenanthrols 1-, 2-, 3-, 4-, and 9-phenanthrol were most likely produced by rearrangement of the postulated arene oxides (reactions: A, H, B, C, and D). After oxidative step in reaction E, a ring cleavage reaction may be involved in the enzymatic attack at C-9 and C-10 positions of 9,10-phenanthrenequinone to form 2,2`-diphenate in reaction F and eventually CO2 by mineralization (reaction G). The enzyme catalyzed step F has not been identified. The white rot fungus Pleurotus ostreatus produces trans-9R,10R-dihydrodiol phenanthrene as the principal enantiomer, which is different from that of the the principal eneantiomer produced by Phanerochaete chrysosporium. P. ostreatus can further cleave the aromatic ring and form 2,2`-diphenic acid and carbon dioxide. Ligninolytic Phanerochaete chrysosporium has been demonstrated to metabolize phenanthrene in a similar way to that of Pleurotus ostreatus (see: Phenanthrene (fungal 9S,10S) Pathway); however different enantiomers are produced in the first metabolic step in the two fungi.", "aliases": [], "predicted": false, "nodes": [{"uuid": "a5cbbeb9-2c72-4637-8dbe-d07a29b3cf27", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/a2a860c7-8ae2-44be-b979-84e11c1d5bd6/node/a5cbbeb9-2c72-4637-8dbe-d07a29b3cf27", "name": "Carbon Dioxide", "description": "no description", "aliases": [], "default_node_label": {"uuid": "b56ca2f4-d95a-41aa-b910-d57e52d27dc9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/05f60af4-0a3f-4ead-9a29-33bb0f123379/structure/b56ca2f4-d95a-41aa-b910-d57e52d27dc9"}, "node_labels": [{"uuid": "b56ca2f4-d95a-41aa-b910-d57e52d27dc9", "url": 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"http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/cb600409-f044-4e55-890c-495269817d55", "name": "Anthracene (fungal)", "description": "Anthracene is a common polycyclic aromatic hydrocarbon (PAH). Although anthracene itself is not carcinogenic, its biodegradation and metabolism are of interest because the same type of fused ring structures are found in higher molecular weight PAHs such as benz[a]anthracene and benzo[a]pyrene, which are carcinogenic. Anthracene and other PAHs are found in crude oil, coal tar and creosote. They are also formed via pyrosynthesis during incomplete combustion. Following fractional distillation of coal tar, the fraction boiling above 270° C is known as \"anthracene oil.\" In addition to anthracene, anthracene oil also contains phenanthrene, fluorene, fluoranthene, pyrene and carbazole. Bacteria can degrade anthracene, as shown elsewhere. Fungi also can degrade anthracene. White rot fungi often prepare aromatic compounds for ring cleavage by first converting them to quinones. The initial oxidation of anthracene (to 9,10-anthraquinone), benzo[a]pyrene (Haemmerli, et al., 1986) and several other PAHs is catalyzed by lignin peroxidases from Phanerochaete chrysporium, Bjerkandera sp. strain BOS55 (Field, J.A. et al., Enzyme and Micro. Tech. 18:300-308, 1996) and other white rot fungi. Manganese peroxidases, another family of lignin degrading peroxidases produced by white rot fungi, can also oxidize anthracene (Eibes et al., 1986). Laccases, copper-containing enzymes that are also involved in lignin degradation by Trametes versicolor, have also been shown to oxidize anthracene (Collins et al., 1986). Not all white rot fungi produce laccases. P. chrysosporium can completely mineralize anthracene. It cleaves 9,10-anthraquinone to phthalate and, here proposed, catechol, though o-benzoquinone or aliphatic compounds are also possible (Hammel et al., 1991). Not all fungi that metabolize anthracene completely mineralize it. Others detoxify anthracene by conjugation followed by secretion. Cunninghamella elegans oxidizes anthracene to anthracene-1,2-oxide using a cytochrome P450 monooxygenase ([http://www.ncbi.nlm.nih.gov/pubmed/9451829|Cerniglia, 1997]). This can be further oxidized to anthracene-trans-1,2-dihydrodiol (Cerniglia and Yang, 1983), or oxidized to 1-anthrol non-enzymatically. 1-Anthrol can form conjugates with xylose, glucuronate and sulfate (Sutherland et al., Myco. 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as an ingredient in cutting oils and petroleum products ([http://www.ncbi.nlm.nih.gov/pubmed/15941012|Whittaker et al., 2004], [http://www.ncbi.nlm.nih.gov/pubmed/9726870|De Wever et al., 1998]). The manufacture of MBT produces wastewaters with high levels of MBT and its derivatives, and these compounds can also be released into water by factories using MBT and by leaching from MBT-containing products, particularly rubber ([http://www.ncbi.nlm.nih.gov/pubmed/9726870|De Wever et al., 1998]). Many other industries also use benzothiazoles, which in some cases degrade to MBT. For example, MBT is a degradation product of a fungicide widely used in the leather and lumber industries, 2-(thiocyanomethylthio)benzothiazole (Reemtsma, Fiehn, Kalnowski, and Jekel (1995) Environ Sci Technol 29:478-485). MBT and some of its degradation products are known to be toxic to humans and other organisms ([http://www.ncbi.nlm.nih.gov/pubmed/15941012|Whittaker et al., 2004], [http://www.ncbi.nlm.nih.gov/pubmed/15750776|Nawrocki et al., 2005]). Both laboratory and epidemiological studies suggest that MBT acts as a carcinogen in mammals ([http://www.ncbi.nlm.nih.gov/pubmed/15941012|Whittaker et al., 2004]). It also has toxic effects on many bacteria, and its presence inhibits biodegradation of other compounds, including some of its own degradation products ([http://www.ncbi.nlm.nih.gov/pubmed/7765737|De Wever et al., 1994], [http://www.ncbi.nlm.nih.gov/pubmed/11778869|De Wever et al., 2001]). MBT is very resistant to biodegradation, and many of its degradation products are also recalcitrant. [http://www.ncbi.nlm.nih.gov/pubmed/11778869|De Wever et al. (2001)] review many of the biotransformations of MBT and other 2-substituted benzothiazoles (shown on the right below; most of the enzymes are postulated). Many bacteria, including strains belonging to Corynebacterium, Pseudomonas, and Escherichia coli, are capable of methylating the thiol group to produce 2-methylthiobenzothiazole (MTBT) ([http://www.ncbi.nlm.nih.gov/pubmed/3662509|Drotar et al., 1987]). MTBT is usually not degraded further, although Reemtsma et al. (1995) report a minor reaction producing 2-(methylsulfinyl)benzothiazole from MTBT, and [http://www.ncbi.nlm.nih.gov/pubmed/6616091|Liu et al. (1983)] describe a culture that can degrade MTBT. De Wever (1995) describes the conversion of MBT to 2,2`-dithio-bis-benzothiazole (DM), benzothiazole-2-sulphonate (BTSO3), a recalcitrant red dye stuff, and recalcitrant polar compounds, as well as the partial mineralization of MBT (De Wever (1995) PhD Thesis, Faculty of Agricultural and Applied Biological Sciences, Katholieke Universiteit Leuven). Reemtsma et al. (1995) also report a very minor reaction producing benzothiazole (BT) from MBT. (This reaction is poorly characterized and thus is only balanced provisionally here.) Of these products, DM is resistant to further degradation, although [http://www.ncbi.nlm.nih.gov/pubmed/8863435|Dufresne et al. (1996)] describe an acidophylic Sulfobacillus disulfidooxidans sp. that can degrade it. BT is readily degraded, and a Rhodococcus erythropolis strain capable of mineralizing BTSO3 has been isolated ([http://www.ncbi.nlm.nih.gov/pubmed/9726870|De Wever et al., 1998]). The degradation pathways for these two metabolites appear to be similar and may share enzymatic machinery. Rhodococcus erythropolis BTSO31 converts both compounds to 2-hydroxybenzothiazole (OBT), which is then further hydroxylated to form 2,6-dihydroxybenzothiazole ([http://www.ncbi.nlm.nih.gov/pubmed/9726870|De Wever et al., 1998], [http://www.ncbi.nlm.nih.gov/pubmed/11282584|Besse et al., 2001]). While most of these conversions require the presence of oxygen, the conversion of BTSO3 to OBT can also be carried out under anaerobic conditions ([http://www.ncbi.nlm.nih.gov/pubmed/9726870|De Wever et al., 1998]). A similar pathway for BT degradation has been observed in Rhodococcus rhodochrous OBT18 ([http://www.ncbi.nlm.nih.gov/pubmed/9726870|De Wever et al., 1998], [http://www.ncbi.nlm.nih.gov/pubmed/11282584|Besse et al., 2001]) and Rhodococcus pyridinovorans PA ([http://www.ncbi.nlm.nih.gov/pubmed/12450835|Haroune et al., 2002]). The latter species uses a catechol 1,2-dioxygenase to open the benzene ring. Another pathway for MBT degradation has been described (shown on the left below; enzymes are postulated) ([http://www.ncbi.nlm.nih.gov/pubmed/15466583|Haroune et al., 2004]). Rhodococcus rhodochrous OBT18 converts MBT into two metabolites, a cis-dihydrodiol derivative and a hydroxylated form, both of which are then converted to a diacid MBT derivative and further mineralized. 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2004]). Along with other branched alkanes, it is used to replace aromatic compounds in gasoline formulations in response to regulations limiting the release of the latter compounds. However, isooctane is itself toxic: in particular, numerous studies have shown that it causes kidney and liver damage in rats (for instance, [http://www.ncbi.nlm.nih.gov/pubmed/3680850|Fowlie et al., 1987]). Its quaternary carbon group makes isooctane one of the most recalcitrant constituents of gasoline. Nonetheless, Mycobacterium austroafricanum IFP 2173 is able to use it as a sole carbon source ([http://www.ncbi.nlm.nih.gov/pubmed/10831416|Solano-Serena et al., 2000]). In addition to isooctane, this strain can degrade a variety of other hydrocarbons, including various n-alkanes, multimethyl-substituted isoalkanes, and monoaromatic hydrocarbons, and some ethers. [http://www.ncbi.nlm.nih.gov/pubmed/15281945|Solano-Serena et al. (2004)] have identified several of the intermediates in isooctane metabolism by M. austroafricanum IFP 2173. Isooctane is oxidized to 2,4,4-trimethylpentanoate, which is then likely ligated to coenzyme A and converted to 2,4,4-trimethyl-3-oxopentanoyl-CoA via beta-oxidation. Cleavage of propanoyl-CoA yields pivalyl-CoA, whose corresponding free form, pivalate, was observed. Pivalate is mineralized by M. austroafricanum IFP 2173, but the mechanism of its degradation is not well understood, and is not shown here. The authors suggest a pathway producing isobutyrate followed by methylmalonate, both of which are mineralized by isooctane-grown cells, as a reasonable hypothesis. [http://www.ncbi.nlm.nih.gov/pubmed/15281945|Solano-Serena et al. (2004)] also detected small amounts of 2,2-dimethyl-3-pentanone and, in some cultures, 3,3-dimethyl-2-butanone produced during isooctane degradation by M. austroafricanum IFP 2173. 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Formation of reactive nitrogen species is presumed to play a major role in neuron death and the presence of free 3-NTyr is considered a marker for this biochemical event. It has been shown that 3-NTyr exhibits neurotoxicity when injected into rat dopaminergic cells. This neurotoxicity has been linked to the metabolism of 3-NTyr via the concerted action of the aromatic amino acid decarboxylase and monoamine oxidase. 3-Nitrotyramine is structurally similar to 3-NTyr, exhibits the same neurotoxic effects and is formed via decarboxylation of 3-NTyr in rat dopaminergic neuronal cells ([http://www.ncbi.nlm.nih.gov/pubmed/16763020|Blanchard-Fillion et al., 2006]). This decarboxylation has not been observed in microbes. 3-Nitrotyramine can be used as a nitrogen source by cultures of Escherichia coli utilizing a periplasmic amine oxidase (TynA) and cytosolic NAD-linked dehydrogenase (FeaB). The biodegradation pathway involves an initial oxidation to 4-hydroxy-3-nitrophenylacetaldehyde which is further oxidized to 4-hydroxy-3-nitrophenylacetate (Rankin et al., 2008). These E. coli cultures did not grow on 3-NTyr. The metabolism of 3-NTyr in Variovorax paradoxus JS171 and Burkholderia sp. strain JS165 is carried out by deamination and subsequent decarboxylation to the above mentioned 4-hydroxy-3-nitrophenylacetate. Monooxygenase-catalyzed denitration of 4-hydroxy-3-nitrophenylacetate yields homoprotocatechuate, for which bacterial metabolism is well established ([http://www.ncbi.nlm.nih.gov/pubmed/16461647|Nishino and Spain, 2006]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "a1a7222c-aeb7-4f11-aed3-14d64ca03e62", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/8296403d-597b-4c86-b888-b9827dac5fa5/node/a1a7222c-aeb7-4f11-aed3-14d64ca03e62", "name": "3,4-Dihydroxyphenylacetate", "description": "no description", "aliases": [], "default_node_label": {"uuid": "a23d37d8-d304-493e-a0bd-13f76daa2f22", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/d7441dee-c9b3-4f65-ba05-c652a8465767/structure/a23d37d8-d304-493e-a0bd-13f76daa2f22"}, "node_labels": [{"uuid": "a23d37d8-d304-493e-a0bd-13f76daa2f22", "url": 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Nitrofen, in its purest form is a colorless and crystalline solid. The technical material is a brown, free flowing solid with a slight aromatic odor. The melting point of the technical material is 64-71C and the density is 1.80g/cm3 at 83C. It is used as a pre or post-emergence contact herbicide. Moderate application rates give selective control in cereals, certain ornamentals, vegetable crops, sugar beet and paddy fields. High application rates will give total vegetation control. Nitrofen requires adequate moisture for full effectiveness. Sphingomonas wittichii RW1 is a very potent diphenyl ether herbicide metabolizing bacterium with broad substrate specificity ([http://www.ncbi.nlm.nih.gov/pubmed/18778066|Keum et al., 2008]). The interesting aspect of the Nitrofen degradation by this strain is the initial reduction of nitro group followed by N-acetylation. As in other Sphingomonads, dissociation of the diaryl ether bond is also found in strain RW1 during Nitrofen metabolism. Although, ether bond clevage is a common metabolic pathway of diaryl ethers in animal, plant, fungi and bacteria, corresponding enzymes of eukaryotes and prokaryotes are different. Bacterial degradation of diphenyl ethers and related environmental contaminants are usually catalyzed by multi-component dioxygenase system, while eukaryotic biodegradation is catalyzed by monooxygenase or peroxidase ([http://www.ncbi.nlm.nih.gov/pubmed/11762605|Hiratsuka et al., 2001]) identified the degradation of diphenyl ether herbicides by the lignin-degrading basidomycete Coriolus versicolor. White-rot basidiomycetous fungi are capable of degrading a variety of environmentally persistent aromatic pollutants. 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Picric acid is mainly used in manufacture of explosives and as an intermediate in dye manufacturing. Both 2,4,6-trinitrophenol and 2,4-dinitrophenol are found in the waste streams released into the environment by aniline production plants. The three nitro groups of picric acid create a highly positive redox potential that is susceptible to reductive rather than oxidative processes. An initial reductive attack on the aromatic ring converts picric acid to the hydride-TNP Meisenheimer complex. In Rhodococcus (opacus) erythropolis HL PM-1 ([http://www.ncbi.nlm.nih.gov/pubmed/1444408|Lenke et al., 1992]), Nocardioides sp. strain CB 22-2 ([http://www.ncbi.nlm.nih.gov/pubmed/10103224|Behrend and Heesche-Wagner, 1999]) and Nocardioides simplex (formerly Arthrobacter) FJ2-1A, ([http://www.ncbi.nlm.nih.gov/pubmed/10217752|Ebert et al., 1999]) elimination of nitrite is thought to proceed through this intermediate. However, [http://www.ncbi.nlm.nih.gov/pubmed/9973345|Rieger et al. (1999)] states this elimination requires an unlikely C-3 to C-2 hydrogen migration. Studies show that C-2 protonation of the hydride species occurs readily at physiological pH and suggests the protonated hydride complex is the reactive intermediate for nitrite elimination to 2-dinitrophenol. Reduction of the aromatic nucleus in 2,4-DNP forms the hydride-DNP Meisenheimer complex. A second pathway involves a two component enzyme system which catalyzes two hydration reactions of picric acid to form a dihydride Meisenheimer-complex ([http://www.ncbi.nlm.nih.gov/pubmed/11882715|Heiss et al. 2002]). The nitro form of this dihydride complex remains as a dead-end metabolite; the aci form undergoes elimination of nitrite, after which the two metabolic pathways of picric acid merge ([http://www.ncbi.nlm.nih.gov/pubmed/11995829|Ebert et al., 2001]). The enzyme catalyzing denitration of the dihydride Meisenheimer-complex of picric acid to form the hydride Meisenheimer-complex of 2,4-dinitrophenol and also the hydrolase enzyme for subsequent reaction have been recently purified ([http://www.ncbi.nlm.nih.gov/pubmed/15128543|Hofmann et al., 2004]). It has been known for more than a decade that 4,6-dinitrohexanoate undergoes further mineralization, with a minor amount remaining as a dead-end metabolite ([http://www.ncbi.nlm.nih.gov/pubmed/1444407|Lenke et al., 1992]). 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Its toxicity can result from three different forms of it, elemental (Hg0), mercuric ion (Hg2+), or organic mercury compounds. It can be absorbed through respiratory tract, skin, or digestive tract, and give rise to poisoning. Mercury toxicity is related to its affinity to form tight coordinate bonds with sulfhydryl groups diffusely disrupting enzyme systems in multiple organs such as brain, kidney, and lung. While mercury poisoning is still seen in some occupations, recently there has been much concern over the potential health hazards brought about by the contamination of many ecosystems. Different forms of mercury in the environment can be interconverted. Methylmercury may be formed in water and soil and accumulated in fish, which could cause mercury poisoning after ingestion. Phenylmercuric acetate has been used as a pesticide, herbicide, fungicide, disinfectant and a preservative in cosmetics. Methylmercury chloride has been used as a fungicide. Some bacteria are resistant to inorganic mercury salts and organomercurials including the above two compounds because they contain two enzymes for mercury conversion. Organomercurial lyase cleaves the C-Hg bond and releases Hg(II) in addition to the respective organic compound ([http://www.ncbi.nlm.nih.gov/pubmed/3542021|Begley et al., 1986]). Mercuric reductase reduces Hg(II) to Hg0, which is less reactive and toxic, and easily volatilizes from the medium ([http://www.ncbi.nlm.nih.gov/pubmed/2067577|Schiering et al., 1991]). In the reactions shown in the graphical pathway map, thiolates act as ligands to the mercury. 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Eighty million pounds are applied to soils annually in the United States, more than any other herbicide. Atrazine is the leading member of a class of triazine ring-containing herbicides that includes simazine and terbuthylazine. The Triazine Metapathway Map contains additional information on triazine metabolism. A number of different bacteria have been identified that are capable of metabolizing atrazine to ammonia and carbon dioxide. Atrazine biodegradation has been found to occur via several different pathways that funnel into cyanuric acid metabolism. A gene region from Pseudomonas sp. strain ADP encoding atrazine degradation enzymes has been cloned and characterized. The initial hydrolytic dechlorination of atrazine to hydroxyatrazine ([http://www.ncbi.nlm.nih.gov/pubmed/7574646|de Souza et al., 1995]) is an animated reaction. Two enzymes belonging to the amidohydrolase protein family catalyze the sequential removal of ethylamine and isopropylamine ([http://www.ncbi.nlm.nih.gov/pubmed/9055410|Boundy-Mills et al., 1997] and [http://www.ncbi.nlm.nih.gov/pubmed/9422605|Sadowsky et al., 1998]). Degradation by Rhodococcus sp. strain N186/21 is initiated by oxidative removal of either the ethyl or isopropyl group ([http://www.ncbi.nlm.nih.gov/pubmed/7646049|Nagy et al., 1995]). Deethylatrazine undergoes a second oxidative removal of the isopropyl group. 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The first metabolite of the propylene degradation pathway is 1,2-Epoxypropane. This compound is an aliphatic epoxide with known stereochemistry of 95% (R)-1,2-Epoxypropane and 5% (S)-1,2-Epoxypropane. Aliphatic epoxides have been extensively studied because of their toxicity, mutagenicity and potential carcinogenicity ([http://www.ncbi.nlm.nih.gov/pubmed/370573|Wade, 1978]). The study of propylene degradation will help to understand the way in which toxic alkene epoxides are degraded by bacteria. Propylene is also a source of carbon and energy for different bacteria such as Xanthobacter Py2. The degradation of propylene leads two compounds that can go into intermediary metabolism, acetoacetone and actetone. The reaction that produces these intermediates is catalyzed by an interesting epoxide carboxylase. In the presence of carbon dioxide this enzyme converts propylene oxide into acetoacetate. 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It is a systemic insecticide that acts by inhibiting cholinesterases, enzymes involved in transmitting nerve impulses. It is not recommended for use by the homeowners because it is extremely toxic and persistent. Because of its persistence in soil it is most useful in controlling soil-dwelling nematodes (microscopic roundworms that suck plant roots and transmit disease to them). Chemically, it is an organophosphate, O,O-diethyl-S-(ethylthio)methylphosphorodithioate. Like all organophosphates, it is related to the nerve gases and is among the most toxic of all pesticides to vertebrates, including humans (Rani et al., 2009). It is among the most widely used pesticides even though it is highly toxic. According to the EXTOXNET Phorate Pesticide Information Profile, single-time exposure at high doses can interfere with cholinesterase activity leading to numbness, headache, dizziness, nausea, a difficulty breathing, and slow heartbeat and if the dose is too high, potentially death. Long-term, low-dose exposure primarily targets the nervous system, with little evidence supporting any teratogenic, carcinogenic, or mutagenic effects. Degradation of phorate occurs in two branches. The left branch is a two-step oxidation of the ethylthio sulfur ([http://www.ncbi.nlm.nih.gov/pubmed/402103|Laveglia and Dahm, 1977]). In the right branch, Ralstonia eutropha strain AAJ1 degrades a high percentage of phorate to phosphate and sulfate anions, with the less toxic diethyl dithiophosphate as one intermediate (Rani et al., 2009). The reaction intermediates diethylthiophosphate, ethylthiophosphate and coproduct ethanol are postulated, though diethylthiophospate is observed in parathion degradation. 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It is a mutagen and suspected carcinogen. It volatilizes from soil very easily, and can contaminate groundwater ([http://www.ncbi.nlm.nih.gov/pubmed/15647563|Yang et al. 2005]). There are several studies examining mammalian degradation, but less is known about its microbial degradation. The microbial metabolism begins when toluene-4-monooxygenase converts NDMA to N-nitrodimethylamine (NTDMA) by oxygenating the nitrogen. Several other enzymes with broad specificity, like alkane monooxygenases, can transform NDMA as well. Some example organisms include: Rhodococcus ruber ENV425P, Mycobacterium vaccae JOB5, and Methylosinus trichospoium OB3b ([http://www.ncbi.nlm.nih.gov/pubmed/15672376|Sharp et al. 2005]). N-Nitrodimethylamine is transformed to N-nitromethylamine (NTMA) and formaldehyde, which funnel to intermediary metabolism. Pseudomonas mendocina KR1 transformed this compound but could not grow on it or mineralize it significant amounts, suggesting the reaction is cometabolic. 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It is successful in 80% of cases and shows very few side effects ([http://www.ncbi.nlm.nih.gov/pubmed/14961135|Gobernato et al., 2003]). Adverse side effects, mainly liver toxicity, have been observed in patients with cystic fibrosis ([http://www.ncbi.nlm.nih.gov/pubmed/11440232|Durupt et al., 2001]). Bacterial resistance has been observed ([http://www.ncbi.nlm.nih.gov/pubmed/14677948|Fillgrove et al., 2003] and Marchese et al., 2003). Because of microbial resistance, some other drugs can no longer be recommended as reliable agents. Fosfomycin remains a drug of choice for the eradication of many uncomplicated infections. This antibiotic is biosynthesized by Streptomyces from (S)-2-hydroxypropylphosphonic acid ([http://www.ncbi.nlm.nih.gov/pubmed/15315444|Liu et al., 2004]). The biodegradation was initially studied in Listeria monocytogenese, but similar degradation pathways occur in many bacterial pathogens. 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"description": "As the highest oxidation state of nitrogen and one of the reactive, or \"fixed\", forms of nitrogen, nitrate can serve both as a source of nitrogen for growth and an electron sink. Under anaerobic conditions, nitrate metabolism occurs in several, competing, microbial processes. Dissimilatory nitrate reduction to ammonia (DNRA) and assimilatory nitrate reduction to ammonia retain the nitrogen in a fixed form, ammonia, keeping it available for further biological processes ([http://www.ncbi.nlm.nih.gov/pubmed/9409151|Zumft, 1997]). In contrast, denitrification ([http://www.ncbi.nlm.nih.gov/pubmed/9409151|Zumft, 1997]) ultimately transforms nitrate to dinitrogen (N2), a gas that removes the nitrogen from the habitat, unless/until nitrogen fixation once again fixes the nitrogen. In the presence of nitrite, the anaerobic ammonium oxidation (anammox) process also produces N2, by effectively combining nitrite with ammonia ([http://www.ncbi.nlm.nih.gov/pubmed/18340342|Keunen, 2008]). DNRA, denitrification, and anammox processes result in energy conservation and provide an electron sink. DNRA also functions to remove excess fixed nitrogen from an organism. Assimilatory nitrate reduction provides ammonia for biosynthesis of nitrogen-containing compounds ([http://www.ncbi.nlm.nih.gov/pubmed/9409151|Zumft, 1997]; [http://www.ncbi.nlm.nih.gov/pubmed/21219945|Kraft et al., 2011]). Nitrate reduction by microorganisms is a major biogeochemical process. The flux through denitrification in the ocean is estimated to be 450 Tg N y-1 (Codispoti, LA, Brandes JA, Christensen, JP, Devol, AH, Naqvi, SWA, Paerl, HW and Yoshinari T, Scientia Marina, 65:Suppl.2, 85-105). In addition, the anammox pathway accounts for roughly 50% of fixed nitrogen turnover in marine environments ([http://www.ncbi.nlm.nih.gov/pubmed/16163345|Arrigo et al., 2005]). Nitrate concentrations are also an important issue in agricultural fertilizer use and wastewater treatment. Although plants can use nitrate as a nitrogen source, excess nitrate in bodies of water and in drinking water supplies can cause algal blooms and lead to public health problems, respectively ([http://www.ncbi.nlm.nih.gov/pubmed/21219945|Kraft et al., 2011]). The first step of the nitrate degradation pathway is the two electron reduction of nitrate to nitrite, which is accomplished by three classes of nitrate reductases in bacteria and archaea. Assimilatory nitrate reductases (NAS) are usually cytoplasmic and enable microbes to use environmental nitrate as a nitrogen source. Periplasmic nitrate reductases (NAP) perform redox balancing, scavenge nitrate in nitrate-limited environments, and serve in aerobic or anaerobic denitrification. Found in the membrane, respiratory nitrate reductases (NAR) enable the use of nitrate as a terminal electron sink in DNRA and in anaerobic denitrification ([http://www.ncbi.nlm.nih.gov/pubmed/16412515|Gonz\ufffdlez et al., 2006]). Subsequently, nitrite can be reduced directly to ammonia, the most negative oxidation state of nitrogen. This reaction is catalyzed by cytochrome c nitrite reductase (NrfA) or octoheme cytochrome c nitrite reductase in DNRA and by NAD(P)H-dependent nitrite reductase (NirB) in nitrite assimilation ([http://www.ncbi.nlm.nih.gov/pubmed/21219945|Kraft et al., 2011]). In denitrification, nitrite is reduced to nitric oxide in a reaction catalyzed by copper nitrite reductase (NirK). The resulting nitric oxide is then reduced to nitrous oxide by nitric oxide reductase. Next, nitrous oxide is reduced to N2 by nitrous oxide reductase. Note that the release to the environment of nitrous oxide, a potent greenhouse gas and ozone layer depleter, can occur before the final reduction step to N2 ([http://www.ncbi.nlm.nih.gov/pubmed/9409151|Zumft, 1997]). In anammox, nitrite is also reduced to nitric oxide, but the reaction is catalyzed by cytochrome cd1 nitrite reductase (NirS). Then, the relatively oxidized nitric oxide is combined with ammonia, which is comparatively reduced, to produce hydrazine in a reaction catalyzed by hydrazine synthase. Hydrazine dehydrogenase next removes electrons and the protons from hydrazine to make N2 ([http://www.ncbi.nlm.nih.gov/pubmed/21964329|Kartal et al., 2011]). Found in the bacterial group Planctomycetes, annamox chemistry occurs in a specialized organelle, the anammoxosome, which has a ladderane lipid membrane, probably structured to protect the cell from the highly reactive pathway intermediates ([http://www.ncbi.nlm.nih.gov/pubmed/18043610|Francis et al., 2007]). 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"url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/47d8d0a3-cc85-4460-afcb-fbe79e595e53", "name": "Testosterone", "description": "Testosterone is a naturally occurring steroid. It has a variety of medical applications, including hormone replacement therapy and treatment of osteoporosis ([http://www.ncbi.nlm.nih.gov/pubmed/16841196|Gao et al., 2006]), and is also widely used as a feed additive in concentrated animal feeding operations (CAFOs) ([http://www.ncbi.nlm.nih.gov/pubmed/15843648|Lorenzen et al. 2005]). Sewage treatment effluent, manure spread onto agricultural fields, and pulp and paper effluent can contain high levels of androgens such as testosterone, which have the potential to contaminate freshwater supplies ([http://www.ncbi.nlm.nih.gov/pubmed/15843648|Lorenzen et al. 2005]). A U.S. Geological Survey study found concentrations of testosterone as high as 0.214 micrograms/L in stream water ([http://www.ncbi.nlm.nih.gov/pubmed/11944670|Kolpin et al., 2002]). The EPA reporting level for this steroid, which is classified as an Endocrine Disrupting Compound (EDC), is 0.005 micrograms/L. Several bacterial species can utilize steroids such as testosterone as a sole carbon source, the best-studied being Nocardia restrictus and Comamonas testosteroni. [http://www.ncbi.nlm.nih.gov/pubmed/16151114|Horinouchi et al. (2005)] have documented the degradation pathway used by Comamonas testosteroni strain TA441. The pathway begins with aromatization of the A ring, followed by metacleavage. The product is then cleaved again to produce 2-hydroxyhexa-2,4-dienoate and 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oate. i The degradation pathway for the latter product is not yet known, although it may be broken down via mechanisms similar to those found in fatty acid metabolism ([http://www.ncbi.nlm.nih.gov/pubmed/15474469|Horinouchi et al., 2004]). 