Reactome pathway alignment: urea_cycle

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Generated by ingest_reactome_pathways.py from R-HSA-70635 using whole_subtree scope.

Counts

Measure	Count
Imported events	19
Imported reaction-like events	17
Activity-level cited event matches	7
Full executor/MF matches	1
Same-reaction rows needing review	6
Reactome-only reaction-like events	10
Module-only activity Reactome IDs	1
Same-executor fuzzy links	1
Reactome-only black-box events	4

Activity-Level Cited Event Matches

Reactome ID	Verdict	Basis	Node	Annoton	Function	Event
R-HSA-70542	same_reaction_executor_unconfirmed	cited_reactome_id, executor_match_via_complex, mf_match	nags_step	nags_activity	GO:0004042	glutamate + acetyl CoA => N-acetyl glutamate + CoA
R-HSA-70555	reaction_id_exact	cited_reactome_id, executor_match_exact, mf_match	cps1_step	cps1_activity	GO:0004087	2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate [mitochondrial]
R-HSA-70560	same_reaction_executor_unconfirmed	cited_reactome_id, executor_match_via_complex, mf_match	otc_step	otc_activity	GO:0004585	carbamoyl phosphate + ornithine => citrulline + orthophosphate
R-HSA-70569	same_reaction_executor_unconfirmed	cited_reactome_id, executor_match_via_complex, mf_match	arg1_step	arg1_activity	GO:0004053	arginine + H2O => ornithine + urea [ARG1]
R-HSA-70573	same_reaction_executor_unconfirmed	cited_reactome_id, executor_match_via_complex, mf_match	asl_step	asl_activity	GO:0004056	argininosuccinate <=> fumarate + arginine
R-HSA-70577	same_reaction_executor_unconfirmed	cited_reactome_id, executor_match_via_complex, mf_match	ass1_step	ass1_activity	GO:0004055	ASS1 tetramer:NMRAL1 dimer:NADPH transforms L-Asp and L-Cit to ARSUA
R-HSA-70634	same_reaction_executor_unconfirmed	cited_reactome_id, executor_match_via_set, mf_match	ornithine_citrulline_transport	slc25a15_activity	GO:0000064	ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic)

Same-Reaction Rows Needing Review

Reactome ID	Verdict	Basis	Node	Annoton	Event
R-HSA-70542	same_reaction_executor_unconfirmed	cited_reactome_id, executor_match_via_complex, mf_match	nags_step	nags_activity	glutamate + acetyl CoA => N-acetyl glutamate + CoA
R-HSA-70560	same_reaction_executor_unconfirmed	cited_reactome_id, executor_match_via_complex, mf_match	otc_step	otc_activity	carbamoyl phosphate + ornithine => citrulline + orthophosphate
R-HSA-70569	same_reaction_executor_unconfirmed	cited_reactome_id, executor_match_via_complex, mf_match	arg1_step	arg1_activity	arginine + H2O => ornithine + urea [ARG1]
R-HSA-70573	same_reaction_executor_unconfirmed	cited_reactome_id, executor_match_via_complex, mf_match	asl_step	asl_activity	argininosuccinate <=> fumarate + arginine
R-HSA-70577	same_reaction_executor_unconfirmed	cited_reactome_id, executor_match_via_complex, mf_match	ass1_step	ass1_activity	ASS1 tetramer:NMRAL1 dimer:NADPH transforms L-Asp and L-Cit to ARSUA
R-HSA-70634	same_reaction_executor_unconfirmed	cited_reactome_id, executor_match_via_set, mf_match	ornithine_citrulline_transport	slc25a15_activity	ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic)

Reactome-Only Reaction-Like Events

Reactome ID	Verdict	Candidate local activities	Class	Catalyst members	Event
R-HSA-452036	same_executor_different_reaction	arg1_step/arg1_activity	Reaction	UniProtKB:P78540	arginine + H2O => ornithine + urea [ARG2]
R-HSA-9955504	reactome_only_event		Reaction	UniProtKB:Q9NXA8	SIRT5 deglutarylates CPS1
R-HSA-9955518	reactome_only_event		Reaction	UniProtKB:Q9NXA8	SIRT5 desuccinylates CPS1
R-HSA-9956502	black_box_event		BlackBoxEvent	no catalyst members	OTC precursor is targeted to the mitochondrial matrix and processed
R-HSA-9959857	reactome_only_event		Reaction	UniProtKB:P04637	TP53 binds ARG1 gene
R-HSA-9959860	reactome_only_event		Reaction	UniProtKB:P04637	TP53 binds CPS1 gene
R-HSA-9959863	reactome_only_event		Reaction	UniProtKB:P04637	TP53 binds OTC gene
R-HSA-9959871	black_box_event		BlackBoxEvent	no catalyst members	ARG1 gene expression
R-HSA-9959874	black_box_event		BlackBoxEvent	no catalyst members	CPS1 gene expression
R-HSA-9959881	black_box_event		BlackBoxEvent	no catalyst members	OTC gene expression

Module-Only Activity Evidence

Reactome ID	Verdict	Candidate imported events	Node	Annoton	Function
R-HSA-372448	module_only_event		citrin_aspartate_supply	slc25a13_activity	GO:0015183