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"Amide groups are common in biological molecules (e.g. peptide bonds), but thioamides are rare. Thioamide groups are found naturally in the copper-chelating compound methanobactin described in Methylosinus trichosporium OB3b ([http://www.ncbi.nlm.nih.gov/pubmed/15361623|Kim et al., 2004]). The antibiotic sulfinemycin, produced by Streptomyces albus NRRL 3384, has a primary thioamide S-oxide moiety ([http://www.ncbi.nlm.nih.gov/pubmed/7730167|Lee et al., 1995]). Thioamide compounds such as 2-ethyl-4-pyridinecarbothioamide (ethionamide) are important second-line drugs in the treatment of multi-drug resistant Mycobacterium tuberculosis and M. leprae ([http://www.ncbi.nlm.nih.gov/pubmed/12164478|Schroeder et al., 2002]; [http://www.ncbi.nlm.nih.gov/pubmed/3910748|Shepard et al., 1985]). Toxicity of thioamides in mammals and Mycobacterium spp. is dependent on metabolic activation of the compounds via sequential oxygenations of the thioamide sulfur atom by flavoprotein monooygenases or cytochromes P450 ([http://www.ncbi.nlm.nih.gov/pubmed/10944230|Debarber et al., 2000]; [http://www.ncbi.nlm.nih.gov/pubmed/10900221|Wang et al., 2000]; [http://www.ncbi.nlm.nih.gov/pubmed/28917|Porter and Neal, 1978]). Thioamide S-oxides are not toxic without further oxygenation and investigators have proposed that thioamide S,S-dioxides (which have not been isolated) or further oxidized species exert the observed toxic effects ([http://www.ncbi.nlm.nih.gov/pubmed/11823459|Vannelli et al., 2002]; [http://www.ncbi.nlm.nih.gov/pubmed/6135576|Hanzlik and Cashman, 1983]; [http://www.ncbi.nlm.nih.gov/pubmed/28917|Porter and Neal, 1978]). This activity results in elimination of the thioamide sulfur and formation of nitrile and/or amide derivatives ([http://www.ncbi.nlm.nih.gov/pubmed/11823459|Vannelli et al., 2002]; [http://www.ncbi.nlm.nih.gov/pubmed/10944230|Debarber et al., 2000]; [http://www.ncbi.nlm.nih.gov/pubmed/28917|Porter and Neal, 1978]). EtaA, a thioamide-oxidizing flavin monooxygenase in Mycobacterium tuberculosis, converted thiobenzamide to thiobenzamide S-oxide and benzamide ([http://www.ncbi.nlm.nih.gov/pubmed/11823459|Vannelli et al., 2002]). Ralstonia pickettii TA, which can grow using thioacetamide as a sole source of nitrogen and carbon ([http://www.ncbi.nlm.nih.gov/pubmed/16997975|Dodge et al., 2006]), converted thiobenzamide sequentially to thiobenzamide S-oxide, benzonitrile, and benzamide. Whole M. tuberculosis cells metabolized ethionamide similarly through the corresponding S-oxide, nitrile, and amide derivatives ([http://www.ncbi.nlm.nih.gov/pubmed/10944230|Debarber et al., 2000]). Sulfur eliminated from thiobenzamide by R. pickettii TA was detected in the medium as sulfur dioxide/sulfite. Release of sulfur at this oxidation state from thiobezamide S,S-dioxide, the proposed intermediate after thiobenzamide S-oxide, requires an additional two-electron oxidation. 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"1,1,1-Trichloro-2,2-bis-(4`-chlorophenyl)ethane (DDT)", "description": "1,1,1-Trichloro-2,2-bis-(4`-chlorophenyl)ethane (DDT), the first of the chlorinated organic insecticides, is a widely distributed and persistent xenobiotic contaminant in the environment. DDT is not metabolized very rapidly by animals; instead, it is deposited and stored in the fatty tissues. The biological half-life of DDT is about eight years; that is, it takes about eight years for an animal to metabolize half of the amount it assimilates. If ingestion continues at a steady rate, DDT builds up within the animal over time. Despite being banned in the United States, DDT continues to be widely used in many developing nations. This page shows only its aerobic pathway. The anaerobic degradation of DDT is documented elsewhere in the EAWAG-BBD. The chemical structure of DDT, including aromatic and alicyclic moieties, offers a variety of possibilities for biochemical attack. Several aerobic pathways for DDT metabolism in different organisms were suggested ([http://www.ncbi.nlm.nih.gov/pubmed/9563945|Quensen et al., 1998], [http://www.ncbi.nlm.nih.gov/pubmed/9603826|Hay et al., 1998], [http://www.ncbi.nlm.nih.gov/pubmed/8117093|Nadeau et al., 1994]). Compounds in brackets were not identified but postulated based on other studies, such as those of the Biphenyl Pathway. The steps labeled A, B, C, D, E are mutiple steps whose intermediates are not identified yet. All descriptions as follows were proposed based on other similar experiments. In A, DDE is attacked by a dioxygenase at the ortho and meta positions. Such an attack would give rise to a 2,3-dihydrodiol-DDE intermediate. In B and D, 2-(4`-Chlorophenyl)-3,3-dichloropropenoate may proceed via decarboxylation to yield 1,1-dichloro-(4`-chlorophenyl)ethane. The latter will undergo oxidation of the aliphatic side chain to yield 1,1-dichloro-(4`-chlorophenyl)ethanol which is further oxidized to yield 4-Chloroacetophenone. The terminal methyl group of 1,1-dichloro-(4`-chlorophenyl)ethane may also undergo oxidation to yield phenylacetic acid. In C, the transformation of 4-Chloroacetophenone to 4-Chlorobenzaldehyde may be via complete oxidation and subsequent decarboxylation of the terminal methyl group. 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It is used in paint removers, degreasing and cleaning fluids, and even as an extraction solvent in the decaffeination of coffee. Although dichloromethane is a potential carcinogen, the EPA Toxic Release Inventory reports that U.S. industrial discharges of dichloromethane amounted to 29,000 metric tons in 1994, down from 46,000 in 1990. The compound has an atmospheric half-life of several months, preventing it from reaching the stratosphere where it would be damaging to ozone. Both aerobic and anaerobic methylotrophic bacteria utilize dichloromethane as a carbon and energy source. A glutathione-dependent substitution which converts dichloromethane to inorganic chloride and formaldehyde (a central metabolite in methylotrophic growth) is the principal metabolic reaction in this degradation pathway. Dichloromethane dehalogenase, the enzyme that catalyzes the first step of this pathway, also known to initiate the degradation of dibromomethane (CH2Br2), chlorofluoromethane (CH2ClF), bromochloromethane (CH2BrCl), and diiodomethane (CH2I2). 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It is commonly found at sites of gas factory pollution. The compound is considered toxic, but toxicology data specific to anthracene is uncommon, or somewhat conflicting. [http://www.ncbi.nlm.nih.gov/pubmed/11682202|Dean-Ross et al. (2001)] state that anthracene is neither genotoxic nor carcinogenic, but is a threat to the environment because of its toxicity to aquatic life, especially through photo-induced toxicity. [http://www.ncbi.nlm.nih.gov/pubmed/12867182|Ma, Zhang, and Wong (2003)] state that anthracene is a priority pollutant because it is carcinogenic, and may cause aberration and mutation in biological tissues. Anthracene biodegradation by Gram-negative and Gram-positive bacteria and numerous fungi has been reported (Cerniglia, CE, 1992. Biodegradation of Polycyclic Aromatic Hydrocarbons. Biodegradation, 3: 351-368). This pathway map is limited to bacterial metabolism of anthracene. Pseudomonas spp. strains with plasmids containing genes for naphthalene degradation were found to mineralize anthracene ([http://www.ncbi.nlm.nih.gov/pubmed/8328809|Sanseverino et al., 1993]). Bacteria initiate anthracene degradation by hydroxylation of the aromatic ring to yield cis-1,2-dihydroanthracene-1,2-diol ([http://www.ncbi.nlm.nih.gov/pubmed/14342521|Evans et al., 1965]; [http://www.ncbi.nlm.nih.gov/pubmed/1239455|Akhtar et al., 1975]; [http://www.ncbi.nlm.nih.gov/pubmed/965633|Jerina et al., 1976]). This intermediate is converted to anthracene-1,2-diol, which is cleaved at the meta position to yield 4-(2-hydroxynaph-3-yl)-2-oxobut-3-enoate ([http://www.ncbi.nlm.nih.gov/pubmed/14342521|Evans et al., 1965]). This compound may spontaneously rearrange to form 6,7-benzocoumarin or be converted to 3-hydroxy-2-naphthoate, from which degradation proceeds through 2,3-dihydroxynaphthalene to phthalate ([http://www.ncbi.nlm.nih.gov/pubmed/10653712|Annweiler et al., 2000]). This pathway has been identified in Gram-negative bacteria ([http://www.ncbi.nlm.nih.gov/pubmed/11682202|Dean-Ross et al., 2001]; [http://www.ncbi.nlm.nih.gov/pubmed/11282593|Moody et al., 2001]). Mycobacterium sp. strain LB501T can degrade 3-hydroxy-2-naphthoate acid through phthalate ([http://www.ncbi.nlm.nih.gov/pubmed/12513994|van Herwijnen et al., 2003]). The Gram-positive bacteria Rhodococcus sp. and Mycobacterium vanbaalenii PYR-1 (formerly Mycobacterium sp. strain PYR-1) also show ortho cleavage of anthracene-1,2-diol to produce 3-[(Z)-2-carboxyvinyl]-2-napthoate ([http://www.ncbi.nlm.nih.gov/pubmed/11682202|Dean-Ross et al., 2001]; [http://www.ncbi.nlm.nih.gov/pubmed/11282593|Moody et al., 2001]). M. vanbaalenii PYR-1 can produce 1-methoxy-2-hydroxyanthracene from anthracene-1,2-diol, representing a third pathway branch from this intermediate (not shown). In addition to initiating anthracene degradation by 1,2-hydroxylation, M. vanbaalenii PYR-1 can catalyze 9,10-hydroxylation of anthracene to produce anthracene-9,10-dihydrodiol, which is converted to 9,10-dihydroxyanthracene and spontaneously oxidized to 9,10-anthraquinone ([http://www.ncbi.nlm.nih.gov/pubmed/11282593|Moody et al., 2001]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "e72febe5-c8cd-4d53-818e-fbd5bafbf722", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/fe417a7c-671a-476b-9fe0-0e73133aa4db/node/e72febe5-c8cd-4d53-818e-fbd5bafbf722", "name": "Phthalate", "description": "no description", "aliases": [], "default_node_label": {"uuid": "f47d5621-9381-4f0d-b3c5-c6bd7ad0536c", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/beeb6652-6ce2-4acf-86dc-75a0ca5d9615/structure/f47d5621-9381-4f0d-b3c5-c6bd7ad0536c"}, "node_labels": [{"uuid": "f47d5621-9381-4f0d-b3c5-c6bd7ad0536c", "url": 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Perchlorate consists of an atom of chlorine surrounded by four atoms of oxygen. It occurs as ammonium, potassium, magnesium or sodium salts. These perchlorate salts bind weakly to soil particles and are not significantly broken down in the environment (EPA, 1998). In water, however, perchlorate salts are extremely soluble and highly mobile, migrating faster and farther than many other water contaminants. Together, these properties make perchlorate a particularly persistent and problematic pollutant once it contaminates groundwater. Perchlorate salts are used in a variety of products as diverse as electronic tubes, car air bags, leather tanning and fireworks. Perchlorate`s main use is as an explosive propellant: Ninety percent of the perchlorate produced goes into solid rocket fuel for Air Force missiles and the NASA space shuttle. Perchlorate impairs normal thyroid function because it is taken up preferentially by the thyroid gland in place of iodide. The thyroid gland is therefore deprived of iodide, a necessary nutrient which it is designed to concentrate; and without iodine, thyroid hormone is inactive. As a result, perchlorate can disrupt the delicate balance of hormone levels in the body which are crucial for healthy metabolism, growth and development. Perchlorate-reducing bacteria use perchlorate ion as a terminal electron acceptor during the anaerobic oxidation of acetate ([http://www.ncbi.nlm.nih.gov/pubmed/10583970|Coates et al., 1999]). Molybdenum is required as a cofactor. The overall stoichiometry of the pathway shown here is: CH3COO- + ClO4- -------> 2HCO3- + H+ + Cl- It is shown here as three discrete steps. However Dr. Coates states (personal communication, 2004) that presently: The perchlorate reductase and chlorate reductase enzymes are not consecutive in any organism. Some organisms reduce chlorate to chlorite using the chlorate reductase while some (the majority) reduce perchlorate to chlorite using the perchlorate reductase. 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It chelates alkaline earth or other heavy metal ions and can substitute for ethylenediaminetetraacetic acid in a variety of applications. The standard synthesis of iminodisuccinate results in a mixture of its three epimers: (R,R)-iminodisuccinate, (S,S)-iminodisuccinate, and the meso (R,S)-iminodisuccinate. Iminodisuccinate degradation is initiated by an epimerase that interconverts the epimers (R,R)-iminodisuccinate, (R,S)-iminodisuccinate, and (S,S)-iminodisuccinate ([http://www.ncbi.nlm.nih.gov/pubmed/16934291|Lohkamp et al., 2006]). The carbon-nitrogen bond in (R,S)-iminodisuccinate or (S,S)-iminodisuccinate, but not (R,R)-iminodisuccinate, is cleaved by iminodisuccinate lyase. This nonhydrolytic cleavage of (S,S)-iminodisuccinate produces fumarate and L-aspartate. 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(1994)]), and the classification therein is based on the time of desulfonation: prior to (two different mechanisms), simultaneous with, or after ring cleavage. Catabolism of toluene-4-sulfonate (TS or TSA), a dye precursor, may progress in accordance with two of the four mechanisms, both involving desulfonation prior to ring cleavage. The left pathway presented below is unique in that the initial step does not involve an oxygenation of the sulfonated carbon, but monooxygenation of the methyl group. However, the final, desulfonating step is a dioxygenation catalyzed by Fe2+-activated 4-sulfobenzoate 3,4-dioxygenase. Alicaligenes sp. strain O-1 ([http://www.ncbi.nlm.nih.gov/pubmed/8075807|Junker et al. (1994)], is thought to contain two independent operons encoding desulfonative pathways, with the enzymes encoded displaying low substrate specificity. The middle pathway below reproduces the initial desulfonation reaction of TS, which can be catalyzed by 2-aminobenzenesulfonate dioxygenase system (2ASDOS) or benzenesulfonate dioxygenase system (BSDOS). There is a EAWAG-BBD reaction page for each enzyme. Little is known about the details of the transformation of TS into 4-hydroxytoluene, although further investigation is currently underway. `Toluene-4-sulfonate monooxygenase` is a proposed name, and 1.14.13.- a proposed E.C. code, for the reaction enzyme. Pseudomonas putida strain S-313 catalyzes only desulfonation of TS, which can serve as its sole source of sulfur. 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"Fluorene, a tricyclic aromatic hydrocarbon, contains a five-membered ring. It is a major component of fossil fuels and their derivatives and is also a byproduct of coal-conversion and energy-related industries. It is commonly found in vehicle exhaust emissions, crude oils, motor oils, coal and oil combustion products, waste incineration, and industrial effluents. Fluorene is one of the compounds on the EPA Priority Pollutants List. This naphthenoaromatic compound bears structural relationships to other chemicals of concern (carbazoles, dibenzothiophenes, dibenzofurans, and dibenzodioxins) and is thus a useful model for biodegradation studies. The chemical structure of fluorene, including aromatic and alicyclic moieties, offers a variety of possibilities for biochemical attack. Two pathways for fluorene metabolism in Arthrobacter sp. strain F101 were suggested by [http://www.ncbi.nlm.nih.gov/pubmed/9055403|Casellas et al., 1997]. Compounds in brackets were not identified but postulated based on other experiments. A nonproductive route, initiated by monooxygenation at C-9, leads to the accumulation of 9-fluorenone. An alternative pathway is initiated by dioxygenation at C-1, C-2 or at C-3, C-4. The corresponding cis-dihydrodiols undergo dehydrogenation and then meta-cleavage which is catalyzed by an extradiol dioxygenase. After the aldolase reaction and decarboxylation of the fission product, the resulting indanones are substrates for a biological Baeyer-Villiger reaction, yielding the aromatic lactones 3-isochromanone and 3,4-dihydrocoumarin. 1-Indanone also appears to be a substrate for aromatic hydroxylation yielding 3-hydroxy-1-indanone, probably a dead-end product. Arene dioxygenases have been reported to act as monooxygenases hydroxylating methylene groups ([http://www.ncbi.nlm.nih.gov/pubmed/3365392|Wackett et al., 1988]). Another pathway, observed in Sphingomonas sp. LB126, Brevibacterium sp. DPO1361, and Pseudomonas sp. F274, was reported by [http://www.ncbi.nlm.nih.gov/pubmed/11766961|Wattiau et. al, 2001]. In this pathway, fluorene is converted to phthalic acid and 2-hydroxypenta-2,4-dienoate by way of 9-fluorenone and a biphenyl intermediate. Other organisms which can metabolize fluorene include Pseudomonas sp. strain NCIB 9816/11 ([http://www.ncbi.nlm.nih.gov/pubmed/8899998|Resnick et al., 1996]), Pseudomonas cepacia F297 ([http://www.ncbi.nlm.nih.gov/pubmed/7487007|Grifoll et al., 1995]), and Staphylococcus auricularis strain DBF63 ([http://www.ncbi.nlm.nih.gov/pubmed/8439154|Monna et al., 1993]). Naphthalene dioxygenase, the enzyme which initiates fluorene metabolism in Ps. strain NCIB 9816/11, is used in a biotechnological process to synthesize the blue jean dye indigo. 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This molecule contains an azoxy group and is being studied to learn more about the synthesis of naturally occurring azoxy compounds ([http://www.ncbi.nlm.nih.gov/pubmed/12688722|Tao et al., 2003]. Valanimycin is synthesized by condensation of L-serine with isobutylhydroxylamine; the latter compound is produced from L-valine via isobutylamine. A key step in the synthesis pathway, the oxidation of isobutylamine to isobutylhydroxylamine, is catalysed by a two-component flavin monooxygenase. The two components are isobutylamine N-hydroxylase and NAD(P)H:FAD oxidoreductase. The second component is required to provide reduced flavin cofactor since isobutylamine N-hydroxylase is unable to reduce FAD or FMN on its own. Purification of isobutylamine N-hydroxylase from Streptomyces viridifaciens has been reported ([http://www.ncbi.nlm.nih.gov/pubmed/9056232|Parry et al., 1997]). The exact mechanism of N-N bond formation is not very clear. 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Extensive deaths and deformities in waterfowl and other wildlife are attributed to micromolar concentrations of selenium at the Kesterton reservoir. The soluble oxyanions selenate (Se(VI)) and selenite (Se(IV)) are the primary forms of selenium in oxic environments. Se(VI) does not readily undergo chemical reduction under physiological conditions of pH and temperature. The toxicity of selenium involves the substitution of selenium for sulfur in thiol-containing proteins. In animals, selenium toxicity is conferred primarily by ingestion of food that is rich in seleniferous compounds (e.g. selenomethionine). Selenium poisoning can result in conditions known as alkali disease and the blind staggers. Plants and microbes can incorporate inorganic selenium oxyanions into their tissues by assimilatory reduction to the level of selenide, followed by their assembly into proteins. At present, only the selenate reductase of Thauera selenatis has been well-characterized. This enzyme is a periplasmic, trimeric enzyme that is very substrate specific and contains molybdenum. It reduces four molecules of selenate to four molecules of selinite ([http://www.ncbi.nlm.nih.gov/pubmed/10525169|Stolz and Oremland, 1999]). Selenate respiring bacteria have been shown to occur in a wide range of environments and not confined to any specific genus. The full impact of their activities on the biogeochemical cycling of selenium is only now being realized. 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Generally a toxic class of compounds ([http://www.ncbi.nlm.nih.gov/pubmed/11306561|Goda, 2001]), isonitriles are unusual in that they contain a formally mono-coordinated carbon atom (similar to the carbon atom in carbon monoxide). Because the isocyano group can react with both electrophiles and nucleophiles attached to the same carbon atom, isonitriles have proven to be versatile reagents in organic synthesis ([http://www.ncbi.nlm.nih.gov/pubmed/12023110|Domling, 2002]). Isonitriles are produced naturally by a variety of organisms, including bacteria, fungi, and marine sponges. They often have antibiotic properties; xanthocillin, a compound produced by Penicillium notatum which has a wide spectrum of antibiotic activity, is an isonitrile (Hagedorn and T\ufffdnjes, Pharmazie, 1957). The metabolism of isonitriles is not well understood. Currently, only one enzyme involved in isonitrile metabolism, isonitrile hydratase, has been identified ([http://www.ncbi.nlm.nih.gov/pubmed/11306561|Goda et al., 2001]; [http://www.ncbi.nlm.nih.gov/pubmed/12244065|Goda et al., 2002]). 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This chemical dissipates primarily by biodegradation in the soil ([http://www.ncbi.nlm.nih.gov/pubmed/9925619|Martin et al., 1999]), or in water ([http://www.ncbi.nlm.nih.gov/pubmed/2604396|Steen and Colette, 1989]). Two of the pathways share the same first step ([http://www.ncbi.nlm.nih.gov/pubmed/9925619|Martin et al., 1999]), and are intiated by Pseudomonas sp. PEM1, Acinetobacter sp. BEM2, and Pseudomonas sp. GH1 ([http://www.ncbi.nlm.nih.gov/pubmed/10698790|Martin et al., 2000]). The other pathway is begun by Moraxella sp. DAK3 and continued by Xanthobacter sp. 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After human consumption, it is excreted via urine mainly as an unchanged compound (90%), with a small percentage of atenolol glucuronide (0.8–4.4%) and hydroxyatenolol (1.1–4.4%, hydroxylation of the benzylic position) ([http://www.ncbi.nlm.nih.gov/pubmed/18922538|Radjenovic et al., 2008]). Atenolol has been found to be partially removed in wastewater treatment plants, which has been shown to be mainly due to biotransformation. In laboratory studies with sludge from both the aerobic stages of full-scale conventional activated sludge treatment plants and sludge from a laboratory-scale membrane bioreactor, it was shown to be quantitatively transformed to the carboxylic acid product of primary amide hydrolysis, atenolol acid ([http://www.ncbi.nlm.nih.gov/pubmed/18922538|Radjenovic et al., 2008]; [http://www.ncbi.nlm.nih.gov/pubmed/20799730|Helbling et al., 2010]). 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"http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/f2391296-24da-4c95-9da9-fc8c47ad423f"}]}], "scenarios": []}, {"uuid": "8ee9cf25-ece9-4c21-886c-23936be81f30", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/8ee9cf25-ece9-4c21-886c-23936be81f30", "name": "(+)-Camphor", "description": "Camphor exists in two enantiomers, but the (+)-isomer is more widely distributed. The bicyclic monoterpene ketone (+)-camphor is one of the major components in the leaves of common sage. Camphor and other terpenoid compounds do not accumulate in the environment due to their ready metabolism by many soil bacteria. The best studied reactions of this type are the early steps of the (+)-camphor degradation pathway which require the cytochrome P-450cam hydroxylase operon (camDCAB) on the CAM plasmid of Pseudomonas putida ATCC 17453. Reactions for the partial oxidation of (+)-camphor have been shown to proceed by an initial hydroxylation at carbon 5, followed by dehydrogenation to form 2,5-diketocamphane. Subsequent ring oxidation by a 1,2-monooxygenase, results in the formation of a 5-oxo-1,2-campholide ([http://www.ncbi.nlm.nih.gov/pubmed/8515237|Jones et al., 1993]). This 5-oxo-1,2-campholide may be unstable and undergo spontaneous cleavage to form 2-oxo-delta3-4,5,5-trimethylcyclopentenylacetate. The synthesis of 2-oxo-delta3-4,5,5-trimethylcyclopentenylacetyl-CoA was detected when an extract of (+)-camphor-grown Pseudomonas putida was incubated with 2-oxo-delta3-4,5,5-trimethylcyclopentenylacetate, CoA, ATP, and CoA ester synthetase ([http://www.ncbi.nlm.nih.gov/pubmed/6848481|Ougham et al., 1983]). The involvement of 2-oxo-delta3-4,5,5-trimethyl-cyclopentenylacetyl-CoA 1,2-monooxygenase was not experimentally established but it is suggested by the accumulation of the delta-lactone of 5-hydroxy-3,4,4-trimethyl-delta2-pimelyate from 2-oxo-delta3 -4,5,5-trimethylcyclopentenylacetate. 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This page describes the microbial degradation of 2-methylnaphthalene under aerobic conditions. An anaerobic 2-methylnaphthalene degradation pathway is presented elsewhere. A soil isolate, Pseudomonas putida CSV86 is able to grow using 1-and 2-Methylnaphthalene as the sole sources of carbon and energy ([http://www.ncbi.nlm.nih.gov/pubmed/8042906|Mahajan et al., 1994]). In the right-most pathway, the aromatic ring adjacent to the one bearing the methyl moiety is oxidized, resulting in the formation of methylsalicylates and methylcatechols. In the left-most pathway the methyl side chain is hydroxylated and further converted resulting in the formation of naphthoic acid. In addition to this, 2-hydroxymethylnaphthalene formed by the hydroxylation of the methyl group of 2-methylnaphthalene undergoes aromatic ring hydroxylation of the methyl group and the resultant dihydrodiol is further oxidized by a series of enzyme catalyzed reactions to form the end product 4-hydroxymethylcatechol ([http://www.ncbi.nlm.nih.gov/pubmed/8042906|Mahajan et al., 1994]). Other organisms able to degrade 2-Methylnaphthalene include Marinobacter sp. NCE312, Vibrio cyclotrophicus, Neptunomonas naphthovorans, Pseudomonas fluorescens LP6a, and Mycobacterium sp. Naphthalene dioxygenase, an enzyme in this pathway, is used in a biotechnological process to synthesize the blue jean dye indigo. 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Furfural can contaminate the product streams of lignocellulose breakdown in production of sugar from biomass. This contaminant inhibits the fermentation of glucose, and thus prevents efficient formation of the product. Methanococcus sp. B can anaerobically degrade 2-methylfurfural and 5-methylfurfural to furfural and methane ([http://www.ncbi.nlm.nih.gov/pubmed/16535410|Boopathy, 1996]). Understanding biodegradation for this compound is important for remediation of paper mill and oatmeal processing effluents, as well as the development of renewable energy sources ([http://www.ncbi.nlm.nih.gov/pubmed/1929367|Rivard, 1991]). Some methanogenic bacteria can degrade furfural to methane and carbon dioxide. Desulfovibrio sp. F-1 anaerobically degrades furfural to acetate (not shown in pathway) ([http://www.ncbi.nlm.nih.gov/pubmed/16346423|Brune, 1983)]. Furfural can be converted by E. coli LYO1, yeast and methanogens to furfuroyl alcohol, which does not inhibit the production of glucose ([http://www.ncbi.nlm.nih.gov/pubmed/16535618|Belay et al., 1997] and [http://www.ncbi.nlm.nih.gov/pubmed/16111779|Gutierrez et al., 2006]). Oxidation of the alcohol yields furfural. Furfural is also degraded to 2-oxoglutaric acid (alpha keto-glutarate) via an activating CoA ester in Pseudomonas putida Fu1 ([http://www.ncbi.nlm.nih.gov/pubmed/16346423|Brune, 1983] and [http://www.ncbi.nlm.nih.gov/pubmed/1929367|Rivard, 1991]). Pseudomonas putida aerobically degrades furfural to produce 2-oxoglutarate. The aldehyde is oxidized to 2-furoate, and subsequent activation via the attachment of a CoA group results in hydroxylation. 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2003]; [http://www.ncbi.nlm.nih.gov/pubmed/9073471|Murata et al., 1997]). Given its potential to contaminate groundwater and other resources, the capacity of microorganisms to degrade it in situ is of considerable interest. 2-Methylnaphthalene is readily metabolized under aerobic conditions ([http://www.ncbi.nlm.nih.gov/pubmed/8042906|Mahajan et al., 1994]), and the well documented aerobic 2-methylnaphthalene degradation pathway is described elsewhere in this database. More recently, an anaerobic degradation pathway has been demonstrated in the laboratory and several of its metabolites found in subsurface petroleum reservoirs, providing evidence for its widespread occurence in nature ([http://www.ncbi.nlm.nih.gov/pubmed/15372028|Aitken et al., 2004]). Although efforts to isolate a particular strain capable of carrying out this pathway have not yet been successful, multiple studies have documented the degradation of 2-methylnaphthalene to 2-naphthoic acid by sulfate-reducing bacterial cultures (e.g., [http://www.ncbi.nlm.nih.gov/pubmed/11097910|Annweiler et al., 2000]; [http://www.ncbi.nlm.nih.gov/pubmed/11440239|Zang et al., 2000]). The pathway listed here, proposed by [http://www.ncbi.nlm.nih.gov/pubmed/15500985|Safinowski and Meckenstock (2004)], begins with the addition of fumerate to the 2-methyl group, followed by conversion to 2-naphthoic acid. The aromatic rings are then reduced and broken ([http://www.ncbi.nlm.nih.gov/pubmed/11823228|Annweiler et al., 2002]). 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NG is toxic to algae, invertebrate, and vertebrates. Nitrosubstituted compounds are widely distributed in the environment because of their use in explosives, dyes, and agricultural chemicals. Pseudomonas putida II-B and Pseudomonas fluorescens I-C are capable of utilizing nitroglycerin as a sole nitrogen source ([http://www.ncbi.nlm.nih.gov/pubmed/9371434|Blehert, D., et al., 1997]). NG reductase catalyzes the NADPH-dependent denitration of NG. The Pseudomonas NG reductases were shown not to be reactive with mononitrate glycerol esters. Yet, nitroglycerin has been shown to be mineralized under anaerobic conditions (C. Chritodoulatos, S. Bhaumik and B. Brodman, 1997, Anaerobic biodegradation of nitroglycerin. Water Res. 31:1462-1470). 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phenylurea herbicide isoproturon (IPU) is used against annual grasses and broad-leaved weeds in cereal production across Europe, resulting in both surface water and ground water pollution ([http://www.ncbi.nlm.nih.gov/pubmed/11722885|Sorensen et al., 2001]). 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Because of its high toxicity and persistence in soil, the use of g-HCH has been prohibited in many countries. g-HCH is degraded rapidly under anaerobic conditions, but is considered extremely persistent in upland soil. Sphingomonas (formerly Pseudomonas) paucimobilis SS86 was isolated from an upland experimental field to which g-HCH was applied once a year for twelve years. The mutant of the strain SS86, named UT26, has nalidixic acid resistance as a genetic marker and utilizes g-HCH as a sole source of carbon and energy under aerobic conditions. The genes and enzymes involved in the g-HCH degradation pathway of S. paucimobilis UT26 have been investigated (Imai et al., 1991; Nagata et al., 1999, J. Ind. Microbiol. Biotechnol. 23: 380-390). The cyanobacteria Anabeana sp. PCC7120 and Nostoc ellipsosporum have also been shown to metabolize lindane. A mixture of 1,2,4- and 1,2,3-trichlorobenzenes is produced ([http://www.ncbi.nlm.nih.gov/pubmed/7534052|Kuritz and Wolk, 1995]). The absolute configuration of 2,4,5-Trichloro-2,5-cyclohexadiene-1-ol and 2,5-Dichloro-2,5-cyclohexadiene-1,4-diol have not yet been determined. 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It is commonly known as TNT and is an explosive used in military shells, bombs, and grenades, in industrial uses, and in underwater blasting. TNT production in the United State occurs solely at military arsenals. Accidental release of TNT has contaminated groundwater and soil at numerous munition manufacturing sites. The U.S. EPA has listed TNT as a priority pollutant and has recommended its removal from contaminated sites. TNT is toxic to algae and invertebrates and chronic exposure to TNT by humans causes harmful health effects, including anemia and abnormal liver function, cataract development, and skin irritation. The EPA has determined that TNT is a possible human carcinogen, based on animal studies. This page shows only its anaerobic pathway. The aerobic degradation of trinitrotoluene is documented elsewhere in the EAWAG-BBD. Few enzymes have been isolated which catalyze the reactions in these pathways. Indeed, most of the reactions are catalyzed by \"non-specific\" NAD(P)H dependent nitroreductases and are uncharacterized. The last reduction steps to produce triaminotoluene occur only under anaerobic conditions and enzymes which can catalyze these reactions have been found in Desufovibrio sp., Clostridium pasteurianum, and Moorella thermoacetica. Many of these nitro group reductions are also catalyzed by purified xenobiotic reductase enzyme ([http://www.ncbi.nlm.nih.gov/pubmed/10515912|Blehert et al., 1999]). A disulfite reductase capable of catalyzing the final reduction to triaminotoluene has only been found in Desulfovibrio sp. There are very few example of TNT mineralization or transformation to a compound in intermediate metabolism by a pure bacterial culture. Generally mineralization is only detected with bacterial consortia. Many of the products of TNT biodegradation are highly reactive and covalently bind to cellular components and any solid supports (such as soil) present in the culture. The latter prevents or prolongs the mineralization process, but also hinders a further spread of TNT contaminants. Several authors have noted the formation of, as yet, unidentified compounds from TNT biodegradation. These have not been included in either the aerobic or anaerobic pathway maps. Prof R. Crawford and co-workers have also identified an adduct formed from methyl glyoxyl and triaminotoluene, however they suggest this product is not a main stream pathway intermediate, but a product produced by a side reaction related to clostridial fermentation. 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S-triazines are characterized by a symmetrical hexameric ring consisting of alternating carbon and nitrogen atoms (pictured below). This meta-pathway will primarily discuss the s-triazine pesticides and similar compounds; however, there are many other groups of s-triazine compounds. In the s-triazine family, atrazine is the most widely used, and the most studied. The pathways below are largely derived from knowledge of the atrazine degradation pathways. Other s-triazines may be degraded by similar mechanisms. In representing the compounds below, we show only the primary ring, amino residues and R-groups. The composition of the R-groups for each compound is designated by the abbreviations employed by Cook (1987, FEMS Microbiol. Rev. 46 93-116) or developed here, as summarized below. The points at which many common triazines feed into the catabolism pathway are shown below. The degree to which these compounds have been studied is indicated by the appearance of the arrow from the compound name to its entry to the pathway. Well Known: Degradation of this compound is well established. Most of the steps and many of the genes catalyzing them have been identified. Known: Degradation of this compound is well established. Many of the steps and a few of the genes catalyzing them have been identified. Partially Known: Degradation of this compound has been observed. Intermediates have been identified which suggest the steps shown here. Putative: Degradation of this compound has been observed. Based on its degradation and the few intermediates identified, it may be degraded through the shown pathway. Unknown: Partial degradation of this compound has been observed. It possibly may be degraded through the shown pathway. Click on a boxed name or phrase for more information. Click on a to see an example of that type of reaction in the atrazine pathway. Click on a boxed name or phrase for more information. Click on a to see an example of that type of reaction in the atrazine pathway.", "aliases": [], "predicted": false, "nodes": [], "edges": [], "scenarios": []}, {"uuid": "9b38552a-5c55-4032-9483-96615fa9c4b7", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/9b38552a-5c55-4032-9483-96615fa9c4b7", "name": "beta-1,2,3,4,5,6-Hexachlorocyclohexane (an/aerobic)", "description": "During the production of the pesticide Lindane (gamma-hexachlorocyclohexane (HCH)), about 85% of the product consisted of isomers such as alpha-, beta- and delta-HCH. They were discarded into the environment, causing serious soil pollution. Aerobic biodegradation mineralizes alpha-, gamma-, and delta-HCH, whereas beta-HCH persists. Therefore, the degradation of beta-HCH and the other isomers was studied under anaerobic conditions by Peter Middeldorp (Environmental Science and Technology (1996) 30(7):2345-2349), in order to develop an anaerobic soil treatment process. beta-HCH was found to anaerobically biodegrade to benzene and chlorobenzene, both of which can undergo further degradation aerobically. The pathway from beta-HCH to benzene and chlorobenzene is the first anaerobic pathway in the EAWAG-BBD. This pathway can be carried out by a Dehalobacter sp. in coculture with a Sedimentibacter sp. ([http://www.ncbi.nlm.nih.gov/pubmed/16329975|van Doesburg et al., 2005]). A second, aerobic, beta-HCH metabolic pathway is mediated by haloalkane dehalogenase LinB in Sphingomonas paucimobilis UT26. The stereochemistry of the 2,3,4,5,6-pentachlorocyclohexanol has not been determined; the stereoisomer shown is based on beta-HCH. The pentachlorocyclohexane is not further metabolized ([http://www.ncbi.nlm.nih.gov/pubmed/15812056|Nagata et al., 2004]). 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It is an emerging water contaminant known to cause respiratory tract and eye irritant. Furthermore, it is considered a possible human carcinogen, having been shown to be one in rats and guinea pigs. The main routes of human exposure are dermal contact, ingestion, and inhalation ([http://www.ncbi.nlm.nih.gov/pubmed/8713712|DeRosa et al., 1996]). Both P. dioxanivorans CB1190 and P. benzenivorans B5 contain putative dioxane monooxygenases induced by 1,4-dioxane or THF. Other strains are capable of cometabolic degradation after growth on THF, propane, and toluene. Based on intermediates identified during degradation, 1,4-dioxane is likely hydroxylated at an ether-bond-associated carbon atom by monooxygenases, resulting in spontaneous oxidizion and ring cleavage to form 2-hydroxyethoxyacetate. A second monooxygenase attack at either the ortho or para position with respect to the carboxylic acid moiety yields a mixture of two dihydroxyethoxyacetates. Spontaneous protonation of the hemiacetal bond results in the progressive formation of various small organic molecules including ethylene gylcol, glyoxylate, glycoaldehyde, oxalate (not shown), and glycolate ([http://www.ncbi.nlm.nih.gov/pubmed/18044507|Mahendra et al., 2007]). The fungus Cordyceps sinensis is able to use 1,4-Dioxane as a sole source of carbon. 1,4-Dioxane is converted to two molecules of ethylene glycol via the proposed formation of two hemiacetals at one side of the dioxane molecule by etherase-type reactions ([http://www.ncbi.nlm.nih.gov/pubmed/15746326|Nakamiya et al., 2005]). Ethylene glycol is degraded via intermediary metabolism. 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Thioamide groups are found naturally in the copper-chelating compound methanobactin described in Methylosinus trichosporium OB3b ([http://www.ncbi.nlm.nih.gov/pubmed/15361623|Kim et al., 2004]). The antibiotic sulfinemycin, produced by Streptomyces albus NRRL 3384, has a primary thioamide S-oxide moiety ([http://www.ncbi.nlm.nih.gov/pubmed/7730167|Lee et al., 1995]). Thioacetamide is used as a sulfur source for organic syntheses and has applications in leather, textile, paper, rubber, and petroleum industries. 2,6-Dichlorothiobenzamide (chlorthiamid) is used as an herbicide. Thioamide compounds such as 2-ethyl-4-pyridinecarbothioamide (ethionamide) are important second-line drugs in the treatment of multi-drug resistant Mycobacterium tuberculosis and M. leprae ([http://www.ncbi.nlm.nih.gov/pubmed/12164478|Schroeder et al., 2002]; [http://www.ncbi.nlm.nih.gov/pubmed/3910748|Shepard et al., 1985]). Toxicity of thioamides in mammals and Mycobacterium spp. is dependent on metabolic activation of the compounds via sequential oxygenations of the thioamide sulfur atom by flavoprotein monooygenases or cytochromes P450 ([http://www.ncbi.nlm.nih.gov/pubmed/10944230|Debarber et al., 2000]; [http://www.ncbi.nlm.nih.gov/pubmed/10900221|Wang et al., 2000]; [http://www.ncbi.nlm.nih.gov/pubmed/28917|Porter and Neal, 1978]). Thioamide S-oxides are not toxic without further oxygenation and investigators have proposed that thioamide S,S-dioxides (which have not been isolated) or further oxidized species exert the observed toxic effects (Vannelli et al., 2002; [http://www.ncbi.nlm.nih.gov/pubmed/6135576|Hanzlik and Cashman, 1983]; [http://www.ncbi.nlm.nih.gov/pubmed/28917|Porter and Neal, 1978]). This activity results in elimination of the thioamide sulfur and formation of nitrile or amide derivatives (Vannelli et al., 2002; [http://www.ncbi.nlm.nih.gov/pubmed/28917|Porter and Neal, 1978]). Ralstonia pickettii TA can grow using thioacetamide as a sole source of nitrogen and carbon ([http://www.ncbi.nlm.nih.gov/pubmed/16997975|Dodge et al., 2006]), but the pathway of degradation has not been completely determined. Thioacetamide S-oxide was detected as a metabolic intermediate, supporting an oxygenase-mediated mechanism. During thioacetamide degradation, 3,5-dimethyl-1,2,4-thiadiazole accumulated in the medium and was not further metabolized. This species did not form when thioacetamide and thioacetamide S-oxide were combined. Therefore it was proposed that a further oxidized species, possibly thioacetamide S,S-dioxide, reacts with thioacetamide to form this dead-end metabolite. Sulfur eliminated from thioacetamide during metabolism was detected in the medium as sulfur dioxide/sulfite. Elimination of sulfur at this oxidation state from thioacetamide S,S-dioxide requires an additional two-electron oxidation, which occurs by an unknown mechanism. Nitrogen released during thioactamide degradation was detected as ammonium ion. Using thiobenzamide metabolism by this strain as a model ([http://www.ncbi.nlm.nih.gov/pubmed/16997975|Dodge et al., 2006]), it was predicted that elimination of the thioacetamide sulfur would generate acetonitrile and/or acetamide. R. pickettii TA grew using acetonitrile or acetamide as the sole source of carbon and nitrogen, but neither could be detected during thioacetamide degradation, possibly because hydrolysis of these substrates was rapid relative to sulfur elimination ([http://www.ncbi.nlm.nih.gov/pubmed/16997975|Dodge et al., 2006]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "7d1c4381-143d-40e9-a7d9-206f032188f9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/869bb223-f969-44d9-ad28-25aff294be0a/node/7d1c4381-143d-40e9-a7d9-206f032188f9", "name": "Acetate", "description": "no description", "aliases": [], "default_node_label": {"uuid": "8e8bf313-62e5-47bc-bf91-26e5a3cd9182", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b545cabc-8c9e-4b20-8848-efa015b481ea/structure/8e8bf313-62e5-47bc-bf91-26e5a3cd9182"}, "node_labels": [{"uuid": "8e8bf313-62e5-47bc-bf91-26e5a3cd9182", "url": 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Extensive necrosis is evident at 85 mumol/kg in kidney and at 170 mumol/kg in testis ([http://www.ncbi.nlm.nih.gov/pubmed/1793801|Lag et al., 1994]). Also 1,2,3-tribromopropane causes DNA damages. It has been shown that 1,2,3-tribromopropane is mutagenic in strains TA1535 and TA100 of Salmonella typhurinum ([http://www.ncbi.nlm.nih.gov/pubmed/1793801|Lag et al., 1991]). Also 1,2,3-tribromopropane induces dominant lethal mutation in the early spermatide stage of SD male rats ([http://www.ncbi.nlm.nih.gov/pubmed/7110159|Saito-Suzuki et al., 1982]). The recombinant strain Agrobacterium radiobacter strain AD1(pTB3) has the ability to utilize 1,2,3-tribromopropane as a sole carbon source. 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A catalase-peroxidase (KatGII) in M. tuberculosis oxidizes INH, generating radical intermediates. These form NAD adducts that inhibit the inhA gene product, an enzyme critical for chain elongation in mycolic acid biosynthesis, which disrupts cell wall formation. Other adducts inhibit dihydrofolate reductase, which is critical for nucleotide biosynthesis ([http://www.ncbi.nlm.nih.gov/pubmed/16648861|Argyrou et al., 2006]). Nitric oxide is also generated and confers antimycobaterial activity as well ([http://www.ncbi.nlm.nih.gov/pubmed/15273113|Timmins, 2004]). Biodegradation of isoniazid occurs in three principle branches: acetylation, hydrolysis, and deamination. Simple acetylation occurs in Pseudomonas aeruginosa, Mycobacterium smegmatis, and Mycobacterium tuberculosis ([http://www.ncbi.nlm.nih.gov/pubmed/15447630|Westwood et al., 2005]). Subsequent hydrolysis by amidase has been demonstrated in rabbits ([http://www.ncbi.nlm.nih.gov/pubmed/10215642|Sarich et al., 1999]), but not yet in microbes. Hydrazinolysis into isonicotinate and hydrazine is carried out by Pseudomonas, Bacillus sp., and Sarcina sp. Deamination occurs in Mycobacterium bovis BCG via a catalase-peroxidase (KatG1). Both hydrazinolysis and deamination liberate isonicotinate. Hydrazine or ammonia ([http://www.ncbi.nlm.nih.gov/pubmed/16563633|Kang et al., 2005]) are the respective coproducts. Hydrazine can be anaerobically degraded to dinitrogen gas in anammoxosome-containing bacteria such as Candidata brocadia anammoxidans ([http://www.ncbi.nlm.nih.gov/pubmed/15098544|van Niftrik et al., 2004;] [http://www.ncbi.nlm.nih.gov/pubmed/11404106|Jetten et al., 2001]). Isonicotinate itself is hydroxylated by Mycobacterium INA1 or Achromobacter sp. to form citrazinate ([http://www.ncbi.nlm.nih.gov/pubmed/9682480|Schrader et al., 1998]). Several branches may then occur. Sarcina sp. carries out a hydrolysis pathway going to aconitamide, whereby deamination leads into common intermediary metabolism (RC Gupta and OP Shukla (1979) J. Biosci. (India), 1: 223-234.). Alternatively, succinic acid semialdehyde can form via ring cleavage of citrazinate by Achromobacter D ([http://www.ncbi.nlm.nih.gov/pubmed/8840783|Kaiser et al., 1996]). Another branch by the same species, as well as Achromobacter 4C1, cleaves the citrazinate ring into maleamate. Pseudomonas and Arthrobacter oxydans indirectly form maleamate from citrazinate via hydroxylation to trihydroxyisonicotinate, decarboxylation to 2,3,6-trihydroxypyridine, and finally ring cleavage ([http://www.ncbi.nlm.nih.gov/pubmed/8840783|Kaiser et al., 1996]). Peroxidation occurs via the catalase-peroxidase enzymes found in Mycobacterium sp. ([http://www.ncbi.nlm.nih.gov/pubmed/15231844|Pierattelli et al., 2004]). The radical intermediates can form at least six different NAD and NADP adducts that are not depicted in this pathway, or may stabilize into isonicotinamide or isonicotinate ([http://www.ncbi.nlm.nih.gov/pubmed/16648861|Argyrou et al., 2006]). There is some uncertainty regarding the catalase peroxidase enzymes, KatGI and KatGII; it is not currently agreed whether they are two subunits of one enzyme, or two separate enzymes ([http://www.ncbi.nlm.nih.gov/pubmed/9371430|Menendez et al., 1997]). The position of the KatG genes on the bacterial genome makes them amenable to mutation, resulting in various structure homologies. 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In the absence of molecular oxygen, the aromatic ring is first reduced prior to ring cleavage. Benzoate is activated to benzoyl-CoA. Dearomatization of the benzene ring is occurs upon a 2 electron reduction of benzoyl-CoA to cyclohex-diene-1-carboxyl-CoA. For subsequent oxidation of cyclohex-diene-1-carboxyl-CoA to 3-hydroxypimelyl-CoA, two metabolic routes are currently discussed, one which involves cyclohex-1-ene-1-carboxyl-CoA as intermediate and another which involves 6-hydroxy-cyclohex-1-ene-1-carboxyl-CoA. For more specific information, see [http://www.ncbi.nlm.nih.gov/pubmed/97144512|Harwood and Gibson (1998)] and [http://www.ncbi.nlm.nih.gov/pubmed/93170297|Koch et al (1993)]. Most studies of anaerobic benzoate degradation have been carried out with the phototrophic bacterium Rhodopseudomonas palustris and with two denitrifying species, Thauera aromatica K172 and Azoarcus evansii (formerly Pseudomonas sp. strain K 172 and KB 740, respectively). Activities of cyclohex-1-ene-1-carboxyl-CoA hydratase, 2-hydroxycyclohexane-1-carboxyl-CoA dehydrogenase and 2-ketocyclohexane-1-carboxyl-CoA hydrolase were not demonstrated directly. The left side of the reactions from 6-Hydroxycyclohex-1-ene-1-carboxyl-CoA to 3-Hydroxypimelyl-CoA is proposed and has not been identified experimentally. The Pimelyl-CoA degradation from Pimelyl-CoA to Acetyl-CoA is also proposed and most of the enzymes of this sequence do not appear to have been directly assayed. This page shows only anaerobic pathway of benzoate degradation. 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It is being studied for apparent benefical effects including cardiovascular protection, anti-cancer activity, anti-ulcer effects, anti-allergy activity, cataract prevention, antiviral activity, and anti-inflammatory effects (Flavonoids in health and disease. Eds C.A. Rice-Evans and L. Packer. New York: Marcel Dekker, 1998). Many of these effects have been attributed to quercetin`s antioxidant activity. These apparent effects have lead to the sale of plant-derived quercetin as a natural remedy and nutritional supplement. The degradation of quercetin is of particular interest since the enzyme quercetin 2,3-dioxygenase is one of the few copper-based dioxygenase enzymes. 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It is also used as grain fumigant and a chemical intermediate in the production of refrigerants. Carbon tetrachloride is a widespread environmental pollutant due to improper disposal. Carbon tetrachloride can be degraded under anaerobic conditions via three different pathways. No enzyme is involved in these pathways; rather, reactions are catalyzed by cofactors present in microorganisms. The left-most pathway is a sequential two-electron reduction process. Carbon tetrachloride is degraded to chloroform, dichoromethane, chloromethane and ultimately methane by hydrogenolytic dechlorinations. Many anaerobic bacteria can catalyze the first two reactions of this pathway using the cofactors heme, factor F430, and corrinoids, such as aquocobalamin and methylcobalamin. These corrinoids can also convert CCl4 to carbon monoxide ([http://www.ncbi.nlm.nih.gov/pubmed/2001359|Krone et al., 1991]). This is part of the middle pathway, a simple two-electron reduction process in which chloroform is only a minor product. Carbon tetrachloride, in the right-most pathway, can be degraded via sulfur and oxygen substitution in one-electron reduction reactions. [http://www.ncbi.nlm.nih.gov/pubmed/10441466|Chang-Ho Lee et al. 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Cr(VI) and its organic copollutants often originate from industrial sources such as leather tanning, photographic-film making, wood preservation, car manufacturing, petroleum refining, and agricultural activity ([http://www.ncbi.nlm.nih.gov/pubmed/11337838|Nkhalambayausi-Chirwa and Wang, 2001]). A common pathway for Cr(VI) reduction to the less toxic Cr(III) is done through the unstable Cr(V) intermediate ([http://www.ncbi.nlm.nih.gov/pubmed/11348688|Cervantes et al, 2001]). This reduction is carried out by many different chromium resistant microorganisms. A less common Cr(VI) reduction involves simultaneous Cr(VI) reduction and phenol degradation, which was observed in a fixed-film bioreactor consisting of a coculture of Pseudomonas putida DMP-1 and Escherichia coli ATCC 33456 ([http://www.ncbi.nlm.nih.gov/pubmed/11337838|Nkhalambayausi-Chirwa and Wang, 2001]). E. coli reduces Cr(VI) under both aerobic and anaerobic conditions ([http://www.ncbi.nlm.nih.gov/pubmed/8285683|Shen and Wang, 1993]), while P. putida is an obligate aerobe capable of degrading phenol (Wang Y. T. and Qu M. Substrate interactions during biodegradation of phenols by a Pseudomonas sp. Proceeding of the 65th Annual Water Environment Federation Conference and Technical Exposition (Alexandria, VA) (1992) 63.). Nkhalambayausi-Chirwa and Wang (2001) believe the spatial and physiological heterogeneity introduced within microbial communities by the formation of biofilms may enhance Cr(VI) reduction by E. coli within the quasi-anaerobic interior of the biofilm while supporting maximum growth of P. putida along the more aerobic surface layers.", "aliases": [], "predicted": false, "nodes": [{"uuid": "383b9292-590b-40f5-8cce-202d06fa20e6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/36f3c2d6-096d-43e9-8220-3d37048ad8d5/node/383b9292-590b-40f5-8cce-202d06fa20e6", "name": "Chromium (III)", "description": "no description", "aliases": [], "default_node_label": {"uuid": "e9464b86-242c-45b4-ba96-72555d204ce2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/495d15cb-66f5-4902-9ad0-114f7997d345/structure/e9464b86-242c-45b4-ba96-72555d204ce2"}, "node_labels": [{"uuid": "e9464b86-242c-45b4-ba96-72555d204ce2", "url": 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"Triazophos is a widely used organophosphorous insecticide, and its presence in the environment is increasing. It induces point mutations in the fruit fly, Drosophila melanogaster ([http://www.ncbi.nlm.nih.gov/pubmed/2123939|Velazquez et al., 1990]). Thus its microbial degradation is of interest. Diaphorobacter sp. TPD-1 can grow on triazophos as its sole source of carbon. The initial step in its degradation involves hydrolysis of the P-O ester to form 1-phenyl-3-hydroxy-1,2,4-triazole (PHT) and o,o-diethylphosphorothioate. Next, the triazole ring of PHT is cleaved to form (E)-1-formyl-2-phenyldiazene, with release of CH3NO2 as one or more compounds in one or more steps. The diazene is tranformed to 2-phenylhydrazinecarboxylate in one or two steps. The latter compound is decarboxylated to phenylhydrazine ([http://www.ncbi.nlm.nih.gov/pubmed/21212954|Yang et al., 2011]). The first reaction is well-characterized; there may be other routes to the other products. Klebsiella sp. E6 can grow on triazophos as its sole source of carbon, nitrogen and phosphorous. The first step in its degradation is the same as above. It can completely mineralize triazophos, but its degradation pathway has not been determined ([http://www.ncbi.nlm.nih.gov/pubmed/16243454|Wang et al., 2005]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "53dd9fd3-4a79-4629-8679-df314e8b48be", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/b8cf9dd2-71c6-4ded-a20c-26b4013471c2/node/53dd9fd3-4a79-4629-8679-df314e8b48be", "name": "Diethylthiophosphoric acid", "description": "no description", "aliases": [], "default_node_label": {"uuid": "edef99ce-744f-4e17-bbd7-3b115902e6cd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/6d1e1628-6483-4e63-9af7-3f273ac23428/structure/edef99ce-744f-4e17-bbd7-3b115902e6cd"}, "node_labels": [{"uuid": "edef99ce-744f-4e17-bbd7-3b115902e6cd", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/6d1e1628-6483-4e63-9af7-3f273ac23428/structure/edef99ce-744f-4e17-bbd7-3b115902e6cd"}], "depth": 1, 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"name": "(E)-1-Formyl-2-phenyldiazene", "description": "no description", "aliases": [], "default_node_label": {"uuid": "d90a1ca4-f070-4912-af8a-0d785e1636be", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a4f4ebe5-670b-42c8-89f2-9f974e055f40/structure/d90a1ca4-f070-4912-af8a-0d785e1636be"}, "node_labels": [{"uuid": "d90a1ca4-f070-4912-af8a-0d785e1636be", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/a4f4ebe5-670b-42c8-89f2-9f974e055f40/structure/d90a1ca4-f070-4912-af8a-0d785e1636be"}], "depth": 2, "stereo_removed": false, "scenarios": []}, {"uuid": "502ad3af-2937-4571-a740-dd83b1cde3f6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/b8cf9dd2-71c6-4ded-a20c-26b4013471c2/node/502ad3af-2937-4571-a740-dd83b1cde3f6", "name": "Triazophos", "description": "no description", "aliases": [], "default_node_label": {"uuid": "0dbdca44-25a9-4605-af4c-67c31d67fd6a", "url": 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"Organoarsenicals can be used in agricultural applications as animal feed additives, cotton defoliants and post-emergence grass herbicides. Extensive research has been undertaken on the mechanism and extent of arsenic bioalkylation. However, still not much is known on the environmental fate of organoarsenicals. [http://www.ncbi.nlm.nih.gov/pubmed/7711909|Quinn and McMullan (1995)] found that strain ASV2, a Gram-negative bacterium isolated from activated sludge, can utilize arsonoacetate as sole carbon and energy source. This is the first report of a microorganism capable of utilizing a compound containing the carbon-arsenic bonds. In the cells of ASV2, arsonoacetate is degraded into arsenite and acetate in C-As bond cleavage reaction. Since arsenite is more toxic than arsenate, it is oxidized to arsenate by arsenite oxidase as an effective means of detoxification. By contrast, some bacteria, such as Escherichia coli and Staphylococcus aureus, are able to reduce arsenate to arsenite. 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It is commercially available under names such as Prefix, Barrier, Casoron, Dyclomec and Norosac. Although dichlobenil does not readily leach to groundwater, it is quickly metabolized to 2,6-dichlorobenzamide (BAM). Due to high water solubility and low sorption affinity in soil ([http://www.ncbi.nlm.nih.gov/pubmed/11455813|Albrechtsen et al., 2001]), the very persistant BAM has been detected in groundwater samples at levels which exceed current regulations ([http://www.ncbi.nlm.nih.gov/pubmed/18970297|Porazzi et al., 2005]). The first step in the microbial degradation of dichlobenil in previously exposed soils involves hydrolysis of the nitrile group to the benzamide. Further hydrolysis of the amide to a carboxylate is found to be much slower. Reductive dechlorination occurs both prior to, and after amide hydrolysis resulting in ortho-chlorobenzoate ([http://www.ncbi.nlm.nih.gov/pubmed/17240021|Holtze et al., 2007]). 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Bis(2-chloroethyl) sulfide, also known as Yperite or mustard gas, is the most produced and stored chemical weapon. It is highly cytotoxic and is a carcinogenic and mutagenic alkylating agent; benzyl sulfide has been used as a non-toxic model for its metabolism. The microbial degradation of benzyl sulfide can be carried out by white-rot (Coriolous versicolor) and brown-rot (Tyromyces palustris) fungi ([http://www.ncbi.nlm.nih.gov/pubmed/9256235|Itoh et al., 1997]). The initial step may be the oxidative cleavage of the C-S bond to yield benzaldehyde and benzyl mercaptan. Benzaldyde can be reduced to benzyl alcohol or oxidized to benzoate. Benzyl mercaptan can be converted to benzyl disulfide in the presense or absence of fungi. Degradation of the disulfide to the mercaptan was observed in the presence of fungi. Benzaldehyde, benzyl alcohol, and benzoate follow the toluene pathway and are finally mineralized to CO2 and H2O. These and several other fungi can also oxide benzyl sulfide to the sulfoxide and the sulfone ([http://www.ncbi.nlm.nih.gov/pubmed/12571066|Van Hamme et al., 2003]), and this may be the primary aerobic route. The first oxidation step is catalyzed by extracellular enzymes such as laccase, but the second step is cytochrome P450 (unspecific monooxygenase) mediated. Rhodococcus sp. strain IGTS8 can perform these same two oxidations using a single sulfide/sulfoxide monooxygenase ([http://www.ncbi.nlm.nih.gov/pubmed/8824615|Lei and Tu, 1996]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "669fca64-0967-4612-80dd-b031a78866c0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/9508ba2f-26d2-422c-888d-da2de9fe6aca/node/669fca64-0967-4612-80dd-b031a78866c0", "name": "Benzyl sulfone", "description": "no description", "aliases": [], "default_node_label": {"uuid": "e9f84062-f698-439d-9aa7-2834a45e67c4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/2103feba-f07b-486d-9a53-b75fe8a6da03/structure/e9f84062-f698-439d-9aa7-2834a45e67c4"}, "node_labels": [{"uuid": "e9f84062-f698-439d-9aa7-2834a45e67c4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/2103feba-f07b-486d-9a53-b75fe8a6da03/structure/e9f84062-f698-439d-9aa7-2834a45e67c4"}], "depth": 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Their degradation serves as a model for bridged PAH metabolism. Rhizobium sp. CU-A1 and Stenotrophomonas sp. RMSK can use acenaphthylene as their sole source of carbon and energy. The pathway involves dioxygenation at the bridge double bond to form 1,2-dihydroxyacenaphthalene, a tautomer of 1-hydroxy-2-ketoacenaphthene. Naphthalene 1,2-dioxygenase, the enzyme which can initiate this route of bacterial acenaphthylene metabolism ([http://www.ncbi.nlm.nih.gov/pubmed/16535238|Selifonov et al., 1996]), has many other catalytic abilities, which are documented in a table of Reactions of Naphthalene 1,2-Dioxygenase. 1-Hydroxy-2-ketoacenaphthene is oxidized to acenaphthenequinone, which is oxidatively cleaved to form naphthalene-1,8-dicarboxylate. This is decarboxylated to 1-naphthoic acid, which is further metabolized to salicylate, which can be transformed to gentisate or catechol ([http://www.ncbi.nlm.nih.gov/pubmed/16957226|Poonthrigpun et al., 2006] and [http://www.ncbi.nlm.nih.gov/pubmed/19543983|Nayak et al., 2009]). A Beijerinckia sp. can metabolize acenaphthylene to acenaphthenequinone by a similar pathway, but no further ([http://www.ncbi.nlm.nih.gov/pubmed/6089663|Schocken & Gibson, 1984]). Acenaphthalene is also degraded through acenaphthenequinone, though the inital metabolites are different. Beijerinchia sp., Pseudomonas sp. BR, BC and A2279, and Sphingomonas sp. A4 can transform acenaphthalene to 1-acenaphthalenol. This compound is either hydroxylated to form 1,2-dihydro-1,2-acenaphthylenediol, or the hydroxyl group is oxidized to form 1-ketoacenaphthene. Both of these compounds are oxidized to 1-hydroxy-2-ketoacenaphthene and from there to acenaphthenequinone ([http://www.ncbi.nlm.nih.gov/pubmed/6089663|Schocken & Gibson, 1984], [http://www.ncbi.nlm.nih.gov/pubmed/9546181|Selifonov et al., 1998], and [http://www.ncbi.nlm.nih.gov/pubmed/16849808|Kouzuma et al., 2006]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "9332cd26-6ce7-409e-8d0e-762685e0d806", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/339a458f-c7b6-458d-866a-1cff4bd68893/node/9332cd26-6ce7-409e-8d0e-762685e0d806", "name": "Acenaphthalene", "description": "no description", "aliases": [], "default_node_label": {"uuid": "cd1f77eb-c5ec-4c80-8ae6-dd19a6398838", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b7e91529-9025-413f-8e0d-1e74f040a90c/structure/cd1f77eb-c5ec-4c80-8ae6-dd19a6398838"}, "node_labels": [{"uuid": "cd1f77eb-c5ec-4c80-8ae6-dd19a6398838", "url": 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The compound is also used in the manufacturing of styrene and synthetic polymers. The anaerobic degradation of ethylbenzene is documented elsewhere in the EAWAG-BBD, and here the aerobic catabolism proceeds via two primary pathways. Pseudomonas sp. strain NCIB 10643 has been shown to utilize a wide range of n-alkylbenzenes (C2-C7), of which ethylbenzene is a single example. This degradation is initiated by a dioxygenation of the aromatic ring, leading to an extradiol ring cleavage. It is reported by [http://www.ncbi.nlm.nih.gov/pubmed/8795196|Lee & Gibson (1996)] that napthalene dioxygenase exhibits a highly relaxed substrate specificity and is capable of aerobically degrading ethylbenzene to styrene and/or 2-hydroxyacetophenone. Information concerning the further degradation of 2-hydroxyacetophenone is not available, though 4-hydroxyacetophenone can undergo aerobic biodegradation. 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It is a selective systemic herbicide, absorbed by germinating shoots and roots. It works by interfering with the plant`s ability to produce protein and elongate roots. When directly applied to soil, it may leach into groundwater and thereby pose a potential health hazard to humans and animals (Sette et al., 2004). Alachlor is degraded by many soil microorganisms, although no pure or mixed cultures able to extensively degrade or mineralize alachlor have been reported. Bacteria and fungi can degrade alachlor through co-metabolism. Sette et al., (2004) used six highly tolerant streptomycete strains in their studies and identified the main biodegradation products as dechlorinated indole compounds, a quinoline derivative compound and a chlorinated indole derivative. Of all the strains reported to degrade alachlor, strain LS182 did not generate the carcinogenic product 2,6-diethylaniline. Hence, LS182 strain may be the best strain to use in bioremediation of alachlor. Reactions A-C, below, all occur spontaneously, in water without microbial inocula. These abiotic reactions are predominently hydrolyses, including dehalogenation and amide hydrolysis, but include more complex reactions as well. The alachlor hydrolase reaction is enzyme-mediated, but also occurs at a slower rate abiotically (Sette et al., 2004). Alachlor can be detoxified by displacement of the chlorine group with a thiol (e.g. glutathione, coenzyme A, cysteine) to produce an alachlor-thiol conjugate. These reactions occur both abiotically and enzymatically via glutathione-S-transferase (GST). Soil microorganisms with GST activity have been shown to product alachlor-cysteine and alachlor-cysteine-glycine conjugates ([http://www.ncbi.nlm.nih.gov/pubmed/16534956|Zablotowicz et al., 1995]). Further enzymatic oxidation of these conjugates produce alachlor-ESA (ethyl sulfonic acid) ([http://www.ncbi.nlm.nih.gov/pubmed/9561822|Stamper et al., 1998]). Possible metabolites of alachlor-ESA found in soil and groundwater include alachlor-OA (oxanilic acid) ([http://www.ncbi.nlm.nih.gov/pubmed/15543734|Postle et al., 2004]) and N-(2,6-Diethylphenyl)-ESA ([http://www.ncbi.nlm.nih.gov/pubmed/12102310|Thurman et al., 2002]). 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Phenylacetate aerobic metabolism in fungi usually proceeds by oxidation to homogentisate ([http://www.ncbi.nlm.nih.gov/pubmed/8919815|Cox et al., 1996]), as shown in the left branch below. In bacteria, this rarely occurs, rather the initial step is ligation with CoA. Pseudomonas putida U uses both pathways; 4-hydroxyphenylacetate is metabolised via oxidation and phenylacetate via ligation with CoA ([http://www.ncbi.nlm.nih.gov/pubmed/8168524|Olivera et al., 1994]). Ligation is followed by epoxide formation, isomerization of the epoxide to an oxepin, and hydrolytic ring cleavage, to eventually produce acetyl-CoA and succinyl-CoA, as shown in the right branch. This pathway is found in 16% of 640 bacteria whose genomes have been sequenced, including Pseudomonas putida and Escherichia coli ([http://www.ncbi.nlm.nih.gov/pubmed/20660314|Teufel et al., 2010]). 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It goes by the trade names Weed-E-Rad, Ansar 170 H.C., Ansar 529 H.C., DiTac and others. Methylarsonate is considered only slightly toxic, having an oral LD50 of 2200 mg/Kg for rats. The inhalation risk is greater with LD50 Rats >20 mg. Long term studies with people exposed to organoarsenicals has shown an increased risk of skin cancer ([http://www.ncbi.nlm.nih.gov/pubmed/11426918|Spiewak, 2001]), lung cancer and some liver cancers, although some recent studies have shown some arsenic containing compounds (specifically Arsine trioxide) may have anticarcinogenic properties ([http://www.ncbi.nlm.nih.gov/pubmed/11587371|Wang, 2001]). In mammals, Methylarsonate is also an intermediate in the detoxification of inorganic arsenic. Arsenic is found in the environment primarily as arsenate and arsenite species. Arsenate is reduced to arsenite by arsenate reductase and can be subsequently methylated to Methylarsonate. This is then reduced and methylated to Dimethylarsinate ([http://www.ncbi.nlm.nih.gov/pubmed/10604879|Zakharyan, 1999]), which can excreted and is considerably less toxic to the organism than any of the previous intermediate compounds. In some bacteria, yeasts and fungi, this process is carried further to yield Trimethylarsine gas ([http://www.ncbi.nlm.nih.gov/pubmed/534956|Cullen et al., 1979]; [http://www.ncbi.nlm.nih.gov/pubmed/7296411|Pickett et al., 1981]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "7abbf64b-999d-4601-8171-e1011b3efcef", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/ca08ca74-e84c-4a51-b41b-fcd1f0736acd/node/7abbf64b-999d-4601-8171-e1011b3efcef", "name": "Trimethylarsine", "description": "no description", "aliases": [], "default_node_label": {"uuid": "82ef0feb-2cfb-4226-8b92-4cdfb41da5b4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/49354e2d-17af-4b5a-8304-65fe9e307c22/structure/82ef0feb-2cfb-4226-8b92-4cdfb41da5b4"}, "node_labels": [{"uuid": "82ef0feb-2cfb-4226-8b92-4cdfb41da5b4", "url": 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This additive reduces the emissions of airborn toxics, carbon monoxide and volatile organic compounds. This compound was first used in the US in the 70`s, but since the 1990 Clean Air Act, its use has gone up immensely. It is now the second most produced chemical in the US with more than 24 billion pounds used per year. There are problems with the storage of MTBE; it is now the second most common contaminant of urban aquifers in the US. MTBE is becoming a problem in drinking water too, and the toxicity of MTBE is not very well known. Some studies show that, in humans exposed to high amounts of MTBE in drinking water, it might induce programmed cell death. While a number of microorganisms are known to metabolize MTBE, not much is known about the mechanism of degradation. The following pathway map is based primarily on [http://www.ncbi.nlm.nih.gov/pubmed/9361407|Steffan et al. (1997)], which examined the mechanism of MTBE degradation in Nocardia sp. ENV425. More recently, [http://www.ncbi.nlm.nih.gov/pubmed/12039730|Francois et al. (2002)] and [http://www.ncbi.nlm.nih.gov/pubmed/12570997|Smith et al. (2003)] have observed that Mycobacterium austroafricanum IFP 2012 and Mycobacterium vaccae JOB5 follow a slightly different pathway in the initial steps of MTBE degradation, converting MTBE to tert-butyl formate, which is then hydrolysed to tert-butyl alcohol and formate. The enzymes shown in these initial steps are those suggested by [http://www.ncbi.nlm.nih.gov/pubmed/12570997|Smith et al. (2003)]. [http://www.ncbi.nlm.nih.gov/pubmed/16622053|Ferreira et al. (2006)] reported the cloning and characterization of several genes from M. austroafricanum IFP 2012 involved in the lower portion of the MTBE pathway (from 2-methyl-2-hydroxy-1-propanol to 2-hydroxyisobutyrate). The exact route of 2-hydroisobutyrate metabolism is not certain; methacrylate, 2-propanol, and 2,3-dihydroxy-2-methyl propionate are all possible next products ([http://www.ncbi.nlm.nih.gov/pubmed/9361407|Steffan et al., 1997]). Wolinella succinogenes can anaerobically reduce methacrylate to isobutyrate ([http://www.ncbi.nlm.nih.gov/pubmed/11685377|Gross et al., 2001]). 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A study dedicated to the isolation and characterization of aromatic compound degrading microbes found 4-fluorobenzoate in freshwater sediment and sewage in concentrations of 50-500 ppm (Horowitz, et al. (1982) Dev Ind Microbiol 23:435-44). Toxicology information is limited for this particular compound but studies on other more common halobenzenes have shown toxicity in high doses. Knowledge of fluorobenzoate metabolism is relatively sparse in comparison to other halobenzoates. Fluorinated organic compounds, such as 4-fluorobenzoate, are more resistant to microbial degradation than other halogenated compounds due to unusual carbon-fluorine bond properties ([http://www.ncbi.nlm.nih.gov/pubmed/12805763|Giesy et al., 2001]). Aerobic metabolism of 4-fluorobenzoate is initiated by an oxygen-dependent ring cleavage in B. cepacia , Pseudomonas sp. B13, A. eutrophus JMP134 and A. eutrophus 335. Cycloisomerization of 3-fluoro-cis,cis-muconate with the addition of a proton yields 4-fluoromuconolactone as the sole major product. Lactone hydrolysis preceeds a secondary dehalogenation reaction and the resulting product enters intermediary metabolism through the TCA cycle ([http://www.ncbi.nlm.nih.gov/pubmed/2394680|Schlomann et al., 1990]). In contrast to chloride and bromide elimination through a carbanionic intermediate ([http://www.ncbi.nlm.nih.gov/pubmed/16345496|Schreiber et al., 1980]), defluorination is not coupled to cycloisomerization and dienelactone formation is negligible ([http://www.ncbi.nlm.nih.gov/pubmed/2394680|Schlomann et al., 1990]). 4-Fluorobenzoate is anaerobically degraded by Aureobacterium sp. strain RHO25. Coenzyme A ligation and dehalogenation yields 4-hydroxybenzoyl-CoA, which enters common intermediary metabolism ([http://www.ncbi.nlm.nih.gov/pubmed/2604392|Oltmanns et al., 1989]). 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The toxicity of malathion is low but acute exposure in high doses may cause a variety of symptoms including nausea, dizziness, or confusion. Malaoxon is a potent cholinesterase inhibitor that can be formed from malathion under certain conditions. Exposure to malaoxon can lead to complications in the central nervous system (Edwards, 2006. US Environmental Protection Agency - Prevention, Pesticides and Toxic Substances EPA 738-R-06-030). The predominant biodegradation pathway for malathion involves formation of mono- and diacid metabolites through carboxylesterase activity. Oxidative desulfurization and demethylation leads to complete mineralization. Other minor routes of metabolism include initial oxidation to remove sulfur and methyl groups ([http://www.ncbi.nlm.nih.gov/pubmed/402103|Laveglia and Dahm, 1977]). Pseudomonas aeruginosa AA112 is able to use malathion as a sole carbon source. 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TBP is not believed to be carcinogenic or mutagenic to humans. However, TBP is toxic to life in aquatic envioronments and has a 50% lethal dose for fish of 0.4 or 0.54 mg/L and 50% effective concentration of 0.96 mg/L for Daphnia magna. A report on TBA and its derivatives has been produced by the International Programme on Chemical Safety. TBP is nonvolatile and is not mobile in the soil partially because TBP is insoluble in water (<1 mg/liter) at a pH of 7.0. In soils with increased pH levels the solubility of TBP is significantly increased and can leach into and contaminate groundwater below contaminated soil. This pathway is based on [http://www.ncbi.nlm.nih.gov/pubmed/10831413|Ronen and Abeliovich, 2000] and [http://www.ncbi.nlm.nih.gov/pubmed/14669869|Arbeli and Ronen, 2003].", "aliases": [], "predicted": false, "nodes": [{"uuid": "9880303d-2752-4ca1-b0c8-096d5c1eed71", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/220c80b8-532c-4f76-ac52-324ebfc91dd8/node/9880303d-2752-4ca1-b0c8-096d5c1eed71", "name": "Bisphenol A", "description": "no description", "aliases": [], "default_node_label": {"uuid": "c0b40456-4723-413b-8b20-836f05464067", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/85ba52bb-d55d-4db8-a14d-2c45e099bdf1/structure/c0b40456-4723-413b-8b20-836f05464067"}, "node_labels": [{"uuid": "c0b40456-4723-413b-8b20-836f05464067", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/85ba52bb-d55d-4db8-a14d-2c45e099bdf1/structure/c0b40456-4723-413b-8b20-836f05464067"}], "depth": 4, 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It is used as an anticonvulsant, sedative, and muscle relaxant, and has a long duration of action (PubChem, 2011). The fungus Aspergillus niger J/8 N-demethylates diazepam to form 7-chloro-5-phenyl-3H-1,4-benzodiazepin-2-one. This demethylation step may be carried out by a transmethylase, hydrolytic demethylase or one of several different types of oxidative demethylases, so the generic \"A\" is used. The diazepin ring in the demethylated compound is then cleaved. It transiently forms 2-amino-N-(2-benzoyl-4-chlorophenyl)acetamide, which is N-acetylated to form N-(2-benzoyl-4-chlorophenyl)-2-acetamidoacetamide. The fungus Penicillium velutinum cleaves the diazepin ring at the same position without prior N-demethylation and performs the same N-acetylation, to form N-(2-benzoyl-4-chlorophenyl-2-acetamido-N-methylacetamide. Other fungi can demethylate diazepam, but this is the first report of fungal diazepam ring cleavage ([http://www.ncbi.nlm.nih.gov/pubmed/1168398|Ambrus et al. 1975]). A mixed microbial culture from activated sludge treatment has also been shown to demethylate diazepam to form 7-chloro-5-phenyl-3H-1,4-benzodiazepin-2-one ([http://www.ncbi.nlm.nih.gov/pubmed/20799730|Helbling et al., 2010]). 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These plastics are used in many food and drink packaging applications. When the resins are inert materials, they are commonly used as lacquers to coat metal products such as food cans, bottle tops and water supply pipes. More information on this compound can be found at the Bisphenol A website from the Bisphenol A Global Industry Group and the Bisphenol A page at the Hormone Disrupting Compounds site. Bisphenol A is metabolized by a Gram-negative aerobic bacterium (strain MV1) via a novel pathway involving oxidative skeletal rearrangement. The metabolism involves two primary pathways: a minor pathway, in which Bisphenol A is first oxidized to a triol, and a major pathway, in which Bisphenol A is metabolized to form the intermediates 4-hydroxybenzoate and 4-hydroxyacetophenone that are converted to carbon dioxide and biomass ([http://www.ncbi.nlm.nih.gov/pubmed/8125948|Spivack et al., 1994]). Sphingobium xenophagium Bayram and Sphingomonas sp. strain TTNP3 can metabolize bisphenol A by an ipso-substitution mechanism that involves ring hydroxylation at the site of the substituent. This proposed hydroxylation product can be cleaved to form hydroquinone and a proposed 2-(4-hydroxyphenyl)-isopropyl cation. The cation can be transformed to 4-(2-hydroxypropan-2-yl)phenol, which can eliminate water to form 4-isopropenylphenol. 4-Isopropenylphenol can be reduced to 4-isopropylphenol. These are the reactions found in both organisms. There are other possible routes (not shown here), including formation of a 2-(4-hydroxyphenyl)-isopropyl anion instead of the cation, to the above products, and other side reactions occur in one organism or the other ([http://www.ncbi.nlm.nih.gov/pubmed/17886831|Gabriel et al., 2007], [http://www.ncbi.nlm.nih.gov/pubmed/17557840|Kolvenbach et al., 2007]). Sphingobium fuliginis TIK-1 can metabolize and grow on 4-isopropylphenol. 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"Triphenyltin (TPT) is a one of the most commercially-important organotin compounds. The major use of TPT is in agriculture in fungicides to protect crops. It can detrimentally impact the environment. Reaction A is non-enzymic, catalyzed by a microbially-associated low-molecular-weight compound called TPT-Degrading Factor (TPT-DF). TPT-DF is most likely a pyoverdine, which is a yellow-green chromopeptide siderophore with a molecular mass of 1,000 to 1,500 Da, or a pyoverdine analog ([http://www.ncbi.nlm.nih.gov/pubmed/10919812|Inoue et al., 2000]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "6cd7edd7-1b3e-454f-923d-04703b330c71", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/234012f2-b78e-401e-964d-5fd7095d064e/node/6cd7edd7-1b3e-454f-923d-04703b330c71", "name": "Diphenyltin", "description": "no description", "aliases": [], "default_node_label": {"uuid": "11670f00-1c05-4ef6-9130-11448e08c3f6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/6c1413cb-d276-4371-9520-740a06ee6d88/structure/11670f00-1c05-4ef6-9130-11448e08c3f6"}, "node_labels": [{"uuid": "11670f00-1c05-4ef6-9130-11448e08c3f6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/6c1413cb-d276-4371-9520-740a06ee6d88/structure/11670f00-1c05-4ef6-9130-11448e08c3f6"}], "depth": 1, "stereo_removed": false, "scenarios": []}, {"uuid": "a133a215-4d1b-4f3f-862e-79bfe3280afe", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/234012f2-b78e-401e-964d-5fd7095d064e/node/a133a215-4d1b-4f3f-862e-79bfe3280afe", "name": "Benzene", "description": "no description", "aliases": [], "default_node_label": {"uuid": "9a1d2089-3a4c-4a5d-bdc0-38271b50e8f2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/51f35ac0-e104-4698-8a4b-e5e01da33af6/structure/9a1d2089-3a4c-4a5d-bdc0-38271b50e8f2"}, "node_labels": [{"uuid": "9a1d2089-3a4c-4a5d-bdc0-38271b50e8f2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/51f35ac0-e104-4698-8a4b-e5e01da33af6/structure/9a1d2089-3a4c-4a5d-bdc0-38271b50e8f2"}], "depth": 1, "stereo_removed": false, "scenarios": []}, {"uuid": "d8d92387-52e3-488d-be9e-e50f6f6d0352", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/234012f2-b78e-401e-964d-5fd7095d064e/node/d8d92387-52e3-488d-be9e-e50f6f6d0352", "name": "Triphenyltin", "description": "no description", "aliases": [], "default_node_label": {"uuid": "316c2ed4-7117-4aba-94a8-fff453b58aa1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b9f2ce65-68d6-472d-a5d5-0dffdd97c86f/structure/316c2ed4-7117-4aba-94a8-fff453b58aa1"}, "node_labels": [{"uuid": "316c2ed4-7117-4aba-94a8-fff453b58aa1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b9f2ce65-68d6-472d-a5d5-0dffdd97c86f/structure/316c2ed4-7117-4aba-94a8-fff453b58aa1"}], "depth": 0, "stereo_removed": false, "scenarios": []}], "edges": [{"uuid": "edbcf43a-b3e1-4c17-a7f8-689f2ba26ded", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/234012f2-b78e-401e-964d-5fd7095d064e/edge/edbcf43a-b3e1-4c17-a7f8-689f2ba26ded", "name": "Eawag BBD reaction r0789", "description": "no description", "aliases": [], "edge_label": {"uuid": "b390ce8f-b3f7-48b9-896a-61c4acc03578", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/b390ce8f-b3f7-48b9-896a-61c4acc03578"}, "start_nodes": [{"uuid": "d8d92387-52e3-488d-be9e-e50f6f6d0352", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/234012f2-b78e-401e-964d-5fd7095d064e/node/d8d92387-52e3-488d-be9e-e50f6f6d0352"}], "end_nodes": [{"uuid": "6cd7edd7-1b3e-454f-923d-04703b330c71", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/234012f2-b78e-401e-964d-5fd7095d064e/node/6cd7edd7-1b3e-454f-923d-04703b330c71"}, {"uuid": "a133a215-4d1b-4f3f-862e-79bfe3280afe", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/234012f2-b78e-401e-964d-5fd7095d064e/node/a133a215-4d1b-4f3f-862e-79bfe3280afe"}], "scenarios": [{"uuid": "9c6b4942-ccc6-4405-a919-0a83a1d6f5ea", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/9c6b4942-ccc6-4405-a919-0a83a1d6f5ea"}]}], "scenarios": []}, {"uuid": "02cf103e-a8a6-42a1-ba55-7481a23afeb6", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/02cf103e-a8a6-42a1-ba55-7481a23afeb6", "name": "Nitrophenol Family (an/aerobic)", "description": "Nitroaromatic compounds are recognized as environmentally hazardous and widely used for the industrial production of dyes, pesticides, plasticizers, explosives and solvents. Both oxidative and reductive mechanisms for degradation of nitrophenol compounds have been reported. A Moraxella sp. utilizes 4-nitrophenol as a sole source of carbon and nitrogen via an initial monooxygenase-catalyzed elimination of nitrite (Spain, J.C.; Gibson, D.T., 1991. Pathway for degradation of p-nitrophenol in a Moraxella sp. Applied and Environmental Microbiology. 57: 812-819; S. Nishino, personal communication, 2003). Similar monooxygenase reactions in Arthrobacter sp. strain JS443 and Arthrobacter protophormiae RKJ100 remove nitrite from 4-nitrophenol or 4-nitrocatechol in preparation for ring cleavage ([http://www.ncbi.nlm.nih.gov/pubmed/8085840|Jain et al., 1994]; [http://www.ncbi.nlm.nih.gov/pubmed/10772893|Chauhan et al., 2000]). Pseudomonas putida B2 and Alcaligenes sp. NyZ215 also employ a monooxygenase for the removal of nitrite from 2-nitrophenol to produce the ring cleavage substrate, catechol ([http://www.ncbi.nlm.nih.gov/pubmed/3752997|Zeyer et al., 1986] and [http://www.ncbi.nlm.nih.gov/pubmed/17616586|Xiao et al., 2007]). Under aneraobic conditions, Ralstonia eutropha JMP 134 and Pseudomonas putida B2 initially reduce the nitro group of 3-nitrophenol to form the hydroxylamino derivative. A mutase reaction, similar to the acid-catalyzed Bamberger rearrangement, converts 3-hydroxyaminophenol to aminohydroquinone ([http://www.ncbi.nlm.nih.gov/pubmed/10049374|Schenzle et al., 1999]) or 4-aminocatechol ([http://www.ncbi.nlm.nih.gov/pubmed/10831408|Zhao et al., 2000]). [http://www.ncbi.nlm.nih.gov/pubmed/8085840|Meulenberg et al. (1996)] reported the formation of 1,2,4-benzenetriol, which is proposed to form via a monooxygenase-type oxidation and elimination of ammonia. Resorcinol is used in the manufacture of adhesives and dyes and as an ingredient in pharmaceutical preparations for the topical treatment of skin conditions. Phenol 2-monooxygenase hydroxylates resorcinol by reducing flavin with molecular oxygen.", "aliases": [], "predicted": false, "nodes": [{"uuid": "4cb9a6fa-78f2-442a-83f9-8031d2ea269b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/02cf103e-a8a6-42a1-ba55-7481a23afeb6/node/4cb9a6fa-78f2-442a-83f9-8031d2ea269b", "name": "Acetyl-CoA", "description": "no description", "aliases": [], "default_node_label": {"uuid": "b72bb376-a570-4a87-8860-1124ad6c7b39", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/57bd5e24-9d14-4b91-bc60-64c8ea6c2d11/structure/b72bb376-a570-4a87-8860-1124ad6c7b39"}, "node_labels": [{"uuid": "b72bb376-a570-4a87-8860-1124ad6c7b39", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/57bd5e24-9d14-4b91-bc60-64c8ea6c2d11/structure/b72bb376-a570-4a87-8860-1124ad6c7b39"}], "depth": 5, "stereo_removed": false, "scenarios": []}, {"uuid": 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Cyanide is usually converted to thiocyanate by the addition reaction of sulfur since thiocyanate is less toxic than cyanide. The resultant thiocyanate is then treated to an activated sludge process, where microbes degrade this substance. Thiobacillus thioparus, which is a chemolithoautotrophic sulfur bacterium, can obtain energy by degradation of thiocyanate. Thiocyanate hydrolase, a newly found enzyme from Thiobacillus thioparus catalyzes the conversion of thiocyanate to carbonyl sulfide and ammonia. A model for the sequential reaction steps for thiocyanate hydrolase was presented, which involves four intermediates ([http://www.ncbi.nlm.nih.gov/pubmed/1577754|Katayama et al., 1992]). Carbonyl sulfide can be reduced by nitrogenase to carbon monoxide in Azotobacter vinelandii. The FeMo cofactor of nitrogenase`s molybdenum-iron protein was proposed to participate in this reaction, which may involve two intermediates ([http://www.ncbi.nlm.nih.gov/pubmed/7727396|Seefeldt et al., 1995]). In addition, carbon disulfide can be oxidized to carbonyl sulfide by an oxygenase in P. denitrificans. This process could be analogous to that seen in rat liver, in which carbon disulfide is oxidized by a P-450-containing NADPH-monoxygenase to produce monothiocarbonate (hydrated COS), rather than free COS itself, and \"active sulfur\" [S]. Carbon monoxide can be oxidized to carbon dioxide by methane monooxygenase in Methylococcus capsulatus, by carbon monoxide oxygenase in Pseudomonas aeruginosa, and by carbon monoxide dehydrogenase in many microbes. Thiocyanate can also be utilized by the heterotrophic bacterium 26B. Thiocyanate is hydrolyzed to cyanate and sulfide by an inducible enzyme in reaction A. Cyanate is hydrolyzed further to carbon dioxide and ammonia by cyanase. Cyanase activity in isolate 26B is also inducible and has been shown to hydrolyze cyanate under anaerobic conditions. Sulfide is oxidized to produce tetrathionate via the formation of thiosulfate. The ability to convert thiosulfate to tetrathionate is constitutive in reactions B and C. No further oxidation of tetrathionate occurred in a variety of heterotrophic bacteria. However, in T. tepidarius, thiosulfate can be oxidized to sulfate with the obligatory formation of tetrathionate as an intermediate. 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"http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/9f9abc75-eee4-4c1b-bd5c-88a4574c56c6"}]}], "scenarios": []}, {"uuid": "be1c8637-b041-4ffd-ad0a-8f0758702009", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/be1c8637-b041-4ffd-ad0a-8f0758702009", "name": "Naphthalene", "description": "Naphthalene is a fused ring bicyclic aromatic hydrocarbon and thus serves as a model for understanding the properties of a large class of environmentally prevalent polycylic aromatic hydrocarbons (PAHs). Naphthalene and its substituted derivatives are commonly found in crude oil and oil products. Certain PAHs are strong human carcinogens leading to widespread interest in the microbial metabolism of these compounds. Several Pseudomonas species can degrade naphthalene starting wtih 1,2 dioxygenation, shown here in the middle branch ([http://www.ncbi.nlm.nih.gov/pubmed/1447127|Eaton et al., 1992]). Naphthalene dioxygenase, the enzyme which initiates this route of bacterial naphthalene metabolism, is used in a biotechnological process to synthesize the blue jean dye indigo. This versatile enzyme has many other catalytic abilities, which are documented in a table of the Reactions of Naphthalene 1,2-Dioxygenase. Bacillus thermoleovorans Hamburg 2 initiates naphthalene degradation with dioxygenation at the 2,3 position ([http://www.ncbi.nlm.nih.gov/pubmed/10653712|Annweiler et al., 2000]), shown here in the left branch. The pathway also includes formation of naphthalene as part of the degradation of 1,2-dihydronaphthalene. 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Its solubility in water is moderate. 1,2,4-TCB has various uses in industry such as a carrier to apply dyes to polyester materials, a heat transfer medium, a degreaser and a lubricant. It also functions as a termite pesticide and an aquatic herbicide. About 93% of 1,2,4-TCB entering the environment through industrial discharges eventually evaporates into atmosphere, about 2.6% and 2.4% leave in terrestrial soil and aquatic sediments respectively, the rest end up in water. 1,2,4-TCB has been found to bioaccumulate in fish tissues. It has high acute toxicity to plants and aquatic life, its chronic toxic effects to aquatic life are also high. The complete microbial mineralization of 1,2,4-TCB as a sole carbon and energy source under aerobic conditions has been observed. The proposed pathway shows that at first 1,2,4-TCB is biodegraded to the corresponding chlorinated catechol by means of dioxygenase and dehydrogenase system, and then channeled into the tricarboxylic acid pathway through ortho cleavage ([http://www.ncbi.nlm.nih.gov/pubmed/1987135|van der Meer et al., 1991]). Under anaerobic conditions, some methanogenic microbial consortia are capable of reductively dechlorinating 1,2,4-TCB to chlorobenzene via 1,4-dichlorobenzene (Middeldorp PJM, De Wolf J, Zehnder AJB, Schraa G Applied and Environmental Microbiology (1997) 63: 1225-1229). 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"http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/a1d3567e-a84f-4b78-8942-82c6441a8d0b"}, "start_nodes": [{"uuid": "f6ce291c-d50a-4e44-bffc-0d67c3d7b6f1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/7dab441c-de7b-4dc1-a8ed-2bd756bec1e3/node/f6ce291c-d50a-4e44-bffc-0d67c3d7b6f1"}], "end_nodes": [{"uuid": "a03b5a7f-d5cd-4a5d-9a34-d6e35148f60e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/7dab441c-de7b-4dc1-a8ed-2bd756bec1e3/node/a03b5a7f-d5cd-4a5d-9a34-d6e35148f60e"}], "scenarios": [{"uuid": "81b324e9-0780-4af9-98f7-322de16cb7ec", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/81b324e9-0780-4af9-98f7-322de16cb7ec"}]}], "scenarios": []}, {"uuid": "ae8cf93f-3e12-44c0-97c5-e6a3150e17a1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/ae8cf93f-3e12-44c0-97c5-e6a3150e17a1", "name": "4-(1-Ethyl-1,4-dimethyl-pentyl)phenol", "description": "4-Alkylphenols are amphiphilic compounds commonly used as surfactants in many industrial production processes. They can have many functions, such as surfactants in a detergent or emulsifying agents in plastic or latex production. 4-Nonylphenols, an important class of 4-alkylphenols, have an estimated use of 650,000 tons annually ([http://www.ncbi.nlm.nih.gov/pubmed/11993862|Guenther et al., 2002]). This is a major concern as 4-nonylphenols are not easily degraded and their buildup can be toxic to an array of species from aquatic organisms to mammals ([http://www.ncbi.nlm.nih.gov/pubmed/9699867|Sonnenschein and Soto, 1998]). There can be as many as or more than forty isomers in technical grade 4-nonylphenol ([http://www.ncbi.nlm.nih.gov/pubmed/16427065|Moeder et al., 2006]). Microbes have evolved to biodegrade some of the relatively resilient 4-nonylphenol isomers. The process appears to depend on molecular oxygen ([http://www.ncbi.nlm.nih.gov/pubmed/15091914|Ekelund et al., 1993]), suggesting activation of the compound by incorporation of oxygen-bearing functional groups. To better understand 4-nonylphenol catabolism, one particular isomer, 4-(1-ethyl-1,4-dimethyl-pentylphenol) or NPL, is shown here in detail, with the R stereoisomer as the initial substrate. Both enantiomers are degraded, but not much is currently known regarding stereoselectivity. Sphingomonas spp. carry out the initial biodegradation of NPL. A major and a minor degradation pathway have been postulated, both ultimately leading to hydroquinone and a nonanol that retains the structure of the original nonyl side chain. Sphingomonas spp. can grow on the aromatic part as a carbon and energy source, but are not capable of further catabolizing the nonyl alcohol, and it is discarded as a non-catabolic byproduct ([http://www.ncbi.nlm.nih.gov/pubmed/15665329|Gabriel et al., 2005]). Both the minor and major pathways are catalyzed initially by an ipso-hydroxylation, i.e., hydroxylation at the anchor carbon atom of the alkyl substituent, forming 4-nonyl-4-hydroxy-cyclohexadienone ([http://www.ncbi.nlm.nih.gov/pubmed/15665329|Gabriel et al., 2005]). 18O-labeling experiments show that the ipso-hydroxy group is derived from molecular oxygen and that the major pathway for cleavage of the alkyl moiety is through cleaving the nonyl chain as alkyl cation (stabilized by the α-quaternary C atom of the nonyl group) and combination of the cation with a molecule of water to yield the nonyl alcohol and hydroquinone. In the minor pathway (not shown), a 1,2-C,O shift of the alkyl moiety is postulated to yield a 4-alkoxyphenol intermediate. A second ipso-hydroxylation leads to a hemiketal, which then spontaneously decomposes to p-benzoquinone and the nonyl alcohol. p-Quinone is quickly converted to hydroquinone by a reducing system ([http://www.ncbi.nlm.nih.gov/pubmed/17369338|Gabriel et al., 2007]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "fbf4b63b-524b-4747-8ec5-2afb92705be1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/ae8cf93f-3e12-44c0-97c5-e6a3150e17a1/node/fbf4b63b-524b-4747-8ec5-2afb92705be1", "name": "3,6-Dimethylheptan-3-ol", "description": "no description", "aliases": [], "default_node_label": {"uuid": "d7c29296-04c1-4912-9f79-06c45a5f8404", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/077bdd7c-964e-4518-b0a9-6b58b4d9f959/structure/d7c29296-04c1-4912-9f79-06c45a5f8404"}, "node_labels": [{"uuid": "d7c29296-04c1-4912-9f79-06c45a5f8404", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/077bdd7c-964e-4518-b0a9-6b58b4d9f959/structure/d7c29296-04c1-4912-9f79-06c45a5f8404"}], "depth": 1, "stereo_removed": false, "scenarios": []}, {"uuid": "75213480-f01b-4bce-ae11-4431b6b91dcf", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/ae8cf93f-3e12-44c0-97c5-e6a3150e17a1/node/75213480-f01b-4bce-ae11-4431b6b91dcf", "name": "Hydroquinone", "description": "no description", "aliases": [], "default_node_label": {"uuid": "b462d42e-e486-4803-b16c-f78676cf2349", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/792b6781-d85c-4c1d-bd82-a082fef85353/structure/b462d42e-e486-4803-b16c-f78676cf2349"}, "node_labels": [{"uuid": "b462d42e-e486-4803-b16c-f78676cf2349", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/792b6781-d85c-4c1d-bd82-a082fef85353/structure/b462d42e-e486-4803-b16c-f78676cf2349"}], "depth": 1, "stereo_removed": false, "scenarios": []}, {"uuid": "9108124f-6868-4c14-9075-301c4f7dc83d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/ae8cf93f-3e12-44c0-97c5-e6a3150e17a1/node/9108124f-6868-4c14-9075-301c4f7dc83d", "name": "4-(1-Ethyl-1,4-dimethyl-pentyl)phenol", "description": "no description", "aliases": [], "default_node_label": {"uuid": "40046efe-70e3-47e9-b4b9-f491fde00069", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ffacf273-3b10-4d1c-bd5b-5be3f1a3aa39/structure/40046efe-70e3-47e9-b4b9-f491fde00069"}, "node_labels": [{"uuid": "40046efe-70e3-47e9-b4b9-f491fde00069", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/ffacf273-3b10-4d1c-bd5b-5be3f1a3aa39/structure/40046efe-70e3-47e9-b4b9-f491fde00069"}], "depth": 0, "stereo_removed": false, "scenarios": []}], "edges": [{"uuid": "964cc0e9-d4dd-4074-b0a9-98885cca3f55", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/ae8cf93f-3e12-44c0-97c5-e6a3150e17a1/edge/964cc0e9-d4dd-4074-b0a9-98885cca3f55", "name": "Eawag BBD reaction r1358", "description": "no description", "aliases": [], "edge_label": {"uuid": "5023ef01-8d88-4a14-97d6-8ee59ade4a2d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/5023ef01-8d88-4a14-97d6-8ee59ade4a2d"}, "start_nodes": [{"uuid": "9108124f-6868-4c14-9075-301c4f7dc83d", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/ae8cf93f-3e12-44c0-97c5-e6a3150e17a1/node/9108124f-6868-4c14-9075-301c4f7dc83d"}], "end_nodes": [{"uuid": "fbf4b63b-524b-4747-8ec5-2afb92705be1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/ae8cf93f-3e12-44c0-97c5-e6a3150e17a1/node/fbf4b63b-524b-4747-8ec5-2afb92705be1"}, {"uuid": "75213480-f01b-4bce-ae11-4431b6b91dcf", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/ae8cf93f-3e12-44c0-97c5-e6a3150e17a1/node/75213480-f01b-4bce-ae11-4431b6b91dcf"}], "scenarios": [{"uuid": "dce781de-26ee-4f74-8986-e420b1bd9174", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/dce781de-26ee-4f74-8986-e420b1bd9174"}]}], "scenarios": []}, {"uuid": "0e09c2f7-12fa-4f31-9ea1-3b3f03536c65", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/0e09c2f7-12fa-4f31-9ea1-3b3f03536c65", "name": "1-Aminocyclopropane-1-carboxylate", "description": "1-Aminocyclopropane-1-carboxylate (ACP) is a natural product found in plant tissues. It is a key intermediate in the biosynthesis of ethylene, a fruit-ripening hormone in plants. Overripening of fruits may cause economic implications. Control of ethylene biosynthesis may delay this. It has been found that several microorganisms such as the bacterium Pseudomonas sp. ACP and the yeast Williopsis saturnus contain ACP deaminase and degrade ACP to 2-oxobutanoate and ammonia ([http://www.ncbi.nlm.nih.gov/pubmed/7326243|Walsh et al., 1981]). This may be a way to reduce ethylene synthesis and delay fruit ripening.", "aliases": [], "predicted": false, "nodes": [{"uuid": "4d62cc03-2402-4461-98fc-79af66f02cf9", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/0e09c2f7-12fa-4f31-9ea1-3b3f03536c65/node/4d62cc03-2402-4461-98fc-79af66f02cf9", "name": "Propanoyl-CoA", "description": "no description", "aliases": [], "default_node_label": {"uuid": "e5abdf0d-c3e9-4924-b041-7d0beaf2ec01", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/4e032169-05c6-49aa-9422-d081d81bc1a6/structure/e5abdf0d-c3e9-4924-b041-7d0beaf2ec01"}, "node_labels": [{"uuid": "e5abdf0d-c3e9-4924-b041-7d0beaf2ec01", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/4e032169-05c6-49aa-9422-d081d81bc1a6/structure/e5abdf0d-c3e9-4924-b041-7d0beaf2ec01"}], "depth": 2, "stereo_removed": false, "scenarios": []}, {"uuid": "424c9ef1-c0d9-4cba-88c1-c7afd1fac424", "url": 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"name": "2-Oxobutanoate", "description": "no description", "aliases": [], "default_node_label": {"uuid": "b465de5e-a44e-4f5b-9197-e665b15af296", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/1d8dba15-23b7-4916-91ba-3b00be5e4e8b/structure/b465de5e-a44e-4f5b-9197-e665b15af296"}, "node_labels": [{"uuid": "b465de5e-a44e-4f5b-9197-e665b15af296", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/1d8dba15-23b7-4916-91ba-3b00be5e4e8b/structure/b465de5e-a44e-4f5b-9197-e665b15af296"}], "depth": 1, "stereo_removed": false, "scenarios": []}], "edges": [{"uuid": "6c0c90cb-427d-424c-967a-bd4fbc8cb0fe", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/0e09c2f7-12fa-4f31-9ea1-3b3f03536c65/edge/6c0c90cb-427d-424c-967a-bd4fbc8cb0fe", "name": "Eawag BBD reaction r0358", "description": "no description", "aliases": [], "edge_label": {"uuid": "0ea9e93a-5df6-4174-b881-9ceb7441ceba", "url": 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Synthetic 5NAA is used as the starting material for other nitroaromatic compounds and dyes (Baxter and Bennion, May 1956, U.S. patent 749,320.23). Bradyrhizobium JS329 can use 5NAA as its sole source of carbon, nitrogen, and energy. The degradation pathway involves an unusual hydrolytic removal of the amino group to form 5-nitrosalicylate, followed by ring cleavage without removal of the nitro group, proposed to produce 4-nitro-6-oxohepta-2,4-dienodioate ([http://www.ncbi.nlm.nih.gov/pubmed/20081004|Qu and Spain, 2010]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "fc241803-0435-472c-a97f-5ad1f48feb79", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/bf1cc03c-a78a-480d-9e69-92fd10bd112d/node/fc241803-0435-472c-a97f-5ad1f48feb79", "name": "4-Nitro-6-oxohepta-2,4-dienedioate", "description": "no description", "aliases": [], "default_node_label": {"uuid": "78fa054a-8b0e-48eb-a323-373949c59b0b", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/c1d0eb67-f8e0-4484-8dee-bf17741c8c59/structure/78fa054a-8b0e-48eb-a323-373949c59b0b"}, "node_labels": [{"uuid": "78fa054a-8b0e-48eb-a323-373949c59b0b", "url": 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Phenylboronic acid is an aromatic boronic acid. Boronic acids are used for a variety of purposes, including insect pest control ([http://www.ncbi.nlm.nih.gov/pubmed/5413091|Settepani et al., 1970]). Plant cell walls and some bacterial quorum-sensing molecules contain borate esters ([http://www.ncbi.nlm.nih.gov/pubmed/11679668|O`Neill et al., 2001], [http://www.ncbi.nlm.nih.gov/pubmed/11823863|Chen et al., 2002]), and antibiotic compounds containing boron are synthesized by some bacteria ([http://www.ncbi.nlm.nih.gov/pubmed/7532644|Irschik et al., 1995], [http://www.ncbi.nlm.nih.gov/pubmed/8695905|Kohno et al., 1996]). The initial step in the degradation of phenylboronic acid can be carried out by Arthrobacter nicotinovorans strain PBA, which converts the compound to phenol under aerobic conditions ([http://www.ncbi.nlm.nih.gov/pubmed/12839810|Negrete-Raymond et al., 2003]). Boron is predicted to be released from phenylboronic acid as orthoboric acid (B(OH)3), although the production of this compound has not yet been experimentally verified. A. nicotinovorans strain PBA has also been shown to oxidize other aromatic boronic acids. The yeast Trichosporon cutaneum ([http://www.ncbi.nlm.nih.gov/pubmed/17425111|Gerginova et al., 2007]) or the bacterium Brevibacterium fuscum ([http://www.ncbi.nlm.nih.gov/pubmed/14478080|Nakagawa & Takeda, 1962]), and several other bacteria, can aerobically degrade phenol to catechol. The anaerobic biodegradation of phenol is covered elsewhere. Diphenyl ether (DE) and its halogenated cogeners are compounds of environmental concern. Polybrominated DEs (PBDEs) are used as flame retardants. Sphingomonas sp. strain SS3 aerobically degrades diphenyl ether and its monochlorinated derivatives through angular dioxygenation to phenol and catechol via cis-1,2-dihydrodihydroxydiphenyl ether ([http://www.ncbi.nlm.nih.gov/pubmed/1444384|Schmidt et al., 1992]). Sphingomonas strain PH-07 aerobically degrades diphenyl ether and its mono-, di-, and tri-brominated derivatives to 2,3-dihydroxydiphenyl ether, which it degrades to phenol and 2-hydroxymuconate ([http://www.ncbi.nlm.nih.gov/pubmed/17694301|Kim et al., 2007]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "3ee55966-18c4-4a64-8d7f-da87f9b1a5fc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/93299316-b92f-4462-9798-648a0b195860/node/3ee55966-18c4-4a64-8d7f-da87f9b1a5fc", "name": "2-Hydroxymuconate", "description": "no description", "aliases": [], "default_node_label": {"uuid": "9c5c1f6b-8249-426e-a94f-88b678533de0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/571b2ca8-e29a-4496-9a09-5b3174ad9019/structure/9c5c1f6b-8249-426e-a94f-88b678533de0"}, "node_labels": [{"uuid": "9c5c1f6b-8249-426e-a94f-88b678533de0", "url": 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Since THF is very soluble in water and has a relatively low boiling point, signficant amounts are often released into the environment, causing contamination problems. Tetrahydrofuran is not considered to be readily degradable, and concerns of environmental contamination have been raised. [http://www.ncbi.nlm.nih.gov/pubmed/1367773| Bernhardt and Diekmann (1991)] performed studied the pathway for tetrahydrofuran degradation by Rhodococcus ruber DSM 44190. The pathway shown below is hypothetical. Not all intermediates (e.g. 2-hydroxytetrahydrofuran) were detected. In fact, the isomerization of 2-hydroxytetrahydrofuran might occur spontaneously and not require an enzyme. However, degradation experiments using the same organism were performed with a similar compound, 2,5-dimethyltetrahydrofuran (Bock, C., Kroppenstedt, R.M., and Diekmann, H., 1996, Appl Microbiol Biotechnol. 45:408-410), and those data support the proposed tetrahydrofuran pathway. [http://www.ncbi.nlm.nih.gov/pubmed/12632259|Thiemer et al. (2003)] characterized the pathway in Pseudonocardia sp. strain K1. 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These isomers are used as a disinfectants, textile scouring agents, surfactants and as intermediates in the manufacture of salicylaldehyde, coumarin, and herbicides. Creosote is a less refined petrochemical mixture containing cresol. It is used as a fungicide and a wood preservative for railroad ties, telephone poles, and marine pilings. Despite their chemical similarity, cresol isomers are degraded by bacteria through different pathways. One intermediate in this pathway, 3-hydroxybenzyl alcohol, is also an intermediate in the biosynthetic pathway of patulin ([http://www.ncbi.nlm.nih.gov/pubmed/6988382|Grootwassink & Gaucher, 1980]), a toxin and antiviral agent produced by some molds such as Penicillium patulinum. When grown on m-cresol as a sole carbon source, P. putida 9869 metabolizes the compound via the meta pathway with 3-methylcatechol as an intermediate ([http://www.ncbi.nlm.nih.gov/pubmed/1123316|Hopper et al., 1975]). It has been shown that Pseudomonas picketti also degrade m-cresol via 3-methylcatechol, as presented in the Toluene Pathway ([http://www.ncbi.nlm.nih.gov/pubmed/1892384|Shields et al., 1991]). [http://www.ncbi.nlm.nih.gov/pubmed/1123316|Hopper and Taylor (1974)] have also reported that P. putida 9869, when grown on 3,5-xylenol as a sole carbon source, metabolizes m-cresol via the gentisate pathway, as depicted in this text map. 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[http://www.ncbi.nlm.nih.gov/pubmed/7783002|Gunther and Schlosser (1994)] report that 4-methylcatechol is also degraded by ortho-cleavage to 4-methylmuconolactone. Ralstonia eutropha JMP134 degrades 4-methylcatechol via this route, converting 4-methylmuconolactone to 4-methyl-3-oxoadipate in several steps ([http://www.ncbi.nlm.nih.gov/pubmed/9461415|Erb et al., 1998]). Rhodococcus sp. strain YU6 is able to metabolize o-xylene via direct ring oxidation and meta-cleavage ([http://www.ncbi.nlm.nih.gov/pubmed/16145546|Jang et al., 2005]). 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Sulfur dioxide emissions can poison catalytic converters, cause acid deposition and increase diesel particulate emissions. Polycyclic aromatic sulfur heterocycles (PASHs), such as benzothiophene, account for a large fraction of this organic sulfur content ([http://www.ncbi.nlm.nih.gov/pubmed/16574137|Liang et al., 2006]). Microbial desulfurization processes are of particular interest as a means to reduce the petroleum sulfur content and minimize pollution. Several microorganisms are able to incorporate the sulfur from benzothiophene into cell biomass. This desulfurization process involves sulfur-specific degradation via the cleavage of carbon-sulfur bonds. Benzothiophene is first oxidized to Benzothiophene-S,S-dioxide and subsequent thiophene ring opening via cleavage of the aryl C-S bond in a mechanism similar to dibenzothiophene desulfurization ([http://www.ncbi.nlm.nih.gov/pubmed/9782503|Gilbert et al., 1998] and [http://www.ncbi.nlm.nih.gov/pubmed/12147483|Kirimura et al., 2002]). The final desulfination step in Gordona sp. strain 213E is thought to occur by oxygenase-catalyzed hydroxylation of the C-S carbon. In this case, an enol product is formed but quickly tautomerizes to the aldehyde upon release from the enzyme ([http://www.ncbi.nlm.nih.gov/pubmed/9782503|Gilbert et al., 1998]). If this aldehyde is oxidized to the carboxylate, it forms 2-hydroxyphenylacetate, a compound found in the styrene pathway. The desulfination product in Paenibacillus sp. strain A11-2 is o-hydroxystyrene via a sulfinase also capable of dibenzothiophene desulfination ([http://www.ncbi.nlm.nih.gov/pubmed/12743754|Konishi et al., 2003]). Dibenzothiophene has both a desulfurization pathway and a pathway for complete metabolism of the compound. 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Lignin is an important part in the terrestrial carbon cycle and is the most abundant of all the aromatic compounds. Lignin is found in the secondary structure of the cell walls of plants, trees and other vegetation ([http://www.ncbi.nlm.nih.gov/pubmed/19167225|Martone et al., 2009]). Its main function is to provide support to the cell walls by integrating into the spaces of the cell walls. Microbial degradation of lignin helps in the conversion of lignin into useful chemical products which are free from toxins. The degradation of Syringate and Gallate lead to the production of pyruvate and oxaloacetate, both of which are critical components involved in multiple pathways, including the Krebs Cycle, amino acid catabolism, fermentation and gluconeogenesis ([http://www.ncbi.nlm.nih.gov/pubmed/16030198|Kasai et al., 2005]). This page shows only aerobic pathway of gallate. 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Epichlorohydrin is a synthetic precursor of DCP, which is used as a general solvent, as an intermediate in organic synthesis and in paints, varnishes, lacquers, water colors, binders and photographic lacquers. Two pathways for the degradation of DCP are found in Corynebacterium sp. strain N-1074 which are catalyzed by two groups of two isoenzymes ([http://www.ncbi.nlm.nih.gov/pubmed/1447132|Nakamura et al., 1992]). One group of two enzymes, originally designated Ia and IIa, catalyzes the non-stereospecific dechlorination and subsequent hydrolyzation of DCP. Both enzymes accept (R)- and (S)-enantiomers as substrates and convert them to racemic product mixtures ([http://www.ncbi.nlm.nih.gov/pubmed/7765275|Nakamura et al., 1994]). The second group of enzymes, designated Ib and IIb, also accept (R)- and (S)-enantiomers, but convert them to (R)-rich products ([http://www.ncbi.nlm.nih.gov/pubmed/1447132|Nakamura et al., 1992]). Comparisons of protein sequences and immunological properties have shown that halohydrin hydrogen-halide-lyase (HHHL) A (enzyme Ia) is similar, but not identical to HHHL B (enzyme Ib) (Nakamura et al., 1994). Epoxide hydrolase A (enzyme IIa) and epoxide hydrolase B (enzyme IIb) have also been shown to have different structural properties ([http://www.ncbi.nlm.nih.gov/pubmed/1447132|Nakamura et al., 1992]). Although Arthrobacter sp. strain AD2 can dechlorinate DCP and 3-Chloro-1,2-propanediol, it does not possess epoxide hydrolase activity and so cannot use either compound as a sole carbon source. Partial sequence comparisons have shown that the HHHL of strain AD2 is very similar to the Corynebacterium HHHL A (Nagasawa et al., 1992, Appl. Microbiol. Biotechnol. 36:478-482). Another species, Agrobacterium radiobacter strain AD1, can use DCP or epichlorohydrin as a sole carbon source. The pathway of degradation is non-enantioselective and similar to that of the Corynebacterium strain. The AD1 epoxide hydrolase has been shown to be very similar to the Corynebacterium epoxide hydrolase A. 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Pure cultures of Sphingomonas haloaromaticamans and some Pseudomonas species can degrade 1,4-dichlorobenzene through similar pathways. 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It has been used to control weeds in cereal, corn, sorghum, onions, flax, mint, turf, and on non-cropland. Anomalies in rat fetuses exposed to bromoxynil suggest that it is a teratogen. Workers chronically exposed to bromoxynil over a year long span showed symptoms of weight loss, fever, vomiting, headache, and urinary problems. Bromoxynil is a Restricted Use Pesticide (RUP), not registered for homeowner use. Bromoxynil has a low persistence in soil (EXTOXNET, June 1996, Bromoxynil Pesticide Information Profile). The left-most pathway for bromoxynil oxidation to 3-oxoadipate is based on [http://www.ncbi.nlm.nih.gov/pubmed/1610174|Topp et al. (1992)], who propose that bromoxynil is degraded by the same enzymes which degrade PCP. The proposed pathway for bromoxynil oxidation to 3,5-dibromo-4-hydroxybenzoate is based on [http://www.ncbi.nlm.nih.gov/pubmed/1505868|Vokounova et al. (1992)], [http://www.ncbi.nlm.nih.gov/pubmed/3530133|McBride et al. (1986)], and [http://www.ncbi.nlm.nih.gov/pubmed/2834373|Stalker et al. (1988)]. [http://www.ncbi.nlm.nih.gov/pubmed/9726864|Verhagen et al. 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"description": "Thiophene-based compounds are relatively abundant in the environment. They can comprise 1-3% of crude petroleum, and they also have specialty uses as building blocks in pharmaceuticals and organic chemistry (Roncali (1992) Chem Rev 92: 711-738). Many different thiophene compounds are naturally produced in plant roots, especially in plants of the Tagetes genus ([http://www.ncbi.nlm.nih.gov/pubmed/12228405|Jacobs et al., 1995]). These compounds include alpha-terthienyl, which appears to be an effective pesticide against a wide variety of organisms (Nivsarkar, Cherian, and Padh (2001) Current Science 81: 667-672). The enzymes involved in microbial degradation of thiophene-2-carboxylate (T2C) are not fully characterized. However, the pathway shown on the left below has been documented for multiple bacterial species, and Aquamicrobium defluvii NKK has been found to use it under both aerobic and anaerobic conditions ([http://www.ncbi.nlm.nih.gov/pubmed/9531630|Bambauer et al., 1998]; [http://www.ncbi.nlm.nih.gov/pubmed/16742794|Cripps, 1973]). In this pathway, T2C is ligated to CoA, oxidized, and then undergoes ring opening with the subsequent loss of sulfide. Hydrolysis releases the intermediary metabolite, 2-oxoglutarate, from the CoA. T2C-CoA thioesterase activity, which regenerates T2C from T2C-CoA, has also been detected ([http://www.ncbi.nlm.nih.gov/pubmed/9531630|Bambauer et al., 1998]). A separate T2C degradation pathway (shown on the right) that does not support growth was described in a photosynthetic bacterium named strain H45-2 (Tanaka, H. et al. (1982) Agric. Biol. Chem. 46:1429-1438). Cells grown photosynthetically and anaerobically on benzoate or succinate transformed T2C to tetrahydrothiophene-2-carboxylate (major product of benzoate-grown cells) and 3-hydroxytetrahydrothiophene-2-carboxylate (major product of succinate-grown cells).", "aliases": [], "predicted": false, "nodes": [{"uuid": "f29e4819-ecf0-4a08-b4d7-2d9f154830f2", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/67fb2172-566c-4e77-a3d4-dbda716703cb/node/f29e4819-ecf0-4a08-b4d7-2d9f154830f2", "name": "2-Oxoglutarate", "description": "no description", "aliases": [], "default_node_label": {"uuid": "710e9b4f-6f5c-4e62-880c-57d93444e869", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/5b0a94f6-d411-44fd-bcc1-fb79b4e697f5/structure/710e9b4f-6f5c-4e62-880c-57d93444e869"}, "node_labels": [{"uuid": "710e9b4f-6f5c-4e62-880c-57d93444e869", "url": 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Although phenanthrene is not mutagenic or carcinogenic, it has been shown to be toxic to marine diatoms, gastropods, mussels, crustaceans, and fish. Phenanthrene is a tricyclic aromatic hydrocarbon. Since it is the smallest aromatic hydrocarbon to have a \"bay-region\" and a \"K-region\", phenanthrene is often used as a model substrate for studies on metabolism of carcinogenic PAHs. Phenanthrene is degraded by some soil bacteria through one of two different routes. In one route,1-hydroxy-2-naphthoic acid is oxidized to 1,2-dihydroxynaphthalene, which is further degraded via the Naphthalene Pathway to salicylate which can be further metabolized. In the other pathway, the ring of 1-hydroxy-2-naphthoic acid is cleaved and further metabolized via the Phthalate Pathway. It has been demonstrated that naphthalene and phenanthrene share a common upper metabolic pathway ([http://www.ncbi.nlm.nih.gov/pubmed/8157614|Kiyohara H, et al. 1994]). In addition, the metabolism of phenanthrene by Streptomyces flavovirens and the marine cyanobacterium Agmenellum quadruplicatum PR-6 is more similar to that reported in mammalian and fungal enzyme systems than those catalyzed by bacteria. Both oxidize phenanthrene to phenanthrene trans-9,10-dihydrodiol via a monooxygenase-epoxide hydrolase-catalyzed reaction rather than by a dioxygenase. The metabolic formation of 1-methoxyphenanthrene from phenanthrene was first reported in Synechococcus sp. PR-6. This organism may detoxify other 1-phenanthrols. The metabolic fate of 1-methoxyphenanthrene in Synechococcus sp. PR-6 remains to be elucidated. Fungi also can metabolize phenanthrene by utilizing monooxygenases and epoxide hydrolases. 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It is commonly known as TNT and is an explosive used in military shells, bombs, and grenades, in industrial uses, and in underwater blasting. TNT production in the United State occurs solely at military arsenals. Accidental release of TNT has contaminated groundwater and soil at numerous munition manufacturing sites. The U.S. EPA has listed TNT as a priority pollutant and has recommended its removal from contaminated sites. TNT is toxic to algae and invertebrates and chronic exposure to TNT by humans causes harmful health effects, including anemia and abnormal liver function, cataract development, and skin irritation. The EPA has determined that TNT is a possible human carcinogen, based on animal studies. This page shows only aerobic TNT degradation pathway. Its anaerobic degradation is documented elsewhere in the EAWAG-BBD. Microbial transformation of TNT usually begins with reduction of one of the nitro groups. The enzymes which catalyze these reductions are \"non-specific\" NAD(P)H dependent nitroreductases and are largely uncharacterized. One exception is a nitrobenzene nitroreducatase, purified from P. pseudoalcaligenes JS52, which can transform TNT to the mono- and dihydroxylamino intermediates. As its name suggests, this enzyme was originally found to reduce nitrobenzene. Aerobic bacteria are able to reduce 2 of the 3 nitro groups of TNT; the reduction of the third nitro group requires anaerobic conditions. While denitration is often a major reaction in the biodegradation of nitrosubstituted compounds, bacterial denitration of TNT or its reduction products has been demonstrated in only a few cases. One example is shown below in which 2-amino-4-nitro-toluene is produced from 2-amino-4,6-dinitrotoluene. In addition, [http://www.ncbi.nlm.nih.gov/pubmed/9198535| Martin et al. (1997)] showed that P. savastanoi can generate 2,4-dinitrotoluene from TNT. The formation of Meisenheimer complexes from TNT has been described in at least 3 bacterial strains, including Rhodococcus erythropolis and Mycobacterium sp. ([http://www.ncbi.nlm.nih.gov/pubmed/16349484|Vorbeck et al., 1998]). These complexes result from the nucleophilic attack by a hydride ion on the aromatic ring. Formation of the hydride complexes could not be identified with the recently isolated TNT-enriched strains TNT-8 and TNT-32, nor with Pseudomonas sp. strain A (2NT-). However, these strains are able to carry out nitro-group reduction, as shown below. [http://www.ncbi.nlm.nih.gov/pubmed/9687442|French et al. (1998)] demonstrated that the enzyme pentaerythritol tetranitrate reductase from Enterobacter cloacae catalyzes the formation of both the hydride- and dihydride-Meisenheimer complexes. Generally, complete mineralization of TNT is only detected with bacterial consortia. Many of the products of TNT biodegradation are highly reactive and covalently bind to cellular components and any solid supports (such as soil) present in the medium. The latter prevents or prolongs the mineralization process, but also hinders a further spread of TNT contaminants. Several authors have noted the formation of, as yet, unidentified compounds during TNT biodegradation. 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Total annual production is about 5.5 million tons worldwide. There are several variations of the polymer, the two most common being nylon 6 and nylon 6,6 (Wikipedia Nylon). Nylon is not considered a hazardous chemical, although its accumulation in landfills renders it a desirable recyclable commodity. Some investigation is under way as to whether nylon dust causes respiratory illness in those exposed to it ([http://www.ncbi.nlm.nih.gov/pubmed/11763480|Warheit et al., 2001]). Furthermore, the synthesis of adipic acid, a chemical used in production of nylon-6,6, produces large emissions of nitrous oxide. Nitrous oxide has a stronger greenhouse effect than carbon dioxide (about 200 times), and is also thought to contribute to ozone layer degradation (Wikipedia Nitrous Oxide). The initial step in the degradation of nylon involves the transport of the compound across the outer membrane of the cell. Nylon 6 exists as a polymer in excess of 100 units. A few different enzymes are known to degrade nylon oligomers via different mechanisms. The endo-type hydrolases can cleave the oligomer in the middle of the molecule, and the exo-type hydrolase can only remove 6-aminohexanoyl groups from the N-terminus. The endo-type 6-aminohexanote oligomer hydrolase can degrade oligomers up to 20 units. It degrades oligomers into various sizes depending on which amide bond is hydrolized ([http://www.ncbi.nlm.nih.gov/pubmed/8285701|Kakudo et al., 1993]). The nylon linear dimer hydrolase is exo-type and can slowly degrade oligomers up to 6 units ([http://www.ncbi.nlm.nih.gov/pubmed/6305910|Negoro et al., 1983]). 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"url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/05cde591-8c91-4a2c-a9be-8e903d71c5b1"}]}], "scenarios": []}, {"uuid": "369ca024-a9c7-4864-bd60-69e32f350aef", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/369ca024-a9c7-4864-bd60-69e32f350aef", "name": "Phenanthrene (fungal 9S,10S)", "description": "Polycyclic aromatic hydrocarbons (PAHs), such as phenanthrene are commonly found as pollutants in soils, estuarine waters and sediments, and other terrestrial and aquatic sites. Phenanthrene has been shown to be toxic to marine diatoms,gastropods, mussels, crustaceans, and fish. Besides the bacterial metabolic pathways of phenanthrene , fungi can also metabolize phenanthrene. Nonligninolytic (i.e., high-N) cultures of Phanerochaete chrysosporium fit the typical eukaryotic pattern. They metabolize phenanthrene to trans-dihydrodiols and phenanthrene conjugates. Phenanthrene trans-9,10- and trans-3,4-dihydrodiols are formed by the successive activities of monooxygenases and epoxide hydrolases. The regiospecificity of P. chrysosporium differs from that of Cunninghamell elegans, which principally produces the trans-1,2- dihydrodiol with smaller amounts of the trans-3,4-dihydrodiol. There was no metabolism at 9, 10- positions (\"K-region\") of phenanthrene as evidenced by the failure to detect trans-9,10-dihydrodiols. The three phenanthrols were most likely produced either by dehydration of the trans-dihydrodiols or by rearrangement of the postulated arene oxides (reactions: A, B, J, K, C and D). Similarly, in Cunninghamell elegans, 1-phenanthrol was produced via dehydration of the corresponing trans-1,2-dihydrodiols (reaction I). The novel 9-phenanthryl-beta -D-glucopyranoside produced by P. chrysosporium differs from the 1-phenanthryl-beta- D-glucopyranoside produced by C. elegans. Those conjugates may be considered detoxification products of phenanthrene. Unlike nonligninolytic Phanerochaete chrysosporium, ligninolytic Phanerochaete chrysosporium does not accumulate trans-dihydrodiols and phenanthrols ([http://www.ncbi.nlm.nih.gov/pubmed/1622259|Hammel KE, et al., 1992]). It gives 2,2`-diphenic acid (DPA) as a major fate of phenanthrene by 9,10-oxidation and ring cleavage (reactions E and F). These two reactions could involve multiple steps. However, no intermediates were reported so far. The oxidation of phenanthrene-9,10-quinone (PQ) to DPA involves both fungal and abiotic mechanisms, and is unaffected by the level of nitrogen added. Phenanthrene degradation by ligninolytic P. chrysosporium involves both ligninolytic and nonligninolytic enzymes and is not initiated by a classical microsomal cytochrome P-450. In reaction H, 2,2`-biphenyldimethanol occurred as a minor phenanthrene metabolite which was probably a reduction product of DPA. Both phenanthrene and PQ could be mineralized to similar extents by this kind of fungus. For reaction G, it is likely that some DPA formed from phenanthrene and PQ was further degraded, but it remains uncertain whether DPA is an obligatory intermediate in phenanthrene. Metabolism of phenanthrene by Phanerochaete chrysosporium, A.quadruplicatum PR-6, and S. flavovirens all produce phenanthrene trans-9S,10S-dihydrodiol as the predominant metabolite. 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A Type I nitroreductase present in enteric bacteria is responsible for the nitroreduction of explosives RDX and TNT ([http://www.ncbi.nlm.nih.gov/pubmed/10749541|Kitts et al., 2000]). 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Carbendazim is quite stable in soil and water, and is a suspected mutagen, carcinogen, and endrocrine disruptor. Thus studies on its biodegradation are of interest ([http://www.ncbi.nlm.nih.gov/pubmed/20228105|Pandey et al., 2010]). Several Pseudomonas species can use benomyl as the sole carbon source for growth. The initial step in the degradation of benomyl is hydrolysis of the butylcarbamoyl side chain to form carbendazim (MBC). The N-butylcarbamate formed is hydrolyzed to n-butylamine. The carbendazim is hydrolyzed to 2-aminobenzimidazole (2-AB). Only small amounts of these compounds are formed; n-butylamine may be the carbon source for growth ([http://www.ncbi.nlm.nih.gov/pubmed/582241|Fuchs and DeVries, 1978]). Rhodococcus jialingiae djl-6-2 is capable of using carbendazim as the sole carbon and nitrogen source for growth. It also hydrolyzes it to 2-aminobenzimidazole, which is converted to 2-hydroxybenzimidazole. This last compound is postulated to be dioxygenated, either by a dioxygenase or two consecutive monoxygenase reactions, to 2,6,7-trihydroxybenzimidazole. Extradiol cleavage forms (2Z)-3-(4-formyl-2-hydroxy-1H-imidazol-5-yl)-2-hydroxyprop-2-enoate. Benzimidazole is also produced in a side reaction, possibly by deamination of carbendazim ([http://www.ncbi.nlm.nih.gov/pubmed/20833408|Wang et al., 2010]). Pseudomonas sp. CBW is capable of using carbendazim as the sole source of carbon and energy for growth. It follows the above pathway through 2-hydroxybenzimidazole. It can metabolize 2-hydroxybenzimidazole and 1,2-diaminobenzene. It is postulated to cleave the heteroring of 2-hydroxybenzimidazole to produce 1,2-diaminobenzene, which might be converted to catechol ([http://www.ncbi.nlm.nih.gov/pubmed/20383655|Fang et al., 2010]). Nocardioides sp. SG-4G is capable of using carbendazim, 2-aminobenzimidazole, and 2-hydroxybenzimidazole as sole carbon and energy sources for growth. The pathway followed is the same as for the above two organisms, through 2-hydroxybenzimidazole. 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Oligomer", "description": "Starch is a polymer of glucose in which the monomers are connected via an alpha-1,4 glucosidic bond. Plants make starch to store glucose, as it can be broken down again to glucose when carbon and energy are needed. For this purpose, animals and fungi make glycogen, an alpha-glucan polymer more highly cross-linked than starch. The starch oligomer maltotriose, which is a glucose trimer connected via alpha-1,4-linkages, serves as a model for starch (or glycogen) degradation. The two most common ways of cleaving alpha-1,4-glucosidic bonds involve glycoside hydrolases or Type-1 polysaccharide lyases (for example, pectate lyase). The third known way to cleave alpha-1,4-glucosidic bonds is found in the Anhydrofructose pathway ([http://www.ncbi.nlm.nih.gov/pubmed/18785261|Yu et al., 2008]), in which the glucosidic bonds in starch (or glycogen) oligomers are cleaved by alpha-1,4-glucan lyase, a Type-2 polysaccharide lyase. From the nonreducing polymer end, alpha-1,4-glucan lyase releases 1,5-anhydro-D-fructose, a central intermediate from which microorganisms can make a variety of end products ([http://www.ncbi.nlm.nih.gov/pubmed/10446355|Yu et al., 1999]). In bacteria, the 1,5-anhydro-D-fructose intermediate is converted to 1,4-anhydro-D-glucitol ([http://www.ncbi.nlm.nih.gov/pubmed/9880813|Shiga et al., 1999]), or 1,4-anhydro-D-mannitol ([http://www.ncbi.nlm.nih.gov/pubmed/16461673|Kuhn et al., 2006]). The 1,4-anhydro-D-glucitol undergoes phosphorylation to 1,4-anhydro-glucitol-6-phosphate and then dehydrogenation to 1,4-anhydro-fructose-6-phosphate. 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Next Baeyer-Villiger oxidation forms 4-hydroxyphenyl 4-hydroxybenzoate, which is hydrolyzed to form 4-hydroxybenzoate and 1,4-hydroquinone ([http://www.ncbi.nlm.nih.gov/pubmed/18024680|Inoue et al., 2008]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "4abe11b5-4f2d-4c4c-aeb4-45c2a725ad60", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/6e4855f5-981a-40b5-9dcc-6fa3865a9d61/node/4abe11b5-4f2d-4c4c-aeb4-45c2a725ad60", "name": "4-Hydroxybenzoate", "description": "no description", "aliases": [], "default_node_label": {"uuid": "86f63ddf-c598-4014-a0af-c59cb11ea956", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/9e05c7cc-e1b3-46a4-93ce-785c0dc04bfa/structure/86f63ddf-c598-4014-a0af-c59cb11ea956"}, "node_labels": [{"uuid": "86f63ddf-c598-4014-a0af-c59cb11ea956", "url": 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In addition, cocaine is a topical anesthetic, potent central nervous system stimulant, adrenergic blocking agent, and abused drug ([http://www.ncbi.nlm.nih.gov/pubmed/12242397|Kutchan, 1995]). Annual production of cocaine is on the order of 800 metric tons (U.S. NDIC, 2006). In bacteria, cocaine breakdown is initiated by cocaine esterase, which creates ecgonine methyl ester and benzoate. Ecgonine methyl esterase cleaves ecgonine methyl ester into ecgonine and methanol. The ecgonine is then transformed to pseudoecgonine by pseudoecgonine epimerase. 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Acetylene can polymerize exothermically, leading to deflagration. Acetylene is relatively nontoxic and has been used as an anesthetic. Inhalation of acetylene can be hazardous because of its action as a simple asphyxiant. Acetylene is also well known for its inhibitory properties and its interactions with microbial processes such as nitrogen fixation, nitrous oxide reduction, ammonium oxidation, methanogenesis and alkane oxidation. Rhodococcus spp. can aerobically metabolize acetylene through reactions catalyzed by the enzyme acetylene hydratase ([http://www.ncbi.nlm.nih.gov/pubmed/6121789|Kanner & Bartha, 1982]), and Klebsiella penumonia can do the same using nitrogenase ([http://www.ncbi.nlm.nih.gov/pubmed/2268290|Lowe et al., 1990]). The strict anaerobe Pelobacter acetylenicus can also carry out the acetylene hydratase reaction ([http://www.ncbi.nlm.nih.gov/pubmed/7592321|Rosner & Schink, 1982]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "ce2f5cfd-bf9a-4cc2-b588-bb678df34e5a", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/a8fc5340-aa47-4c8f-b354-7941b0cacd49/node/ce2f5cfd-bf9a-4cc2-b588-bb678df34e5a", "name": "Acetyl-CoA", "description": "no description", "aliases": [], "default_node_label": {"uuid": "b72bb376-a570-4a87-8860-1124ad6c7b39", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/57bd5e24-9d14-4b91-bc60-64c8ea6c2d11/structure/b72bb376-a570-4a87-8860-1124ad6c7b39"}, "node_labels": [{"uuid": "b72bb376-a570-4a87-8860-1124ad6c7b39", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/57bd5e24-9d14-4b91-bc60-64c8ea6c2d11/structure/b72bb376-a570-4a87-8860-1124ad6c7b39"}], "depth": 1, 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Dimethyl ether has also been shown to be oxidized by methanotrophic bacteria but it does not serve as a growth substrate for those bacteria [http://www.ncbi.nlm.nih.gov/pubmed/6802804|(Meyers, 1982).]", "aliases": [], "predicted": false, "nodes": [{"uuid": "35bc1e1f-424c-43c2-ad7e-90d13c87ab0f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/51e7bbdf-3d63-491a-97b2-8babec8192c0/node/35bc1e1f-424c-43c2-ad7e-90d13c87ab0f", "name": "Methanol", "description": "no description", "aliases": [], "default_node_label": {"uuid": "54eebfe8-d5ea-4695-909a-05b33bf1fb71", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b5522308-bb5c-41bb-a11a-e9b9ae61da85/structure/54eebfe8-d5ea-4695-909a-05b33bf1fb71"}, "node_labels": [{"uuid": "54eebfe8-d5ea-4695-909a-05b33bf1fb71", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/b5522308-bb5c-41bb-a11a-e9b9ae61da85/structure/54eebfe8-d5ea-4695-909a-05b33bf1fb71"}], "depth": 1, "stereo_removed": false, "scenarios": []}, {"uuid": "b0ee0b86-4539-4333-900d-f7a93a172ad4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/51e7bbdf-3d63-491a-97b2-8babec8192c0/node/b0ee0b86-4539-4333-900d-f7a93a172ad4", "name": "Formaldehyde", "description": "no description", "aliases": [], "default_node_label": {"uuid": "ffd9c907-48f5-4563-89b9-b97fb3193441", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/8ee6f55a-4488-4606-b65f-5aead102ccfc/structure/ffd9c907-48f5-4563-89b9-b97fb3193441"}, "node_labels": [{"uuid": "ffd9c907-48f5-4563-89b9-b97fb3193441", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/8ee6f55a-4488-4606-b65f-5aead102ccfc/structure/ffd9c907-48f5-4563-89b9-b97fb3193441"}], "depth": 1, "stereo_removed": false, "scenarios": []}, {"uuid": "1f5fbcaa-f178-40c1-afa8-1976b8844503", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/51e7bbdf-3d63-491a-97b2-8babec8192c0/node/1f5fbcaa-f178-40c1-afa8-1976b8844503", "name": "Dimethyl ether", "description": "no description", "aliases": [], "default_node_label": {"uuid": "66795f60-7d19-4376-8552-d6155de61dcc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/6a9270a6-9543-4210-8dcb-f8c42dfee1bf/structure/66795f60-7d19-4376-8552-d6155de61dcc"}, "node_labels": [{"uuid": "66795f60-7d19-4376-8552-d6155de61dcc", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/6a9270a6-9543-4210-8dcb-f8c42dfee1bf/structure/66795f60-7d19-4376-8552-d6155de61dcc"}], "depth": 0, "stereo_removed": false, "scenarios": []}], "edges": [{"uuid": "e3a2b7d0-a4a6-47f5-b76c-3febcd71111f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/51e7bbdf-3d63-491a-97b2-8babec8192c0/edge/e3a2b7d0-a4a6-47f5-b76c-3febcd71111f", "name": "Eawag BBD reaction r0082", "description": "no description", "aliases": [], "edge_label": {"uuid": "f16eff8e-0fb9-466c-9759-ce0c61792f37", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/reaction/f16eff8e-0fb9-466c-9759-ce0c61792f37"}, "start_nodes": [{"uuid": "1f5fbcaa-f178-40c1-afa8-1976b8844503", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/51e7bbdf-3d63-491a-97b2-8babec8192c0/node/1f5fbcaa-f178-40c1-afa8-1976b8844503"}], "end_nodes": [{"uuid": "35bc1e1f-424c-43c2-ad7e-90d13c87ab0f", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/51e7bbdf-3d63-491a-97b2-8babec8192c0/node/35bc1e1f-424c-43c2-ad7e-90d13c87ab0f"}, {"uuid": "b0ee0b86-4539-4333-900d-f7a93a172ad4", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/51e7bbdf-3d63-491a-97b2-8babec8192c0/node/b0ee0b86-4539-4333-900d-f7a93a172ad4"}], "scenarios": [{"uuid": "f7087b19-7f00-43a4-a2c9-014933c2d9df", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/f7087b19-7f00-43a4-a2c9-014933c2d9df"}]}], "scenarios": []}, {"uuid": "f1aa12e8-f2be-4f22-918a-b3a2a13170d1", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/f1aa12e8-f2be-4f22-918a-b3a2a13170d1", "name": "1,1,1-Trichloroethane (an/aerobic)", "description": "1,1,1-Trichloroethane (TCA) is a synthetic organic solvent widely used in industrial processes and is a major environmental pollutant commonly found in soil, groundwater, and the atmosphere. TCA is present in at least 696 of the 1430 National Priorities List sites identified by the U.S. Environmental Protection Agency (EPA). Because of TCA\ufffds adverse effects on human health, the EPA has set a maximum contaminant level of 200 ppb in drinking water. TCA is also listed as an ozone-depleting substance by the United Nations Environment Programme. Even when released into soil or leached into groundwater, the primary environmental fate of TCA is volatilization to the atmosphere, where it interacts with ozone and contributes to the erosion of the ozone layer. TCA can be reductively dechlorinated under anaerobic conditions to 1,1,-dichloroethane (DCA) by Desulfobacterium autotrophicum (C. Egli, R. Scholtz, A. M. Cook, & T. Leisinger (1987) FEMS Microbiol. Lett. 43:257-261.) and a Clostridium sp. ([http://www.ncbi.nlm.nih.gov/pubmed/2729985|Galli and McCarty, 1989]). Reductive dechlorination of TCA to DCA and chloroethane (CA) has been documented in methanogenic consortia (J. H. de Best, A. Hage, H. J. Doddema, D. B. Janssen, & W. Harder (1999) Appl. Environ. Microbiol. 51:277-283.) and a putative Dehalobacter sp. (designated strain TCA1) ([http://www.ncbi.nlm.nih.gov/pubmed/12411705|Sun et al., 2002]). [http://www.ncbi.nlm.nih.gov/pubmed/10633545|Chen et al. (1999)] reported the complete dehalogenation of TCA, DCA, and CA to ethane by an anaerobic consortium in sewage sludge, but ethane was a minor product in all cases (< 5%, < 3%, and < 1% of the initial substrate degraded to ethane, respectively). The enzymes that catalyze the reductive dehalogenation of TCA have not been identified. TCA can be aerobically transformed to 2,2,2-trichloroethanol by the methanotroph Methylosinus trichosporium OB3b expressing a soluble methane monooxygenase ([http://www.ncbi.nlm.nih.gov/pubmed/2624462|Oldenhuis et al., 1989]), and by ethane-utilizing Mycobacterium spp. isolated from soil ([http://www.ncbi.nlm.nih.gov/pubmed/10508110|Yagi et al., 1999]). Further study revealed that one of the Mycobacterium strains produced trichloroacetic acid and dichloroacetic acid as minor products (12.7% and 1.2%, respectively, vs. 85.5% of TCA converted to 2,2,2-trichloroethanol) during the aerobic transformation of TCA ([http://www.ncbi.nlm.nih.gov/pubmed/11999413|Hashimoto et al., 2002]). Oldenhuis et al (1989) found that M. trichosporium expressing soluble methane monooxygenase completely dechlorinated DCA, but degradation intermediates were not identified. [http://www.ncbi.nlm.nih.gov/pubmed/12355460|Kim et al. (2000)] observed partial dechlorination of DCA (~37% of initial solvent) by an aerobic butane-grown mixed culture. In Nitrosomonas europea, an ammonia monooxygenase catalyzed the oxidation of CA to acetaldehyde, with 2-Chloroethanol produced as a minor product (1-2% 2-chloroethanol vs. 98% acetaldehyde) ([http://www.ncbi.nlm.nih.gov/pubmed/2394686|Rasche et al., 1990]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "31be846f-b68e-4163-856c-97df66671ab0", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/f1aa12e8-f2be-4f22-918a-b3a2a13170d1/node/31be846f-b68e-4163-856c-97df66671ab0", "name": "Trichloroethanol", "description": "no description", "aliases": [], "default_node_label": {"uuid": "d0b3b9b8-1fdf-4ed2-b8e5-78b667eb50fb", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/810724b8-88e9-4307-835c-e3773582fad5/structure/d0b3b9b8-1fdf-4ed2-b8e5-78b667eb50fb"}, "node_labels": [{"uuid": "d0b3b9b8-1fdf-4ed2-b8e5-78b667eb50fb", "url": 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Pseudomonas fluorescens KU-7, Arthrobacter protophormiae RKJ100, and other strains are capable of utilizing o-nitrobenzoate as the sole carbon, nitrogen and energy source ([http://www.ncbi.nlm.nih.gov/pubmed/11034277|Hasegawa et al., 2000]; [http://www.ncbi.nlm.nih.gov/pubmed/10623604|Chauhn et al., 2000]; [http://www.ncbi.nlm.nih.gov/pubmed/12620844|Muraki et al., 2003]). o-Nitrobenzoate is degraded by a two electron reduction of the nitro moiety, yielding o-Hydroxylaminobenzoate. Ps. fluorescens KU-7 ([http://www.ncbi.nlm.nih.gov/pubmed/11034277|Hasegawa et al., 2000]), and more recently A. protophormiae RKJ100 ([http://www.ncbi.nlm.nih.gov/pubmed/14680704|Pandey et al., 2003]), were shown to transform o-Hydroxylaminobenzoate to 3-Hydroxyanthranilate. In addition, A. protophormiae RKJ100 can transform it to 2-Aminobenzoate (anthranilic acid). This oxygen-insensitive reductive catabolic pathway of o-nitrobenzoate provides evidence that 2-Aminobenzoate is not produced as a side reaction but is an obligate intermediate in a direct energy yielding metabolic pathway by Arthrobacter protophormiae RKJ100 ([http://www.ncbi.nlm.nih.gov/pubmed/10623604|Chauhan et al., 2000]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "c29eb863-b995-4a9e-94eb-91ffc142d0c3", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/3ec3ecf5-c3b2-4820-8753-edfe57ef48a4/node/c29eb863-b995-4a9e-94eb-91ffc142d0c3", "name": "2-Amino-3-carboxymuconate-6-semialdehyde", "description": "no description", "aliases": [], "default_node_label": {"uuid": "77f02cdd-25ba-4397-b935-a49ea221f3ae", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/574c32c5-4e08-48e4-a59c-1a94a433c4cb/structure/77f02cdd-25ba-4397-b935-a49ea221f3ae"}, "node_labels": [{"uuid": "77f02cdd-25ba-4397-b935-a49ea221f3ae", 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It is widely used in commercial products such as toothpaste, mouthwashes, cigarettes, foods, and medicines ([http://www.ncbi.nlm.nih.gov/pubmed/10460066|Gelal et al., 1999]). In 1984, world production of this popular compound was estimated to be 3500 tons. Thauera terpenica strain 21Mol is able to grow on (-)-menthol, as well as on (-)-menthone, (+)-isomenthol, (+)-isopulegol, and (+)-pulegone [http://www.ncbi.nlm.nih.gov/pubmed/9841126|(Foss and Harder, 1998)]. Based on the bacterium`s apparent requirement for an oxygen functional group at the C-3 atom, [http://www.ncbi.nlm.nih.gov/pubmed/9990726|Hylemon and Harder (1998)] suggest that the menthol degradation pathway resembles the anaerobic oxidation and cleavage of cyclohexanol described by [http://www.ncbi.nlm.nih.gov/pubmed/2505723|Dangel et al. (1989)]. In this proposed pathway, menthol and the related substrates listed above are first converted to menth-2-enone, which is then oxidized to mentha-1,2-dione. 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"url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/2bded979-d91b-40d3-a4e0-6145abed76e3"}]}], "scenarios": []}, {"uuid": "4f571a2c-184b-45ae-a366-11c06ca5a778", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/4f571a2c-184b-45ae-a366-11c06ca5a778", "name": "Parathion (an/aerobic)", "description": "Parathion (O,O-diethyl-O-p-nitrophenyl phosphorothioate) is an organophosphate compound and is one of the most toxic insecticides registered with the U.S. Environmental Protection Agency (EPA). On agricultural crops it was used widely as a broad spectrum insecticide, acaricide, fumigant and nematocide. In 1991 parathion became a Restricted Use Pesticide (RUP). Parathion is well tolerated by crops, does not easily leach through soil and may be degraded by soil microorganisms within weeks. Degradation of parathion by sunlight or liver enzymes results in the active compound paraoxon which interferes with the nervous system through cholinesterase inhibition. Extreme toxicity combined with the ease of exposure has resulted in numerous human and non-pest species deaths. The immediate aerobic metabolic breakdown product of parathion, PNP or p-nitrophenol, was listed as a priority pollutant in 1979 by the US EPA. The main aerobic pathway involves initial hydrolysis of parathion to para-nitrophenol and diethylthiophosphoric acid (middle branch). The oxidation of parathion to paraoxon was observed, but was a minor contribution (right branch). It was not determined whether this reaction was enzyme-mediated or not; it is shown here as being enzyme-mediated, based on the known enzymic oxidation of diethtylthiophosphoric acid to diethylphosphoric acid, though since the reactions are not well-characterized, both reactions cannot be balanced. 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It is used in cultivated agriculture and in pasture and rangeland applications, forest management, home and garden situations and for the control of aquatic vegetation. The wide use of this compound has prompted interest in its biodegradation. Alcaligenes eutrophus and other bacteria can degrade 2,4-D through 2,4-dichlorophenol, 3,5-dichlorocatechol, and ortho cleavage of this catechol ([http://www.ncbi.nlm.nih.gov/pubmed/8226980|Fukumori & Hausinger, 1993]). Alternatively, Axotobacter chroococcum first removes the chloride in the 2 position to produce 4-chlorophenoxyacetate, 4-chlorophenol, and 4-chlorocatechol, again with ortho cleavage of this catechol ([http://www.ncbi.nlm.nih.gov/pubmed/2219955|Balajee and Mahadevan, 1993]). 2,4-D biodegradation by this pathway branch may produce a byproduct antibiotic protoanemonin, which can be degraded to cis-acetylacrylate by a dienelactone hydrolase of Pseudomonas sp. strain B13 ([http://www.ncbi.nlm.nih.gov/pubmed/9440530|Brueckmann et al., 1998]). Comamonas testosteroni JH5 can cleave 4-chlorocatechol by a meta pathway, forming 5-chloro-2-hydroxymuonate semialdehyde which can be further transformed by a 2-hydroxymuconic semialdehyde dehydrogenase or a 2-hydroxymuconic semialdehyde hydrolase. Dehydrogenation is the major route, however the hydrolase step is also of physiological significance. Both branches lead to 5-chloro-2-oxopent-4-eneoate. This does not accumulate, and stoichiometric chloride is quickly released, but the exact route of chloride elimination is not known ([http://www.ncbi.nlm.nih.gov/pubmed/1510672|Hollender et al., 1997]). Pseudomonas cepacia P166 can move the chloride in 5-chloro-2-oxopent-4-eneoate through 5-chloro-4-hydroxy-2-oxopentanate to chloroacetate. 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At 47% of waste sites containing these materials, BaP has been detected as a soil contaminant at concentrations up to 1300 ppb (Aspelin, A. L. & Grube, A. H., 2000, in Report 733-R-99 C001, U.S. Environmental Protection Agency, Office of Pesticide Programs, Washington, DC.). There is evidence for BaP carcinogenicity from animal tests, and it is classified as a compound that is probably carcinogenic to humans ([http://www.ncbi.nlm.nih.gov/pubmed/6835251|Georgian et al., 1983]). BaP degradation pathways have been studied in the Gram-positive bacteria Mycobacterium sp. RJGII-135M ([http://www.ncbi.nlm.nih.gov/pubmed/8572690|Schneider et al., 1996]), M. vanbaalenii ([http://www.ncbi.nlm.nih.gov/pubmed/14711661|Moody et al., 2004]), and the Gram-negative bacterium Sphingomonas yanoikuyae B8/36 (formerly Beijerinckia sp. strain B8/36) ([http://www.ncbi.nlm.nih.gov/pubmed/11423945|Gibson, 1999]). The pathways are initiated by mono- or di-oxygenation at different positions, followed by dehydration of the resulting dihydrodiols, and then oxidative cleavage, usually at the meta-position. Cleavage products are then decarboxylated to form chrysene derivatives. Sphingomonas sp. CHY-1 can grow on chrysene as its sole carbon and energy source ([http://www.ncbi.nlm.nih.gov/pubmed/15598525|Willison 2004]). 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When ingested by humans, caffeine stimulates the central nervous system, elevates blood pressure, increases metabolic rate, and acts as a diuretic ([http://www.ncbi.nlm.nih.gov/pubmed/16507475|Higdon and Frei, 2006]). Caffeine consumption may reduce the risk of Parkinson`s disease. However, adverse reactions to caffeine consumption can include anxiety, insomnia, heart palpitations, abdominal pain, and nausea, and high caffeine intake has been linked with increased risk of osteoporosis and complications in pregnancy ([http://www.ncbi.nlm.nih.gov/pubmed/17009088|Dash and Gummadi, 2006]). Caffeine is also mildly addictive. Withdrawal symptoms can include headache, fatigue, depressed mood, difficulty concentrating, irritability, nausea, and muscle pain ([http://www.ncbi.nlm.nih.gov/pubmed/16507475|Higdon and Frei, 2006]). Coffee pulp, a waste product produced during coffee processing, is a major pollutant in water bodies near coffee plants. Even though it is high in nutrients, it cannot be used as animal feed due to the high levels of caffeine and other unwanted compounds ([http://www.ncbi.nlm.nih.gov/pubmed/10959086|Pandey et al., 2000]). Solvents commonly used to produce caffeine-free products are either very expensive to use or toxic ([http://www.ncbi.nlm.nih.gov/pubmed/17009088|Dash and Gummadi, 2006]). However, a number of bacterial and fungal strains capable of degrading caffeine have been identified ([http://www.ncbi.nlm.nih.gov/pubmed/14977550|Mazzafera, 2004]). The pathway described below has been documented for members of the fungal species Penicillium commune and Aspergillus tamarii (Hakil et al. 1998. Enzyme Microb Technol 22: 355-359), other members of these two genera, and the bacterial species Pseudomonas putida CBB5 ([http://www.ncbi.nlm.nih.gov/pubmed/19447909|Yu et al., 2009]). In the major fungal pathway, caffeine degrades via theophylline (1,3-dimethylxanthine) and 3-methylxanthine to xanthine. Bacterial and minor fungal pathway branches funnel through paraxanthine and theobromine. 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Gallate is used in photographic ink, dyeing, paper manufacture, and engraving and lithography. The toxicological properties of gallate have not been fully investigated. It may cause eye, skin, respiratory and digestive tract irritation. Polyphenolic compounds such as gallate, pyrogallol, and 1,2,4-trihydroxybenzene are stabilized by resonance and meta-substituted hydroxyl groups. Natural sources of theses compounds include plant flavonoids, tannins and lignin. Biodegradation occurs by aerobic pathways and anaerobic pathways in the absence of terminal electron acceptors. The initial step in the anaerobic gallate pathway used by Eubacterium oxidoreducens G41 is the decarboxylation of the ring ([http://www.ncbi.nlm.nih.gov/pubmed/87194560|Krumholz et al., 1987]). Acetate, butyrate and carbon dioxide are end products of gallate fermentation. Oxidation of formate or hydrogen is required for growth on gallate to provide electrons for reduction of the ring prior to ring cleavage ([http://www.ncbi.nlm.nih.gov/pubmed/2925649|Haddock and Ferry, 1989]). Pelobacter acidigallici degrades gallate anaerobically, but produces only acetate ([http://www.ncbi.nlm.nih.gov/pubmed/2298693|Brune et al., 1990]). The reaction that transforms 3-hydroxy-5-oxohexanoate to 3-hydroxy-5-oxohexanoyl-CoA is proposed and still not well understood. This page shows only anaerobic pathway of gallate. 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Because of their widespread use, phthalates have become one of the most abundant industrial pollutants in the environment. Several phthalates are classified as toxic chemicals in the EPA`s Toxics Release Inventory Program. Phthalic acid (phthalate) is used industrially as a plasticizer. Terephthalate is used in the synthesis of polyethylene terephthalate (abbreviated PET or PETE), a plastic polymer with many commercial uses including the production of plastic beverage bottles. Phthalates in the environment show a moderate resistance to bacterial degradation, but are easily degraded in the laboratory. Pseudomonas cepacia, Mycobacterium vanbaalenii PYR-1, and Arthrobacter keyseri 12B all convert phthalate to a cis-dihydrodiol. Ps. cepacia produces the 4,5-dihydrodiol ([http://www.ncbi.nlm.nih.gov/pubmed/2841671|Ballou & Batie, 1988]), and M. vanbaalenii PYR-1 ([http://www.ncbi.nlm.nih.gov/pubmed/17085566|Kim et al., 2007]) and A. keyseri 12B ([http://www.ncbi.nlm.nih.gov/pubmed/11371533|Eaton, 2001]) produce the 2,3-dihydrodiol. These are transformed into the respective dihydroxy compounds, both of which can be decarboxylated to 3,4-dihydroxybenzoate (protocatechuate). Comanonas testosteroni strains can convert terephthalate ([http://www.ncbi.nlm.nih.gov/pubmed/8565920|Wang et al., 1995]) and 4-hydroxyphthalate ([http://www.ncbi.nlm.nih.gov/pubmed/29563|Nakazawa & Hayashi, 1978]) to protocatechuate. A Micrococcus sp. strain can decarboxylate 3,4-dihydroxyphthalate to 2,3-dihydroxybenzoate ([http://www.ncbi.nlm.nih.gov/pubmed/7125802|Eaton & Ribbons, 1982]). Rhodococcus jostii RHA1 is able to use monoalkyl esters including methyl, butyl, hexyl and 2-ethylhexyl phthalates as its sole carbon and energy source. Suspensions of cells grown on phthalate could degrade dimethyl, diethyl, dipropyl, dibutyl, dihexyl and di-(2-ethylhexyl) phthalates. The major metabolites of the dialkyl esters are corresponding monoalkyl esters and phthalate. Demethylation of the alkyl side chains was also observed as a concurrent minor process. The degradation of dibutyl phthalate is provided here as an example and other phthalate esters follow similar pathways ([http://www.ncbi.nlm.nih.gov/pubmed/20038686|Hirofumi et al., 2010]). 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Triethanolamine is widely used as an ingredient in emulsifiers, thickeners, wetting agents, detergents, and alkalinizing agents in cosmetic products; as a chemical intermediate for anionic and nonionic surfactants and surface active agents in household cleaning agents, textiles, herbicides, pharmaceutical ointments, and other products; as a vulcanization accelerator in the manufacture of rubber; and in many other industrial applications. The National Cancer Institute nominated triethanolamine for study because of its widespread use in cosmetics and other consumer products, its high potential for worker exposure due to its many industrial uses, and its potential for conversion to the carcinogen N-nitrosodiethanolamine. Triethanolamine is degraded by the enzyme triethanolamine lyase. A corronoid-dependent shifting of the terminal hydroxyl group to the subterminal carbon atom occurs to form an unstable intermediate that forms diethanolamine and releases acetaldehyde. It is believed that the diethanolamine formed by this reaction undergoes a similar degradation route to form ethanolamine. Ethanolamine ammonia-lyase degrades the ethanolamine to acetaldehyde and ammonia. A strictly anaerobic, gram-positive, rod-shaped bacterium, strain LuTria 3, was used to degrade the triethanolamine. Acetobacterium sp. LuTria 3 was enriched and isolated with triethanolamine as sole source of energy and carbon. The new isolate differs from other species of the genus described so far by its capacity to grow with triethanolamine and its inability to utilize ethylene glycol or fructose ([http://www.ncbi.nlm.nih.gov/pubmed/8085913|Frings et al., 1994]).", "aliases": [], "predicted": false, "nodes": [{"uuid": "04f54a1b-5e35-4278-be5e-9f1c9c04564e", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/e5b1165d-7cec-4104-be15-075ac38a4163/node/04f54a1b-5e35-4278-be5e-9f1c9c04564e", "name": "Ethanolamine", "description": "no description", "aliases": [], "default_node_label": {"uuid": "cfb90bfc-d534-48f3-b132-e557d7254b80", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/9cee8877-412f-4ce0-a56d-b7c5de20969e/structure/cfb90bfc-d534-48f3-b132-e557d7254b80"}, "node_labels": [{"uuid": "cfb90bfc-d534-48f3-b132-e557d7254b80", "url": 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RW1 and several other organisms, multiple isofunctional enzymes have been discovered for each of the steps in the degradation of dibenzofuran. It has been postulated ([http://www.ncbi.nlm.nih.gov/pubmed/9288905|Armengaud and Timmis, 1997]) that this may be due to the common expression of two separate pathways for dibenzofuran and biphenyl, the latter of which is also a growth source for some dibenzofuran-degrading microorganisms.", "aliases": [], "predicted": false, "nodes": [{"uuid": "c26ae486-f9e7-4967-9848-ef857856ac10", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/b41738ce-c67e-414f-b048-00bd331d3bfb/node/c26ae486-f9e7-4967-9848-ef857856ac10", "name": "2-Oxopent-4-enoate", "description": "no description", "aliases": [], "default_node_label": {"uuid": "5d30c9a4-3058-4c41-a176-7a53cdcbd484", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/compound/55aaa3f5-5d56-42a7-a0aa-04c0ab74e738/structure/5d30c9a4-3058-4c41-a176-7a53cdcbd484"}, "node_labels": [{"uuid": "5d30c9a4-3058-4c41-a176-7a53cdcbd484", "url": 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In the chemical production industry it is found as an intermediate in the synthesis of agrochemicals (e.g., pesticides, herbicides) and pharmaceuticals. Toxicity data for compounds structurally similar to DCTs indicate that it likely exhibits moderate toxicity to aquatic organisms, and will have a moderate potential for bioaccumulation in the environment. 2,4-DCT is hydrophobic, meaning it may be subject to soil and sediment adsorption. 2,4-DCT is also volatile and has been characterized by the EPA as a hazardous air pollutant (HAP). The aerobic pathway for biodegradation of 2,4-DCT is initiated by Ralstonia sp. strain PS12 ([http://www.ncbi.nlm.nih.gov/pubmed/12218011|Pollman et al., 2002]). Ring dioxygenation is followed by intradiol cleavage to form 3,5-dichloro-3-methylmuconate. Subsequent degradation involves two different methods for dechlorination. The methylmaleylacetate derivates listed here are the last known intermediates, and are assumed to enter more common intermediary metabolism, but their further metabolism is not well-characterized. 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It and trichloroethene (TCE) are suspected carcinogens and some of the most abundant environmental pollutants of groundwater in the United States. In some groundwater, they undergo reductive dechlorination catalyzed by anaerobic bacteria that yields vinyl chloride, a potent human carcinogen. Removal by dumping or air stripping is now largely disallowed and this has focused efforts on biological methods of PCE and TCE remediation in soil and water. Aerobic TCE biodegradation pathways are found in the EAWAG-BBD. Anaerobic pathways are less well-understood. Only the first enzyme in this pathway has been isolated; in Dehalospirillum multivorans it also catalyzes the reductive dehalogenation of trichloroethene to cis-1,2-dichloroethene ([http://www.ncbi.nlm.nih.gov/pubmed/8663199|Neumann et al., 1996]). Other organisms implicated in anerobic PCE biodegradation include Sporomusa ovata ([http://www.ncbi.nlm.nih.gov/pubmed/7988892|Terzenbach & Blaut, 1994]), and Dehalobacter restrictus TEA ([http://www.ncbi.nlm.nih.gov/pubmed/9188197|Wild et al., 1996]). Most organisms studied convert trichloroethene to cis-1,2-dichloroethene (DCE); Dehalococcoides ethenogenes 195 is reported to also produce the trans isomer. TCE can be reductively dehalogenated (through both cis and trans DCE) by the CO dehydrogenase from Methanosarcina thermophila ([http://www.ncbi.nlm.nih.gov/pubmed/1526465|Jablonski & Ferry, 1992]). 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Little attention has been given to the biodegradation of these compounds. The uses of fluorinated aromatic compounds include herbicides, pesticides, insecticides, refrigerants, and anesthetics (B. D. Key, R. D. Howell, & C. S. Criddle (1997) Environ Sci Technol 31:2445-2454). Fluoroorganics are more stable than their chlorine analogues due to the stability of the C-F bond, which is 25 kcal/mol stronger than the C-Cl bond (D. F. McMillen & D. M. Golden (1982) Ann Rev Phys Chem 33:493). Fluoroorganics pose a potential human health concern. Industrial workers exposed to fluroorganics were shown to have higher serum organic fluorine concentrations than individuals not exposed to fluroorganics ([http://www.ncbi.nlm.nih.gov/pubmed/7405826|Ubel et al., 1980]). The health effects of acute fluoride toxicity are well known; however, it is unclear whether fluorinated organic compounds result in the same problems (Akiniwa. K. (1997) Fluoride 30(2): 89-104). In organisms that have been surveyed, metabolism of 2-fluorobenzoate and 4-fluorobenzoate is more common than that of 3-fluorobenzoate ([http://www.ncbi.nlm.nih.gov/pubmed/10919805|Song et al., 2000]). Two pathways of 3-fluorobenzoate degradation have been described. In one pathway, degradation is initiated by 1,2-dioxygenation of 3-fluorobenzoate to give 3-fluorohexadiene-cis,cis-1,2-diol-1-carboxylate. This is converted to 3-fluorocatechol, which is slowly metabolized to 2-fluoro-cis,cis-muconate, which is not metabolized further ([http://www.ncbi.nlm.nih.gov/pubmed/16345496|Schreiber et al., 1980]) , leading to accumulation of cytotoxic 3-fluorocatechol. Alternatively, metabolism can begin with 1,6-dioxygenation of 3-fluorobenzoate, which is converted to 5-fluorocyclohexadiene-cis,cis-1,2-diol-1-carboxylate and then sequentially to 4-fluorocatechol, 3-fluoro-cis,cis-muconate, and eventually oxoadipate, which can enter central metabolism (K. H. Engesser, G. Auling, J. Busse, & H.-J. Knackmuss (1990) Arch Microbiol 153:193-199). Fluoride is also released in this pathway. Both pathways are present in strains that metabolize 3-fluorobenzoate, but metabolic flux through each pathway varies among the organisms (Engesser et al., 1990). Cells of Acinetobacter calcoaceticus NCIB 8250 ([http://www.ncbi.nlm.nih.gov/pubmed/1182155|Clarke et al., 1975]) and Pseudomonas sp. B13 ([http://www.ncbi.nlm.nih.gov/pubmed/16345496|Schreiber et al., 1980]) grown on benzoate or 3-chlorobenzoate, respectively, metabolized 3-fluorobenzoate, but the strains could not grow on the compound as a carbon and energy source. In these organisms, the major pathway of 3-fluorobenzoate degradation begins with 1,2-dioxygenation. Strain FLB 300 (alpha-2-subclass of Proteobacteria, Agrobacterium-Rhizobium branch) (Engesser et al., 1990) and Sphingomonas sp. HB-1 ([http://www.ncbi.nlm.nih.gov/pubmed/15321683|Boersma et al., 2004]) were able to grow using 3-fluorobenzoate as a sole carbon and energy source. 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Though it is generally thought that azo dyes are degraded only anaerobically, there have been recent reports to suggest otherwise. This is the first aerobic bacterial stain reported to utilize an azo dye as its sole source of carbon and energy ([http://www.ncbi.nlm.nih.gov/pubmed/9603860|Blumel et al., 1998]). In the first step of the pathway, the S5 strain cleaves 4-Carboxy-4`-Sulfoazobenze aerobically to 4-aminobenzoate and 4-aminobenzenesulfonate. 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"url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/scenario/2fb08ea8-0a02-4e18-b70f-cbac80fabf9f"}]}], "scenarios": []}, {"uuid": "9daec55c-eb02-4a7d-b4bb-4f0848a8a997", "url": "http://localhost:8000/package/32de3cf4-e3e6-4168-956e-32fa5ddb0ce1/pathway/9daec55c-eb02-4a7d-b4bb-4f0848a8a997", "name": "N,N-Diethyl-m-toluamide", "description": "N,N-Diethyl-m-toluamide, commonly known as DEET, is broadly used as an active ingredient in insect repellents ([http://www.ncbi.nlm.nih.gov/pubmed/17337538|Rivera-Cancel et al., 2007]). In the United States, 30% of people use an insect repellent containing DEET at least once a year ([http://www.ncbi.nlm.nih.gov/pubmed/11693870|McGready et al., 2001]). Annual domestic use equals approximately 1,800 tons ([http://www.ncbi.nlm.nih.gov/pubmed/17337538|Rivera-Cancel et al., 2007]). DEET was originally patented by the United States Army for use in insect-infested areas and was later registered for use by the general public. DEET is not known to have carcinogenic effects on humans (EXTOXNET; Pesticide Information Profile: DEET). While not carcinogenic, exposure to N,N-diethyl-m-toluamide does have human health effects including skin reactions and in rare cases of high-level exposure, seizures, toxic encephalopathy, acute manic psychosis and death (TOXNET; Hazardous Substances Data Bank; DEET). Hydrolysis of the amide bond in N,N-Diethyl-m-toluamide yields 3-methylbenzoate and diethylamine. This transformation is catalyzed by the enzyme DEET hydrolase under aerobic conditions by the bacterium P. putida DTB. The resulting 3-methylbenzoate is then converted to 3-methylcatechol which can be further metabolized through the meta cleavage pathway of Pseudomonas putida ([http://www.ncbi.nlm.nih.gov/pubmed/17337538|Rivera-Cancel et al., 2007]). Diethylamine and ethylamine are both hydrolyzed to acetaldehyde before entering central metabolism ([http://www.ncbi.nlm.nih.gov/pubmed/1268229|Steenkamp et al., 1976]). 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"[H:10][#8:9]-[c:4]1[c;R1:5][c;R1:6][c:1]([H])[c;R1:7][c;R1:8]1>>[H:10][#8:9]-[c:4]1[c;R1:5][c;R1:6][c:1](-[#8])[c;R1:7][c;R1:8]1", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "412d2e1e-dd6c-4160-ac4d-24bd5f6bb308", "name": "bt0103-3648", "description": "Dithiophosphate diester + Thiophosphate diester + Thiophosphate triester > Thiophosphate diester + Phosphate diester + Phosphate triester", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/412d2e1e-dd6c-4160-ac4d-24bd5f6bb308", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[#8:4][P:2]([#8:6])([#8,#16:5])=S>>[#8:6][P:2]([#8:4])([#8,#16:5])=O", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "4aeb53b3-d40a-4acb-a4e7-4fb2c26f2c96", "name": "bt0259-3814", "description": "Monoalkylthiol + disubstituted Sulfide + Thiol alkene + Monoalkylthiophosphate > Aldehyde + H2S + Aldehyde + Sulfide + Alcohol + Aldehyde + Thiophosphate", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/4aeb53b3-d40a-4acb-a4e7-4fb2c26f2c96", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[H][#6:3](-[#1,#6:7])-[#16;v2:1]-[#1,#6,#15:2]>>[#1,#6:7]-[#6:3]=O.[H][#16;v2:1]-[#1,#6,#15:2]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "4e58e4ef-9f13-48c1-ac7e-ccdc527b0df4", "name": "bt0255-2690.4", "description": "vic-Dihydrodihydroxyaromatic > vic-Dihydroxyaromatic", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/4e58e4ef-9f13-48c1-ac7e-ccdc527b0df4", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[#6:9]:[#6:10]@-[C:6]([H])([#8:2][H:11])[C:5]([H])(@-[#6:7]:[#6:8])[#8:1][H:12]>>[H:12][#8:1]-[#6:5](-[#6:7]:[#6:8])=[#6:6](-[#8:2][H:11])-[#6:10]:[#6:9]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "5c001cb6-114b-4835-b8a8-84a9d18fb769", "name": "bt0389-3302", "description": "Phenylcarbamate derivative > Phenol derivative + Amine", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/5c001cb6-114b-4835-b8a8-84a9d18fb769", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[#7:3]-[#6](=O)-[#8:2]-[c:1]1[c:6][c:7][c:8][c:9][c:10]1>>[#8:2]-[c:1]1[c:10][c:9][c:8][c:7][c:6]1.[#7:3]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "5e787976-dfca-48f8-b1f7-3691f3f70948", "name": "bt0073-3591", "description": "2-unsubstituted Cyclic ether > 2-Hydroxy cyclic ether", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/5e787976-dfca-48f8-b1f7-3691f3f70948", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[#6:5]-[#6:1]([H])([H])@-[#8:4]@-[#6:2]>>[#6:2]@-[#8:4]@-[#6:1]([H])(-[#6:5])-[#8]([H])", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "61ad33ae-748d-4e04-b6df-951b908f2ce1", "name": "bt0104-2854", "description": "Arylphosphotriester + Arylphosphodiester + Arylphosphoester > Phenol derivative + Phosphodiester + Phenol derivative + Phosphoester + Phenol derivative", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/61ad33ae-748d-4e04-b6df-951b908f2ce1", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[#8:1][P:4]([#8:6])(=[O:5])[#8:2]-[c:7]:[c:8]>>[#8:2]-[c:7]:[c:8].[#8:1][P:4]([#8:6])([#8])=[O:5]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "66a0ffcc-2a99-4051-9497-efaa38b05e65", "name": "bt0435-4212", "description": "Thiol > RH + H2S", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/66a0ffcc-2a99-4051-9497-efaa38b05e65", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[H:6][C:1]([#6:4])([#16;H1v2])[#1,#6:5]>>[H:6][C:1]([H])([#6:4])[#1,#6:5]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "6bdb093f-73b8-4a16-be03-0c3ed1648246", "name": "bt0061-2451", "description": "N-aliphatic-hydroxy-s-Triazine > hydroxy-s-Triazine", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/6bdb093f-73b8-4a16-be03-0c3ed1648246", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[H:10][#8:9]-[c:4]1[n:5][c:6][n:7][c:2](-[#7:1]-[#6:11])[n:8]1>>[H:10][#8:9]-[c:4]1[n:5][c:6][n:7][c:2](-[#8])[n:8]1.[H][#7:1]-[#6:11]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "828328d0-3629-4198-9c22-99545d34d1c9", "name": "bt0434-4149", "description": "Hemiacetal > Alcohol + Aldehyde", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/828328d0-3629-4198-9c22-99545d34d1c9", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[#6:4]-[#8:1]-[#6:3](-[#6:5])-[#8:2]([H])>>[#6:4]-[#8:1].[#6:5]-[#6:3]=[O:2]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "833bb289-f276-4a8e-80fc-eec1ee7a1a41", "name": "bt0260-2032", "description": "disubstituted Disulfide > two Thiols", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/833bb289-f276-4a8e-80fc-eec1ee7a1a41", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[#6:3]-[#16:2]-[#16:1]-[#6:4]>>[#6:4]-[#16:1]([H]).[#6:3]-[#16:2]([H])", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "8d8513a5-72c8-46e2-906c-e726e87684e9", "name": "bt0316-4136", "description": "Xanthine derivative > Uric acid derivative", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/8d8513a5-72c8-46e2-906c-e726e87684e9", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[H][c:1]1:[n;X2:2]:[c:8]2[n:12][c:11](=[O:14])[n:10][c:9](=[O:13])[c:7]2[n:4]1>>[H][n:2]1[c:8]2[n:12][c:11](=[O:14])[n:10][c:9](=[O:13])[c:7]2[n:4][c:1]1=O", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "8f6745ba-f4a5-4c63-96c7-4e1a31cd2eb0", "name": "bt0432-4254", "description": "Phosphorofluoridate derivative + Cyanophosphate derivative + Phosphonofluoridate derivative + Thiophosphate derivative > Phosphate derivative + Phosphate derivative + cyanide + Phosphonate derivative + Phosphate derivative + Thiol", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/8f6745ba-f4a5-4c63-96c7-4e1a31cd2eb0", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[#6,#7,#8,#16:4][P:2]([#9,#16,#17,#35,#53:1])([#6,#8:5])=[#8,#16:6]>>[#8]([H])[P:2]([#6,#7,#8,#16:5])([#6,#8:4])=[#8,#16:6].[#9,#16,#17,#35,#53:1]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "901c97b4-6f72-4f7b-b9a6-386b1c918c70", "name": "bt0024-2218", "description": "Ester + Lactone > Alcohol + Carboxylate + Hydroxycarboxylate", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/901c97b4-6f72-4f7b-b9a6-386b1c918c70", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[#6:2]-[#8:1]-[#6:6](-[#1,#6:3])=[O:7]>>[H][#8]-[#6:2].[#8-:1]-[#6:6](-[#1,#6:3])=[O:7]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "91233f28-7424-461d-980d-0ca90319972c", "name": "bt0241-3580", "description": "tertiary Aliphatic > tertiary Alcohol", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/91233f28-7424-461d-980d-0ca90319972c", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[H:2][C:1]([#6:5])([#6:6])[#6:7]>>[H:2][#8][C:1]([#6:5])([#6:7])[#6:6]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "96269406-6813-4056-bef1-d39ba5c7e9a8", "name": "bt0399-3488", "description": "1-Methylcyclohexene derivative > 1,2-Epoxy-1-Methylcyclohexane derivative", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/96269406-6813-4056-bef1-d39ba5c7e9a8", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[#6:8]([H])([H])([H])-[#6:1]-1=[#6:2]([H])-[#6:7]([H])([H])-[#6:6]-[#6:5]([H])([H])-[#6:4]-1>>[#6:8]([H])([H])([H])[C:1]12[#6:4]-[#6:5]([H])([H])-[#6:6]-[#6:7]([H])([H])-[#6:2]([H])1-[#8]2", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "96df26f9-4b90-493d-8e6c-dd3c2ddeef1e", "name": "bt0003-1196", "description": "Aldehyde > Carboxylate", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/96df26f9-4b90-493d-8e6c-dd3c2ddeef1e", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[H][#6:1](-[#6:5])=[O:4]>>[#6:5]-[#6:1](-[#8-])=[O:4]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "a412cc4c-3454-4c44-8e33-a5a31cd47c85", "name": "bt0330-3929", "description": "1-halo or 1-pseudohalo-s-Triazine > 1-hydroxy-s-Triazine", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/a412cc4c-3454-4c44-8e33-a5a31cd47c85", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[H][#7]([H])-[c:1]1[n:6][c:7](-[$([N]-[C]-1-[C]-[C]-1),$(O),$([N]):8])[n:9][c:10](-[$([N]),$(O),$(Cl):11])[n:12]1>>[#8]-[c:1]1[n:6][c:7](-[$([N]-[C]-1-[C]-[C]-1),$(O),$([N]):8])[n:9][c:10](-[$([N]),$(O),$(Cl):11])[n:12]1", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "b0a4ec71-0d9c-4c17-9713-ca190d612b2d", "name": "bt0022-2833", "description": "Dihalomethyl derivative + Halomethyl derivative > 1-Halo-1-methylalcohol derivative + 1-Methylalcohol derivative", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/b0a4ec71-0d9c-4c17-9713-ca190d612b2d", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[H:5][C:1]([#6:6])([#1,#9,#17,#35,#53:4])[#9,#17,#35,#53]>>[H:5][C:1]([#6:6])([#8])[#1,#9,#17,#35,#53:4]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "c33a2f93-402a-441c-834b-0855b7a9ae32", "name": "bt0067-4013", "description": "Lactam + secondary Amide > Aminecarboxylate + Carboxylate + primary Amine", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/c33a2f93-402a-441c-834b-0855b7a9ae32", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[H:5][#7:1](-[#6,#7:7])-[#6:3](-[#1,#6:6])=[O:4]>>[#8-]-[#6:3](-[#1,#6:6])=[O:4].[H:5][#7:1]-[#6,#7:7]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "c80a23d3-3986-49d7-84db-0e0bb92f1ff7", "name": "bt0173-1376", "description": "Stilbene derivative > Aldo/Keto derivative + Aldo/Keto derivative", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/c80a23d3-3986-49d7-84db-0e0bb92f1ff7", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[H:21][#8:20]-[c:16]1[c:5][c:8][c:14](\\[#6:2]=[#6:1](/[#6:15])-[c:10]2[c:11][c:12][c:17](-[#8:18][H:19])[c:13][c:9]2)[c:7][c:6]1>>[H:21][#8:20]-[c:16]1[c:6][c:7][c:14](-[#6:2]=O)[c:8][c:5]1.[H:19][#8:18]-[c:17]1[c:13][c:9][c:10]([c:11][c:12]1)-[#6:1](-[#6:15])=O", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "cccbc049-91e9-4dd9-84c1-b7b9f88ac691", "name": "bt0257-3855.4", "description": "Cyclic 1,2-epoxide > 1-Hydroxyaromatic", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/cccbc049-91e9-4dd9-84c1-b7b9f88ac691", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[#6:1]:[#6:2]@-[#6:3]([H])-2-[#8:6]-[#6:4]([H])-2@-[#6:5]=[#6:7]>>[#6:1]:[#6:2]-[#6:3](-[#8:6])=[#6:4]([H])-[#6:5]=[#6:7]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "cd0f874b-364f-455e-814f-8f9f7d27600b", "name": "bt0352-4297.2", "description": "1-Methyl-2-oxo derivative + 2-Oxopent-4-enoate derivative > Acetate + RH + Pyruvate derivative + Acetaldehyde or Ketone", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/simple-ambit-rule/cd0f874b-364f-455e-814f-8f9f7d27600b", "kv": {}, "aliases": [], "scenarios": [], "rule_type": "SimpleAmbitRule", "smirks": "[#8:4]=[#6;D3,D4H1;R0:1](-[#6:2])!@-[#6:3]-[#6:8](=[O:10])-[#6:7](-[#8-:6])=[O:9]>>[#6:3]-[#6:8](=[O:10])-[#6:7](-[#8-:6])=[O:9].[#6:2]-[#6:1](-[#8-])=[O:4]", "reactant_filter_smarts": "", "product_filter_smarts": ""}, {"uuid": "cda01c72-86ec-42f7-89fa-82ebdcccd474", "name": "bt0063-3938", "description": "Methylammonium derivative + tertiary Amine + primary Amine + secondary Amine > 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Bis(2-chloroethyl) sulfide, also known as Yperite or mustard gas, is the most produced and stored chemical weapon. It is highly cytotoxic and is a carcinogenic and mutagenic alkylating agent; benzyl sulfide has been used as a non-toxic model for its metabolism. The microbial degradation of benzyl sulfide can be carried out by white-rot (Coriolous versicolor) and brown-rot (Tyromyces palustris) fungi ([http://www.ncbi.nlm.nih.gov/pubmed/9256235|Itoh et al., 1997]). The initial step may be the oxidative cleavage of the C-S bond to yield benzaldehyde and benzyl mercaptan. Benzaldyde can be reduced to benzyl alcohol or oxidized to benzoate. Benzyl mercaptan can be converted to benzyl disulfide in the presense or absence of fungi. Degradation of the disulfide to the mercaptan was observed in the presence of fungi. Benzaldehyde, benzyl alcohol, and benzoate follow the toluene pathway and are finally mineralized to CO2 and H2O. These and several other fungi can also oxide benzyl sulfide to the sulfoxide and the sulfone ([http://www.ncbi.nlm.nih.gov/pubmed/12571066|Van Hamme et al., 2003]), and this may be the primary aerobic route. The first oxidation step is catalyzed by extracellular enzymes such as laccase, but the second step is cytochrome P450 (unspecific monooxygenase) mediated. Rhodococcus sp. strain IGTS8 can perform these same two oxidations using a single sulfide/sulfoxide monooxygenase ([http://www.ncbi.nlm.nih.gov/pubmed/8824615|Lei and Tu, 1996]).", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/0dffa556-25a2-42a2-b424-ac2dbc0847c6", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "24e2dce8-b918-43dd-9469-9349608cc259", "name": "Dimethylisophthalate", "description": "Dimethyl isophthalate (DMI) is a white flaked solid, soluble in most organic solvents and belongs to a category of compounds called dimethyl phthalate esters (DMPE). DMI is used to modify the structural integrity of plastics such as polyethylene terephthalate (PET). Health concerns may be warranted due to the estrogenic mimicking properties of DMI ([http://www.ncbi.nlm.nih.gov/pubmed/17462710|Cheung et al., 2007]). The complementary metabolism of Klebsiella oxytoca Sc and Methylobacterium mesophilicum Sr can degrade DMI to non toxic metabolites ([http://www.ncbi.nlm.nih.gov/pubmed/17258288|Li et al., 2007]). Variovorax paradoxus T4 and Xanthobacter sp. ([http://www.ncbi.nlm.nih.gov/pubmed/17462710|Cheung et al., 2007]), and Rhodococcus erythropolis 5D and R. ruber 1B (Aleshchenkova et al., Microbiol. 66: 515-518, 1997) can also degrade DMI by the same pathway. Other phthalate degradation pathways are found on the Phthalate Family Map.", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/24e2dce8-b918-43dd-9469-9349608cc259", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "257b013f-0343-4ddc-91c3-9abc5f9de62d", "name": "Limonene", "description": "Limonene (4-isopropenyl-1-methyl-cyclohexene), a monocyclic monoterpene, is the most widespread terpene in the world and is formed by more than 300 plants. (+)-(4R)-limonene is its most widespread form ([http://www.ncbi.nlm.nih.gov/pubmed/10224006|van der Werf et al., 1999]). Limonene is the major constituent of citrus essential oils and is used as a raw material for the chemical synthesis of terpene resin adhesives and flavor materials, such as menthol and carvone. So far, five different microbial biotransformation pathways for limonene have been proposed. In the middle branch, a soil Pseudomonassp. degradates limonene in the same way as Rhodococcus erythropolis DCL14, but its final product is 1-hydroxy-2-oxolimonene rather than 3-isopropenyl-6-oxoheptanoyl-CoA. The middle branch shows a pathway for (+)-(4R)-limonene; a similar pathway using many of the same enzymes is known for (-)-(4S)-limonene ([http://www.ncbi.nlm.nih.gov/pubmed/10224006|van der Werf et al., 1999]).", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/257b013f-0343-4ddc-91c3-9abc5f9de62d", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "3022a7f1-9d3c-4780-ac90-8e1c11c886f2", "name": "Caffeine (fungal)", "description": "Caffeine (1,3,7-trimethylxanthine) is found naturally in coffee, tea and cocoa and used as a food and drug additive. When ingested by humans, caffeine stimulates the central nervous system, elevates blood pressure, increases metabolic rate, and acts as a diuretic ([http://www.ncbi.nlm.nih.gov/pubmed/16507475|Higdon and Frei, 2006]). Caffeine consumption may reduce the risk of Parkinson`s disease. However, adverse reactions to caffeine consumption can include anxiety, insomnia, heart palpitations, abdominal pain, and nausea, and high caffeine intake has been linked with increased risk of osteoporosis and complications in pregnancy ([http://www.ncbi.nlm.nih.gov/pubmed/17009088|Dash and Gummadi, 2006]). Caffeine is also mildly addictive. Withdrawal symptoms can include headache, fatigue, depressed mood, difficulty concentrating, irritability, nausea, and muscle pain ([http://www.ncbi.nlm.nih.gov/pubmed/16507475|Higdon and Frei, 2006]). Coffee pulp, a waste product produced during coffee processing, is a major pollutant in water bodies near coffee plants. Even though it is high in nutrients, it cannot be used as animal feed due to the high levels of caffeine and other unwanted compounds ([http://www.ncbi.nlm.nih.gov/pubmed/10959086|Pandey et al., 2000]). Solvents commonly used to produce caffeine-free products are either very expensive to use or toxic ([http://www.ncbi.nlm.nih.gov/pubmed/17009088|Dash and Gummadi, 2006]). However, a number of bacterial and fungal strains capable of degrading caffeine have been identified ([http://www.ncbi.nlm.nih.gov/pubmed/14977550|Mazzafera, 2004]). The pathway described below has been documented for members of the fungal species Penicillium commune and Aspergillus tamarii (Hakil et al. 1998. Enzyme Microb Technol 22: 355-359), other members of these two genera, and the bacterial species Pseudomonas putida CBB5 ([http://www.ncbi.nlm.nih.gov/pubmed/19447909|Yu et al., 2009]). In the major fungal pathway, caffeine degrades via theophylline (1,3-dimethylxanthine) and 3-methylxanthine to xanthine. Bacterial and minor fungal pathway branches funnel through paraxanthine and theobromine. In contrast to other known bacterial pathways, no methyluric acids are reported as degradation products.", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/3022a7f1-9d3c-4780-ac90-8e1c11c886f2", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "3ed539af-69b0-4295-8dd2-76f881bf5b9f", "name": "Parathion (an/aerobic)", "description": "Parathion (O,O-diethyl-O-p-nitrophenyl phosphorothioate) is an organophosphate compound and is one of the most toxic insecticides registered with the U.S. Environmental Protection Agency (EPA). On agricultural crops it was used widely as a broad spectrum insecticide, acaricide, fumigant and nematocide. In 1991 parathion became a Restricted Use Pesticide (RUP). Parathion is well tolerated by crops, does not easily leach through soil and may be degraded by soil microorganisms within weeks. Degradation of parathion by sunlight or liver enzymes results in the active compound paraoxon which interferes with the nervous system through cholinesterase inhibition. Extreme toxicity combined with the ease of exposure has resulted in numerous human and non-pest species deaths. The immediate aerobic metabolic breakdown product of parathion, PNP or p-nitrophenol, was listed as a priority pollutant in 1979 by the US EPA. The main aerobic pathway involves initial hydrolysis of parathion to para-nitrophenol and diethylthiophosphoric acid (middle branch). The oxidation of parathion to paraoxon was observed, but was a minor contribution (right branch). It was not determined whether this reaction was enzyme-mediated or not; it is shown here as being enzyme-mediated, based on the known enzymic oxidation of diethtylthiophosphoric acid to diethylphosphoric acid, though since the reactions are not well-characterized, both reactions cannot be balanced. Under anerobic conditions, parathion was reduced to aminoparathion, which is hydrolyzed to p-aminophenol and diethylthiophosphoric acid (left branch) ([http://www.ncbi.nlm.nih.gov/pubmed/8005|Munnecke & Hsieh, 1976]).", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/3ed539af-69b0-4295-8dd2-76f881bf5b9f", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "523b8c04-5050-4dbd-9e72-d7231fb1b9e9", "name": "3-Fluorobenzoate", "description": "3-Fluorobenzoic acid is a fluorinated organic compound. Little attention has been given to the biodegradation of these compounds. The uses of fluorinated aromatic compounds include herbicides, pesticides, insecticides, refrigerants, and anesthetics (B. D. Key, R. D. Howell, & C. S. Criddle (1997) Environ Sci Technol 31:2445-2454). Fluoroorganics are more stable than their chlorine analogues due to the stability of the C-F bond, which is 25 kcal/mol stronger than the C-Cl bond (D. F. McMillen & D. M. Golden (1982) Ann Rev Phys Chem 33:493). Fluoroorganics pose a potential human health concern. Industrial workers exposed to fluroorganics were shown to have higher serum organic fluorine concentrations than individuals not exposed to fluroorganics ([http://www.ncbi.nlm.nih.gov/pubmed/7405826|Ubel et al., 1980]). The health effects of acute fluoride toxicity are well known; however, it is unclear whether fluorinated organic compounds result in the same problems (Akiniwa. K. (1997) Fluoride 30(2): 89-104). In organisms that have been surveyed, metabolism of 2-fluorobenzoate and 4-fluorobenzoate is more common than that of 3-fluorobenzoate ([http://www.ncbi.nlm.nih.gov/pubmed/10919805|Song et al., 2000]). Two pathways of 3-fluorobenzoate degradation have been described. In one pathway, degradation is initiated by 1,2-dioxygenation of 3-fluorobenzoate to give 3-fluorohexadiene-cis,cis-1,2-diol-1-carboxylate. This is converted to 3-fluorocatechol, which is slowly metabolized to 2-fluoro-cis,cis-muconate, which is not metabolized further ([http://www.ncbi.nlm.nih.gov/pubmed/16345496|Schreiber et al., 1980]) , leading to accumulation of cytotoxic 3-fluorocatechol. Alternatively, metabolism can begin with 1,6-dioxygenation of 3-fluorobenzoate, which is converted to 5-fluorocyclohexadiene-cis,cis-1,2-diol-1-carboxylate and then sequentially to 4-fluorocatechol, 3-fluoro-cis,cis-muconate, and eventually oxoadipate, which can enter central metabolism (K. H. Engesser, G. Auling, J. Busse, & H.-J. Knackmuss (1990) Arch Microbiol 153:193-199). Fluoride is also released in this pathway. Both pathways are present in strains that metabolize 3-fluorobenzoate, but metabolic flux through each pathway varies among the organisms (Engesser et al., 1990). Cells of Acinetobacter calcoaceticus NCIB 8250 ([http://www.ncbi.nlm.nih.gov/pubmed/1182155|Clarke et al., 1975]) and Pseudomonas sp. B13 ([http://www.ncbi.nlm.nih.gov/pubmed/16345496|Schreiber et al., 1980]) grown on benzoate or 3-chlorobenzoate, respectively, metabolized 3-fluorobenzoate, but the strains could not grow on the compound as a carbon and energy source. In these organisms, the major pathway of 3-fluorobenzoate degradation begins with 1,2-dioxygenation. Strain FLB 300 (alpha-2-subclass of Proteobacteria, Agrobacterium-Rhizobium branch) (Engesser et al., 1990) and Sphingomonas sp. HB-1 ([http://www.ncbi.nlm.nih.gov/pubmed/15321683|Boersma et al., 2004]) were able to grow using 3-fluorobenzoate as a sole carbon and energy source. In these strains that can assimilate 3-fluorobenzoate, the major pathway begins with 1,6-dioxygenation of the substrate, thereby reducing the amount of the toxic 3-fluorocatechol intermediate that is produced.", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/523b8c04-5050-4dbd-9e72-d7231fb1b9e9", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "52d72f19-910b-469c-ad60-5c3afce72cb6", "name": "4-Fluorobenzoate (an/aerobic)", "description": "Fluorinated hydrocarbons are most commonly used in herbicides, fungicides, and pharmaceuticals. A study dedicated to the isolation and characterization of aromatic compound degrading microbes found 4-fluorobenzoate in freshwater sediment and sewage in concentrations of 50-500 ppm (Horowitz, et al. (1982) Dev Ind Microbiol 23:435-44). Toxicology information is limited for this particular compound but studies on other more common halobenzenes have shown toxicity in high doses. Knowledge of fluorobenzoate metabolism is relatively sparse in comparison to other halobenzoates. Fluorinated organic compounds, such as 4-fluorobenzoate, are more resistant to microbial degradation than other halogenated compounds due to unusual carbon-fluorine bond properties ([http://www.ncbi.nlm.nih.gov/pubmed/12805763|Giesy et al., 2001]). Aerobic metabolism of 4-fluorobenzoate is initiated by an oxygen-dependent ring cleavage in B. cepacia , Pseudomonas sp. B13, A. eutrophus JMP134 and A. eutrophus 335. Cycloisomerization of 3-fluoro-cis,cis-muconate with the addition of a proton yields 4-fluoromuconolactone as the sole major product. Lactone hydrolysis preceeds a secondary dehalogenation reaction and the resulting product enters intermediary metabolism through the TCA cycle ([http://www.ncbi.nlm.nih.gov/pubmed/2394680|Schlomann et al., 1990]). In contrast to chloride and bromide elimination through a carbanionic intermediate ([http://www.ncbi.nlm.nih.gov/pubmed/16345496|Schreiber et al., 1980]), defluorination is not coupled to cycloisomerization and dienelactone formation is negligible ([http://www.ncbi.nlm.nih.gov/pubmed/2394680|Schlomann et al., 1990]). 4-Fluorobenzoate is anaerobically degraded by Aureobacterium sp. strain RHO25. Coenzyme A ligation and dehalogenation yields 4-hydroxybenzoyl-CoA, which enters common intermediary metabolism ([http://www.ncbi.nlm.nih.gov/pubmed/2604392|Oltmanns et al., 1989]). These pathways may be relevant for the degradation of other fluoroaromatic compounds.", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/52d72f19-910b-469c-ad60-5c3afce72cb6", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "535789b9-f6e6-45fc-9bfa-5b57f6655c54", "name": "Carbofuran", "description": "Carbofuran is a common agricultural pesticide belonging to the N-methylcarbamate family. It is used to control soil dwelling and leaf feeding insects. It has a high mammalian toxicity due to acetylcholinesterase inhibition. The oral LD50 value of carbofuran in mice and other animals has been reported to vary from 2 to 9 mg/kg bodyweight. Since it is water soluble and mobile in soil environments, it is very likely to contaminate lakes and ground water, so a major exposure to it is by drinking contaminated water. Because of this, it is important to find out ways to biodegrade it. Sphingomonas sp. strain SB5, can degrade carbofuran into carbofuran-7-phenol and methylamine, hydrolyze carbofuran-7-phenol to 3-(2-hydroxy-2-methylpropyl)benzene-1,2-diol (DP-1), and then degrade DP-1 into a red metabolite (DP-2). More study is needed to identify this red metabolite ([http://www.ncbi.nlm.nih.gov/pubmed/15080638|Kim et al., 2004]). Pseudomonas sp. 50432 is capable of hydroxylating carbofuran at the 4-position; further metabolites are unknown ([http://www.ncbi.nlm.nih.gov/pubmed/12351226|Chaudhry et al., 2002]). Carbofuran may also be hydroxylated at the 5 position by Novosphingobium sp. FND-3 and Rhodococcus TEI ([http://www.ncbi.nlm.nih.gov/pubmed/17425661|Yan et al., 2006]). Fungal degradation of carbofuran may occur via hydroxylation at the three position and oxidation to 3-ketocarbofuran ([http://www.ncbi.nlm.nih.gov/pubmed/9604338|Salama et al., 1998]).", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/535789b9-f6e6-45fc-9bfa-5b57f6655c54", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "5b80be8c-a8ba-4b2d-9745-950693bb44d2", "name": "Bisphenol A", "description": "Bisphenol A is widely used as a monomer for the production of polymers, such as epoxy resins and polycarbonate plastics. These plastics are used in many food and drink packaging applications. When the resins are inert materials, they are commonly used as lacquers to coat metal products such as food cans, bottle tops and water supply pipes. More information on this compound can be found at the Bisphenol A website from the Bisphenol A Global Industry Group and the Bisphenol A page at the Hormone Disrupting Compounds site. Bisphenol A is metabolized by a Gram-negative aerobic bacterium (strain MV1) via a novel pathway involving oxidative skeletal rearrangement. The metabolism involves two primary pathways: a minor pathway, in which Bisphenol A is first oxidized to a triol, and a major pathway, in which Bisphenol A is metabolized to form the intermediates 4-hydroxybenzoate and 4-hydroxyacetophenone that are converted to carbon dioxide and biomass ([http://www.ncbi.nlm.nih.gov/pubmed/8125948|Spivack et al., 1994]). Sphingobium xenophagium Bayram and Sphingomonas sp. strain TTNP3 can metabolize bisphenol A by an ipso-substitution mechanism that involves ring hydroxylation at the site of the substituent. This proposed hydroxylation product can be cleaved to form hydroquinone and a proposed 2-(4-hydroxyphenyl)-isopropyl cation. The cation can be transformed to 4-(2-hydroxypropan-2-yl)phenol, which can eliminate water to form 4-isopropenylphenol. 4-Isopropenylphenol can be reduced to 4-isopropylphenol. These are the reactions found in both organisms. There are other possible routes (not shown here), including formation of a 2-(4-hydroxyphenyl)-isopropyl anion instead of the cation, to the above products, and other side reactions occur in one organism or the other ([http://www.ncbi.nlm.nih.gov/pubmed/17886831|Gabriel et al., 2007], [http://www.ncbi.nlm.nih.gov/pubmed/17557840|Kolvenbach et al., 2007]). Sphingobium fuliginis TIK-1 can metabolize and grow on 4-isopropylphenol. S. fuliginis is proposed to hydroxylate 4-ispropylphenol to 4-isopropylcatechol, which is metabolized by a meta-cleavage pathway. 3-Methyl-2-butanone was the major degradation product observed ([http://www.ncbi.nlm.nih.gov/pubmed/20802076|Toyama et al., 2010]).", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/5b80be8c-a8ba-4b2d-9745-950693bb44d2", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "65783708-db79-40fb-878e-9526a7537165", "name": "Atrazine", "description": "Atrazine is a broad-leaf, pre-emergence herbicide. Eighty million pounds are applied to soils annually in the United States, more than any other herbicide. Atrazine is the leading member of a class of triazine ring-containing herbicides that includes simazine and terbuthylazine. The Triazine Metapathway Map contains additional information on triazine metabolism. A number of different bacteria have been identified that are capable of metabolizing atrazine to ammonia and carbon dioxide. Atrazine biodegradation has been found to occur via several different pathways that funnel into cyanuric acid metabolism. A gene region from Pseudomonas sp. strain ADP encoding atrazine degradation enzymes has been cloned and characterized. The initial hydrolytic dechlorination of atrazine to hydroxyatrazine ([http://www.ncbi.nlm.nih.gov/pubmed/7574646|de Souza et al., 1995]) is an animated reaction. Two enzymes belonging to the amidohydrolase protein family catalyze the sequential removal of ethylamine and isopropylamine ([http://www.ncbi.nlm.nih.gov/pubmed/9055410|Boundy-Mills et al., 1997] and [http://www.ncbi.nlm.nih.gov/pubmed/9422605|Sadowsky et al., 1998]). Degradation by Rhodococcus sp. strain N186/21 is initiated by oxidative removal of either the ethyl or isopropyl group ([http://www.ncbi.nlm.nih.gov/pubmed/7646049|Nagy et al., 1995]). Deethylatrazine undergoes a second oxidative removal of the isopropyl group. Hydrolytic removal of s-triazine ring substituents from deisopropylatrazine and deisopropyldeethylatrazine yields cyanuric acid.", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/65783708-db79-40fb-878e-9526a7537165", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "67859a8d-3ce2-44ad-ae91-399cf6c07665", "name": "alpha-Pinene", "description": "Alpha-Pinene is a monoterpene that may be a significant factor affecting bacterial activities in nature. It is a major component in tea-tree oils, and gives off a piney smelling odor. Terpenes are widely used as flavorings, deodorants, and medicines (as in the treatment of acne). It is not clear whether the enzymes from B. pallidus here named \"alpha-pinene dehydrogenase\" and \"alpha-pinene monooxygenase\" are the same enzyme or two different enzymes. Indeed, these pathways may be catalyzed by a limited number of isomerase, monooxygenase and dehydrogenase enzymes with broad substrate specificities. Glycine mediates the isomerization of cis-2-Methyl-5-isopropylhexa-2,5-dienoic acid to trans-2-Methyl-5-isopropylhexa-2,5-dienoic acid. The beta-oxidation reactions transforming cis/trans-2-Methyl-5-isopropylhexa-2,5-dienoic acid to 3-Isopropylbut-3-enoic acid are postulated (Savithiry et al., 1998).", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/67859a8d-3ce2-44ad-ae91-399cf6c07665", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "809882b1-6377-4e63-8166-42cf7a7b222e", "name": "Orcinol", "description": "Benzene compounds with dihydroxylated rings, e.g. catechol (1,2-benzenediol) and hydroquinone (1,4-benzenediol), are important intermediates in bacterial catabolism of aromatic compounds. The bacterial catabolism of orcinol (5-methyl-1,3-benzenediol) can be used as a model for the metabolism of other members of the resorcinol (1,3-benzenediol) compound family. This family includes many commercially-important compounds; for example, 4-hexylresorcinol is used medicinally as a topical antiseptic. This pathway is based on [http://www.ncbi.nlm.nih.gov/pubmed/1254564|Chapman and Ribbons (1976)].", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/809882b1-6377-4e63-8166-42cf7a7b222e", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "80b5312b-43d7-4e7b-94fd-4074cf3abd1f", "name": "Trichloroethylene", "description": "Trichloroethylene (TCE) is a good solvent and is used in manufacturing to clean grease from machinery. It is one of the most abundant environmental pollutants of groundwater in the United States. In some groundwater, TCE undergoes reductive dechlorination catalyzed by anaerobic bacteria that yields vinyl chloride, a potent human carcinogen. TCE removal by dumping or air stripping is now largely disallowed and this has focused efforts on biological methods of TCE remediation in soil and water. The enzyme that starts one branch of this pathway, toluene 1,2-dioxygenase, has many other catalytic abilities, which are documented in a table of the Reactions of Toluene 1,2-Dioxygenase. The spontaneous degradation of trichloroethylene epoxide can produce as many as four products: dichloroacetate, carbon monoxide, glyoxylate, and formate. The number, type, and proportion of products seen depends on the local environment.", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/80b5312b-43d7-4e7b-94fd-4074cf3abd1f", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "a0ce66fa-3058-4ddb-b6a8-e4bbe78ad66f", "name": "1,1,1-Trichloroethane (an/aerobic)", "description": "1,1,1-Trichloroethane (TCA) is a synthetic organic solvent widely used in industrial processes and is a major environmental pollutant commonly found in soil, groundwater, and the atmosphere. TCA is present in at least 696 of the 1430 National Priorities List sites identified by the U.S. Environmental Protection Agency (EPA). Because of TCA\ufffds adverse effects on human health, the EPA has set a maximum contaminant level of 200 ppb in drinking water. TCA is also listed as an ozone-depleting substance by the United Nations Environment Programme. Even when released into soil or leached into groundwater, the primary environmental fate of TCA is volatilization to the atmosphere, where it interacts with ozone and contributes to the erosion of the ozone layer. TCA can be reductively dechlorinated under anaerobic conditions to 1,1,-dichloroethane (DCA) by Desulfobacterium autotrophicum (C. Egli, R. Scholtz, A. M. Cook, & T. Leisinger (1987) FEMS Microbiol. Lett. 43:257-261.) and a Clostridium sp. ([http://www.ncbi.nlm.nih.gov/pubmed/2729985|Galli and McCarty, 1989]). Reductive dechlorination of TCA to DCA and chloroethane (CA) has been documented in methanogenic consortia (J. H. de Best, A. Hage, H. J. Doddema, D. B. Janssen, & W. Harder (1999) Appl. Environ. Microbiol. 51:277-283.) and a putative Dehalobacter sp. (designated strain TCA1) ([http://www.ncbi.nlm.nih.gov/pubmed/12411705|Sun et al., 2002]). [http://www.ncbi.nlm.nih.gov/pubmed/10633545|Chen et al. (1999)] reported the complete dehalogenation of TCA, DCA, and CA to ethane by an anaerobic consortium in sewage sludge, but ethane was a minor product in all cases (< 5%, < 3%, and < 1% of the initial substrate degraded to ethane, respectively). The enzymes that catalyze the reductive dehalogenation of TCA have not been identified. TCA can be aerobically transformed to 2,2,2-trichloroethanol by the methanotroph Methylosinus trichosporium OB3b expressing a soluble methane monooxygenase ([http://www.ncbi.nlm.nih.gov/pubmed/2624462|Oldenhuis et al., 1989]), and by ethane-utilizing Mycobacterium spp. isolated from soil ([http://www.ncbi.nlm.nih.gov/pubmed/10508110|Yagi et al., 1999]). Further study revealed that one of the Mycobacterium strains produced trichloroacetic acid and dichloroacetic acid as minor products (12.7% and 1.2%, respectively, vs. 85.5% of TCA converted to 2,2,2-trichloroethanol) during the aerobic transformation of TCA ([http://www.ncbi.nlm.nih.gov/pubmed/11999413|Hashimoto et al., 2002]). Oldenhuis et al (1989) found that M. trichosporium expressing soluble methane monooxygenase completely dechlorinated DCA, but degradation intermediates were not identified. [http://www.ncbi.nlm.nih.gov/pubmed/12355460|Kim et al. (2000)] observed partial dechlorination of DCA (~37% of initial solvent) by an aerobic butane-grown mixed culture. In Nitrosomonas europea, an ammonia monooxygenase catalyzed the oxidation of CA to acetaldehyde, with 2-Chloroethanol produced as a minor product (1-2% 2-chloroethanol vs. 98% acetaldehyde) ([http://www.ncbi.nlm.nih.gov/pubmed/2394686|Rasche et al., 1990]).", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/a0ce66fa-3058-4ddb-b6a8-e4bbe78ad66f", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "a9029787-5381-455d-ba4f-5283aa527c2c", "name": "Malathion", "description": "Malathion is an organophosphate pesticide commonly used in the United States for controlling mosquito populations. The toxicity of malathion is low but acute exposure in high doses may cause a variety of symptoms including nausea, dizziness, or confusion. Malaoxon is a potent cholinesterase inhibitor that can be formed from malathion under certain conditions. Exposure to malaoxon can lead to complications in the central nervous system (Edwards, 2006. US Environmental Protection Agency - Prevention, Pesticides and Toxic Substances EPA 738-R-06-030). The predominant biodegradation pathway for malathion involves formation of mono- and diacid metabolites through carboxylesterase activity. Oxidative desulfurization and demethylation leads to complete mineralization. Other minor routes of metabolism include initial oxidation to remove sulfur and methyl groups ([http://www.ncbi.nlm.nih.gov/pubmed/402103|Laveglia and Dahm, 1977]). Pseudomonas aeruginosa AA112 is able to use malathion as a sole carbon source. [http://www.ncbi.nlm.nih.gov/pubmed/17896475|Abo-Amer (2007)] observed the formation of diethylsuccinate and succinate metabolites. The intermediate steps in this pathway have not been characterized. However, the reduction of -SH to -H (diethyl 2-mercaptosuccinate -> diethylsuccinate) may be abiotic ([http://www.ncbi.nlm.nih.gov/pubmed/12713326|Hebting et al., 2003]).", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/a9029787-5381-455d-ba4f-5283aa527c2c", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "b8b3f751-a922-4398-8a52-a3dcf7c36867", "name": "Caffeine", "description": "Caffeine (1,3,7-trimethylxanthine) is found naturally in coffee, tea and cocoa and used as a food and drug additive. When ingested by humans, caffeine stimulates the central nervous system, elevates blood pressure, increases metabolic rate, and acts as a diuretic ([http://www.ncbi.nlm.nih.gov/pubmed/16507475|Higdon and Frei, 2006]). Caffeine consumption may reduce the risk of Parkinson`s disease. However, adverse reactions to caffeine consumption can include anxiety, insomnia, heart palpitations, abdominal pain, and nausea, and high caffeine intake has been linked with increased risk of osteoporosis and complications in pregnancy ([http://www.ncbi.nlm.nih.gov/pubmed/17009088|Dash and Gummadi, 2006]). Caffeine is also mildly addictive. Withdrawal symptoms can include headache, fatigue, depressed mood, difficulty concentrating, irritability, nausea, and muscle pain ([http://www.ncbi.nlm.nih.gov/pubmed/16507475|Higdon and Frei, 2006]). Coffee pulp, a waste product produced during coffee processing, is a major pollutant in water bodies near coffee plants. Despite the fact that it is high in nutrients, it cannot be used as animal feed due to the high levels of caffeine and other unwanted compounds ([http://www.ncbi.nlm.nih.gov/pubmed/10959086|Pandey et al., 2000]). Solvents commonly used to produce caffeine-free products are either very expensive to use or toxic ([http://www.ncbi.nlm.nih.gov/pubmed/17009088|Dash and Gummadi, 2006]). However, a number of bacterial and fungal strains capable of degrading caffeine have been identified ([http://www.ncbi.nlm.nih.gov/pubmed/14977550|Mazzafera, 2004]). There are multiple possible pathways depending on the genus, species and strain of organism degrading the caffeine. In the bacteria Psuedomonas putida and Serratia marcescens, the major pathway is through theobromine to 7-methylxanthine to xanthine ([http://www.ncbi.nlm.nih.gov/pubmed/14977550|Mazzafera, 2004]). Minor branches produce methyluric acids; it has been proposed that these degrade to uric acid ([http://www.ncbi.nlm.nih.gov/pubmed/17009088|Dash and Gummadi, 2006]), but this has not been confirmed. Another bacterial pathway, found in Rhodococcus and Klebsiella spp., requires oxidation to yield 1,3,7-trimethyluric acid ([http://www.ncbi.nlm.nih.gov/pubmed/9705852|Madyastha and Sridhar, 1998]). Caffeine can also be degraded via alternative pathways found in several fungal and one bacterial species.", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/b8b3f751-a922-4398-8a52-a3dcf7c36867", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "bbd9ef3c-5d42-4af9-a1ca-fceaa0fa13ae", "name": "Pyrene", "description": "Pyrene is a four-ringed polycyclic aromatic hydrocarbon (PAH). Although not a carcinogen, pyrene is a byproduct of the manufactured gas process and other incomplete combustion processes. Pyrene is present at thousands of sites throughout the United States and pyrene has been shown to be involved in the bacterial cometabolism of the potent carcinogen benzo[a]pyrene ([http://www.ncbi.nlm.nih.gov/pubmed/10698765|Boonchan et al., 2000]), whose metabolism is shown elsewhere on this site. The biodegradation of benzo[a]pyrene is known to proceed through substituted pyrene intermediates (e.g., [http://www.ncbi.nlm.nih.gov/pubmed/8572690|Schneider et al., 1996]). Pyrene can be biodegraded by bacteria and fungi through initial dioxygenase (bacteria) and monooxygenase (bacteria and fungi) reactions.", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/bbd9ef3c-5d42-4af9-a1ca-fceaa0fa13ae", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "c6a2135b-e067-48eb-ae2c-062743ff3ec9", "name": "Isoproturon", "description": "The phenylurea herbicide isoproturon (IPU) is used against annual grasses and broad-leaved weeds in cereal production across Europe, resulting in both surface water and ground water pollution ([http://www.ncbi.nlm.nih.gov/pubmed/11722885|Sorensen et al., 2001]). Isoproturon in soil is degraded, producing carbon dioxide and degradation products ([http://www.ncbi.nlm.nih.gov/pubmed/11482681|Perrin-Gainer et al., 2001]). The major biodegradation pathway of isoproturon is isoproturon -> mono-demethyl-isoproturon -> hydroxy-monodemethyl-isoproturon -> 4`-(2-hydroxyisopropylphenyl)urea -> 4`-(2-hydroxyisopropylphenyl)aniline. Other minor pathways exist. Through one of these, 4,4`-diisopropylazobenzene can accumulate in soil ([http://www.ncbi.nlm.nih.gov/pubmed/11482681|Perrin-Ganier et al., 2001]). Attempts to isolate microorganisms which metabolize isoproturon have often failed. Recently, Sphingomnas sp. strain SRS2 was found to mineralize isoproturon. Sphingomnas sp. strain SRS2 is auxotrophic; it requires strain SRS1 to supply amino acids needed for the pathway ([http://www.ncbi.nlm.nih.gov/pubmed/12089031|Sorensen et al., 2002]).", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/c6a2135b-e067-48eb-ae2c-062743ff3ec9", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "d201269f-a284-4737-a7dd-55d1606bc0af", "name": "N,N-Diethyl-m-toluamide", "description": "N,N-Diethyl-m-toluamide, commonly known as DEET, is broadly used as an active ingredient in insect repellents ([http://www.ncbi.nlm.nih.gov/pubmed/17337538|Rivera-Cancel et al., 2007]). In the United States, 30% of people use an insect repellent containing DEET at least once a year ([http://www.ncbi.nlm.nih.gov/pubmed/11693870|McGready et al., 2001]). Annual domestic use equals approximately 1,800 tons ([http://www.ncbi.nlm.nih.gov/pubmed/17337538|Rivera-Cancel et al., 2007]). DEET was originally patented by the United States Army for use in insect-infested areas and was later registered for use by the general public. DEET is not known to have carcinogenic effects on humans (EXTOXNET; Pesticide Information Profile: DEET). While not carcinogenic, exposure to N,N-diethyl-m-toluamide does have human health effects including skin reactions and in rare cases of high-level exposure, seizures, toxic encephalopathy, acute manic psychosis and death (TOXNET; Hazardous Substances Data Bank; DEET). Hydrolysis of the amide bond in N,N-Diethyl-m-toluamide yields 3-methylbenzoate and diethylamine. This transformation is catalyzed by the enzyme DEET hydrolase under aerobic conditions by the bacterium P. putida DTB. The resulting 3-methylbenzoate is then converted to 3-methylcatechol which can be further metabolized through the meta cleavage pathway of Pseudomonas putida ([http://www.ncbi.nlm.nih.gov/pubmed/17337538|Rivera-Cancel et al., 2007]). Diethylamine and ethylamine are both hydrolyzed to acetaldehyde before entering central metabolism ([http://www.ncbi.nlm.nih.gov/pubmed/1268229|Steenkamp et al., 1976]). In laboratory batch experiments with activated sludge from a membrane bioreactor, the two main products observed were the product of enzymatic dealkylation and the product of enzymatic oxidation.", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/d201269f-a284-4737-a7dd-55d1606bc0af", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "d80622c2-0d8c-459f-8068-73543a341912", "name": "Tetrabromobisphenol A", "description": "3,3`,5,5`-Tetrabromobisphenol A (TBP) is a chemical used in industry as a flame retardant treatment for paper and textiles as well as an additive during the manufacture of plastics, polymers and circuit boards. TBP is not believed to be carcinogenic or mutagenic to humans. However, TBP is toxic to life in aquatic envioronments and has a 50% lethal dose for fish of 0.4 or 0.54 mg/L and 50% effective concentration of 0.96 mg/L for Daphnia magna. A report on TBA and its derivatives has been produced by the International Programme on Chemical Safety. TBP is nonvolatile and is not mobile in the soil partially because TBP is insoluble in water (<1 mg/liter) at a pH of 7.0. In soils with increased pH levels the solubility of TBP is significantly increased and can leach into and contaminate groundwater below contaminated soil. This pathway is based on [http://www.ncbi.nlm.nih.gov/pubmed/10831413|Ronen and Abeliovich, 2000] and [http://www.ncbi.nlm.nih.gov/pubmed/14669869|Arbeli and Ronen, 2003].", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/d80622c2-0d8c-459f-8068-73543a341912", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "d9148295-4aaf-499c-a305-71c964702f8e", "name": "Tetrahydrofuran", "description": "Tetrahydrofuran (THF) is one of the most polar ethers and is a widely used solvent for polar reagents. Since THF is very soluble in water and has a relatively low boiling point, signficant amounts are often released into the environment, causing contamination problems. Tetrahydrofuran is not considered to be readily degradable, and concerns of environmental contamination have been raised. [http://www.ncbi.nlm.nih.gov/pubmed/1367773| Bernhardt and Diekmann (1991)] performed studied the pathway for tetrahydrofuran degradation by Rhodococcus ruber DSM 44190. The pathway shown below is hypothetical. Not all intermediates (e.g. 2-hydroxytetrahydrofuran) were detected. In fact, the isomerization of 2-hydroxytetrahydrofuran might occur spontaneously and not require an enzyme. However, degradation experiments using the same organism were performed with a similar compound, 2,5-dimethyltetrahydrofuran (Bock, C., Kroppenstedt, R.M., and Diekmann, H., 1996, Appl Microbiol Biotechnol. 45:408-410), and those data support the proposed tetrahydrofuran pathway. [http://www.ncbi.nlm.nih.gov/pubmed/12632259|Thiemer et al. (2003)] characterized the pathway in Pseudonocardia sp. strain K1. This strain only uses the left pathway branch.", "url": "http://localhost:8000/package/1869d3f0-60bb-41fd-b6f8-afa75ffb09d3/pathway/d9148295-4aaf-499c-a305-71c964702f8e", "kv": {}, "aliases": [], "scenarios": [], "setting": null}, {"uuid": "f47cc15b-6ef8-4fc3-97e4-6c8b2a6b055b", "name": "Nitrofen", "description": "Nitrofen is a potent herbicide and has the ability to induce various physiological effects, including master cell activation, organ morphogenesis and severe endocrine disruptor activities. Nitrofen, in its purest form is a colorless and crystalline solid. The technical material is a brown, free flowing solid with a slight aromatic odor. The melting point of the technical material is 64-71C and the density is 1.80g/cm3 at 83C. It is used as a pre or post-emergence contact herbicide. Moderate application rates give selective control in cereals, certain ornamentals, vegetable crops, sugar beet and paddy fields. High application rates will give total vegetation control. Nitrofen requires adequate moisture for full effectiveness. Sphingomonas wittichii RW1 is a very potent diphenyl ether herbicide metabolizing bacterium with broad substrate specificity ([http://www.ncbi.nlm.nih.gov/pubmed/18778066|Keum et al., 2008]). The interesting aspect of the Nitrofen degradation by this strain is the initial reduction of nitro group followed by N-acetylation. As in other Sphingomonads, dissociation of the diaryl ether bond is also found in strain RW1 during Nitrofen metabolism. Although, ether bond clevage is a common metabolic pathway of diaryl ethers in animal, plant, fungi and bacteria, corresponding enzymes of eukaryotes and prokaryotes are different. Bacterial degradation of diphenyl ethers and related environmental contaminants are usually catalyzed by multi-component dioxygenase system, while eukaryotic biodegradation is catalyzed by monooxygenase or peroxidase ([http://www.ncbi.nlm.nih.gov/pubmed/11762605|Hiratsuka et al., 2001]) identified the degradation of diphenyl ether herbicides by the lignin-degrading basidomycete Coriolus versicolor. White-rot basidiomycetous fungi are capable of degrading a variety of environmentally persistent aromatic pollutants. 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select.select[multiple] { display: block; white-space: normal; } + +p a { + @apply underline; +} diff --git a/static/js/alpine/pagination.js b/static/js/alpine/pagination.js index aaa5d9ca..4b858543 100644 --- a/static/js/alpine/pagination.js +++ b/static/js/alpine/pagination.js @@ -5,6 +5,126 @@ */ document.addEventListener('alpine:init', () => { + + const basePagination = ( + items, + currentPage, + totalPages, + totalItems, + perPage, + isReviewed, + instanceId + ) => ({ + items, + currentPage, + totalPages, + totalItems, + perPage, + isReviewed, + instanceId, + + get paginatedItems() { + return this.items; + }, + + get showingStart() { + if (this.totalItems === 0) return 0; + return (this.currentPage - 1) * this.perPage + 1; + }, + + get showingEnd() { + if (this.totalItems === 0) return 0; + return Math.min((this.currentPage - 1) * this.perPage + this.items.length, this.totalItems); + }, + + nextPage() { + if (this.currentPage < this.totalPages) { + this.fetchPage(this.currentPage + 1); + } + }, + + prevPage() { + if (this.currentPage > 1) { + this.fetchPage(this.currentPage - 1); + } + }, + + goToPage(page) { + if (page >= 1 && page <= this.totalPages) { + this.fetchPage(page); + } + }, + + get pageNumbers() { + const pages = []; + const total = this.totalPages; + const current = this.currentPage; + + if (total === 0) { + return pages; + } + + if (total <= 7) { + for (let i = 1; i <= total; i++) { + pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` }); + } + } else { + pages.push({ page: 1, isEllipsis: false, key: `${this.instanceId}-page-1` }); + + let rangeStart; + let rangeEnd; + + if (current <= 4) { + rangeStart = 2; + rangeEnd = 5; + } else if (current >= total - 3) { + rangeStart = total - 4; + rangeEnd = total - 1; + } else { + rangeStart = current - 1; + rangeEnd = current + 1; + } + + if (rangeStart > 2) { + pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-start` }); + } + + for (let i = rangeStart; i <= rangeEnd; i++) { + pages.push({ page: i, isEllipsis: false, key: `${this.instanceId}-page-${i}` }); + } + + if (rangeEnd < total - 1) { + pages.push({ page: '...', isEllipsis: true, key: `${this.instanceId}-ellipsis-end` }); + } + + pages.push({ page: total, isEllipsis: false, key: `${this.instanceId}-page-${total}` }); + } + + return pages; + } + }); + + Alpine.data('paginatedList', + (items, options = {}) => ({ + ...basePagination(items,1, 0, 0, options.perPage || 50, options.isReviewed || false, options.instanceId || Math.random().toString(36).substring(2, 9),), + + init() { + this.fetchPage(1); + }, + + async fetchPage(page) { + this.totalItems = this.items.length; + this.totalPages = Math.ceil(this.items.length / this.perPage); + this.currentPage = page + + const start = page * this.perPage - this.perPage; + const end = page * this.perPage; + return this.items.slice(start, end); + } + + }) + ); + Alpine.data('remotePaginatedList', (options = {}) => ({ items: [], currentPage: 1, diff --git a/static/js/pw.js b/static/js/pw.js index 59abe8cc..1ef18f49 100644 --- a/static/js/pw.js +++ b/static/js/pw.js @@ -67,6 +67,9 @@ function draw(pathway, elem) { const horizontalSpacing = 75; // horizontal space between nodes const depthMap = new Map(); + // Avoid leaving unconnected Nodes leaving the viewport + nodes.forEach(node => {if (node.depth < 0) node.depth = 0;}); + // Sort nodes by depth first to minimize crossings const sortedNodes = [...nodes].sort((a, b) => a.depth - b.depth); @@ -154,6 +157,11 @@ function draw(pathway, elem) { }); node.attr("transform", d => `translate(${d.x},${d.y})`); + + linkText + .attr("x", d => (d.source.x + d.target.x) / 2) + .attr("y", d => (d.source.y + d.target.y) / 2); + } function dragstarted(event, d) { @@ -256,7 +264,7 @@ function draw(pathway, elem) { } // Wait before showing popup (ms) - var popupWaitBeforeShow = 1000; + var popupWaitBeforeShow = 750; // Custom popover element let popoverTimeout = null; @@ -488,7 +496,7 @@ function draw(pathway, elem) { if (n.stereo_removed) { popupContent += "Removed stereochemistry for prediction"; } - popupContent += "" + n.name + "
"; + popupContent += "" + n.plain_name + "
"; popupContent += "Depth " + n.depth + "
" if (appDomainViewEnabled) { @@ -528,6 +536,21 @@ function draw(pathway, elem) { popupContent += 'Half-lives and related scenarios:
' for (var s of n.scenarios) { popupContent += "" + s.name + "
"; + for (var prop in n.proposed) { + if (n.proposed[prop].scenarioId === s.url) { + if("proposed" in n.proposed[prop]){ + popupContent += "This compound is a proposed intermediate" + "
"; + } + if("Confidence" in n.proposed[prop]){ + popupContent += "Confidence: " + n.proposed[prop]["Confidence"] + "
"; + } + if("Transformation product importance" in n.proposed[prop]){ + popupContent += "Transformation product importance: " + n.proposed[prop]["Transformation product importance"] + "
"; + } + } + } + popupContent += "
"; + } } @@ -540,7 +563,7 @@ function draw(pathway, elem) { } function edge_popup(e) { - popupContent = "" + e.name + "

"; + popupContent = "" + e.plain_name + "

"; if (e.reaction.rules) { for (var rule of e.reaction.rules) { @@ -591,7 +614,7 @@ function draw(pathway, elem) { // Add background rectangle FIRST to enable pan/zoom on empty space // This must be inserted before zoomable group so it's behind everything - svg.insert("rect", "#zoomable") + const rect = svg.insert("rect", "#zoomable") .attr("x", 0) .attr("y", 0) .attr("width", width) @@ -600,6 +623,30 @@ function draw(pathway, elem) { .attr("pointer-events", "all") .style("cursor", "grab"); + // Click on empty SVG space (not on a node or link) + rect.on("click", function(event) { + // Only treat it as a background click if the direct target is the rect itself + // (clicks on nodes/links bubble up but originate from different elements) + const target = event.target; + const isNode = target.closest && ( + target.closest("circle") !== null || + target.closest("image") !== null || + target.closest(".node") !== null + ); + const isLink = target.closest && ( + target.closest("path.link") !== null || + target.closest("path.link_no_arrow") !== null + ); + if (!isNode && !isLink) { + // console.log("Clicked outside a node or link"); + // Clear all highlights + d3.selectAll("circle").classed("highlighted", false); + d3.selectAll("path").classed("highlighted", false); + d3.selectAll("path").classed("inedge", false); + d3.selectAll("path").classed("outedge", false); + } + }); + // Zoom Funktion aktivieren const zoom = d3.zoom() .scaleExtent([0.5, 5]) @@ -646,22 +693,32 @@ function draw(pathway, elem) { .force("center", d3.forceCenter(width / 2, height / 4)) .on("tick", ticked); - // Kanten zeichnen - const link = zoomable.append("g") - .selectAll("path") - .data(links) - .enter().append("path") - // Check if target is pseudo and draw marker only if not pseudo - .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link") - .attr("marker-end", d => { - if (d.target.pseudo) return ''; - if (d.source.id === d.target.id) return 'url(#curve-arrow)'; // Use curve arrow for self-loops - return d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)'; - }) - .attr("fill", "none") - .on("click", function(event, d) { + // Draw Edges + const linkGroup = zoomable.append("g") + .selectAll("g") + .data(links) + .enter() + .append("g") + .attr("class", "link-group"); + + const link = linkGroup + .append("path") + .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link") + .attr("marker-end", d => d.target.pseudo ? "" : "url(#arrow)") + .attr("fill", "none") + + // Check if target is pseudo and draw marker only if not pseudo + .attr("class", d => d.target.pseudo ? "link_no_arrow" : "link") + .attr("marker-end", d => { + if (d.target.pseudo) return ''; + if (d.source.id === d.target.id) return 'url(#curve-arrow)'; // Use curve arrow for self-loops + return d.multi_step ? 'url(#doublearrow)' : 'url(#arrow)'; + } + ) + .attr("fill", "none") + .on("click", function(event, d) { const wasHighlighted = d3.select(this).classed("highlighted"); - d3.selectAll("path").classed("highlighted", false); + d3.selectAll("path").classed("highlighted", false); if (!wasHighlighted) { const toHighlight = []; toHighlight.push(d.el); @@ -688,6 +745,32 @@ function draw(pathway, elem) { } }); + function reaction_name(d) { + const to_pseudo = d?.to_pseudo || false; + + if (to_pseudo) { + return ""; + } + + var suffix = ""; + if ("reaction_probability" in d && d["reaction_probability"] !== null) { + suffix = " (p= " + d["reaction_probability"].toFixed(2) + ")" + } + return d.plain_name + suffix; + } + + const linkText = linkGroup + .append("text") + .attr("class", "link-label") + .attr("text-anchor", "middle") + .attr("dy", -6) + .style("font-size", "4px") + .style("pointer-events", "none") + .style("display", "none") + .text(d => reaction_name(d)) + .attr("x", d => (d.source.x + d.target.x) / 2) + .attr("y", d => (d.source.y + d.target.y) / 2); + // add element to links array link.each(function (d) { d.el = this; // attach the DOM element to the data object @@ -695,7 +778,7 @@ function draw(pathway, elem) { pop_add(link, "Reaction", edge_popup); - // Knoten zeichnen + // Draw Nodes const node = zoomable.append("g") .selectAll("g") .data(nodes) diff --git a/templates/objects/node.html b/templates/objects/node.html index 5f5515f9..043342b4 100644 --- a/templates/objects/node.html +++ b/templates/objects/node.html @@ -55,6 +55,14 @@ + + {% if node.description and node.description != "no description" %} +
+ +
Description
+
{{ node.description }}
+
+ {% endif %} {% epdb_slot_templates "epdb.objects.node.viz" as viz_templates %} {% for tpl in viz_templates %} diff --git a/templates/objects/pathway.html b/templates/objects/pathway.html index 9cd9cf58..2ec30a49 100644 --- a/templates/objects/pathway.html +++ b/templates/objects/pathway.html @@ -21,12 +21,13 @@ .link { stroke: #999; stroke-opacity: 0.6; - /* marker-end: url(#arrow); */ + stroke-width: 1.5px; } .link_no_arrow { stroke: #999; stroke-opacity: 0.6; + stroke-width: 1.5px; } .node image { @@ -177,6 +178,52 @@ tabindex="0" class="dropdown-content menu bg-base-100 rounded-box z-50 w-60 p-2" > +
  • + + + + + + Compound Names + +
    • +
  • + + + + + + Reaction Names + +
    • {% if pathway.setting.model.app_domain %}
  • @@ -495,6 +542,10 @@ {{ pathway.d3_json|json_script:"pathway" }}