Activator convergence audit

Generated by audit_activator_convergence.py; do not edit by hand. Part of EXECUTABLE_MODELS. Full detail, including each connection's description, is in activator_convergence_audit.yaml.

Every step with two or more activating regulators, which the Boolean translation would OR together by default. ALTERNATIVE_VARIANTS steps are settled by the module's own structure (the activators are alternative variants); DECLARED steps carry activation_logic; UNDECIDED steps need a curator to read the module.

274 steps in 150 modules: ALTERNATIVE_VARIANTS 40, DECLARED 8, UNDECIDED 226.

module	step	classification	default rule	declared rule
`adrenal_steroidogenesis`	17alpha-hydroxylation and 17,20-lyase (to 17OH-steroids and DHEA/androstenedione)	UNDECIDED	`(cyp11a1_step \| hsd3b2_step)`
`adrenal_steroidogenesis`	21-hydroxylation (progesterone to DOC; 17OH-progesterone to 11-deoxycortisol)	UNDECIDED	`(cyp17a1_step \| hsd3b2_step)`
`alginate_polymerization_export`	AlgK secretion scaffold	UNDECIDED	`(alg8_alg44_synthase \| algG_maturation)`
`aliphatic_glucosinolate_myrosinase_defense`	Methylthioalkylmalate synthase (MAM)	UNDECIDED	`(ipmdh_decarboxylation \| met_deamination)`
`aliphatic_glucosinolate_myrosinase_defense`	Myrosinase (thioglucosidase) hydrolysis	UNDECIDED	`(alkenylation \| sulfation)`
`arginine_biosynthesis`	N-acetyl-L-glutamate to N-acetyl-L-glutamyl 5-phosphate	UNDECIDED	`(argJ_transacetylation_variant \| glutamate_acetylation_step)`
`arginine_biosynthesis`	L-ornithine to L-citrulline	UNDECIDED	`(argE_deacetylation_variant \| argJ_transacetylation_variant \| carbamoyl_phosphate_synthetase_a_step)`
`auxin_polar_transport`	PIN-mediated polar auxin efflux	UNDECIDED	`(abcb_auxin_export \| auxin_influx \| pin_kinase_regulation)`
`bacterial_c_di_amp_signaling`	Phosphodiesterase hydrolysis of c-di-AMP to pApA	UNDECIDED	`(c_di_amp_synthesis \| papa_clearance)`
`bacterial_chemotaxis_signal_transduction`	Flagellum-dependent motility output	UNDECIDED	`(c_ring_motor_switch \| flagellar_stator_conductance)`
`bacterial_chromosomal_dna_replication`	DNA polymerase III alpha-epsilon core	UNDECIDED	`(beta_clamp_processivity \| dnag_priming)`
`bacterial_cytochrome_c_maturation_system_i`	CcmE heme chaperone	UNDECIDED	`(ccmc_heme_handling_subunit \| ccmd_accessory_subunit)`
`bacterial_cytochrome_c_maturation_system_i`	CcmF/CcmH heme-ligation machinery	UNDECIDED	`(ccmab_energy_coupling \| ccmh_redox_component)`
`bacterial_flagellar_assembly_export`	Hook-filament junction, flagellin filament, and cap	UNDECIDED	`(flagellar_late_transcription \| rod_hook_assembly)`
`bacterial_rna_degradation`	Processive 3'-to-5' RNA degradation	UNDECIDED	`(degradosome_helicase_assistance \| rne_endonucleolytic_cleavage)`
`bacterial_rna_polymerase_core`	RpoB/RpoC catalytic cleft	UNDECIDED	`(rpoa_alpha_dimer_platform \| rpoz_omega_assembly_subunit)`
`bacterial_ruvabc_holliday_junction_processing`	RuvC cleavage and resolution of the Holliday junction	UNDECIDED	`(recg_branch_migration \| ruvb_branch_migration)`
`bacterial_twin_arginine_translocation`	Active Tat translocon assembly	UNDECIDED	`(tatb_receptor_organization \| tatc_substrate_recognition)`
`bacterial_type_ii_secretion`	Type II secretion pseudopilus	UNDECIDED	`(inner_membrane_platform \| secretion_atpase)`
`bile_acid_biosynthesis`	3-beta-hydroxy-Delta5-C27-steroid dehydrogenase (HSD3B7)	UNDECIDED	`(cholesterol_7a_hydroxylation \| oxysterol_7a_hydroxylation)`
`bile_acid_synthesis_ring_modification`	7-alpha-hydroxycholesterol to 7-alpha-hydroxy-4-cholesten-3-one	UNDECIDED	`(cyp7a1_step \| cyp7b1_step)`
`bile_acid_synthesis_sidechain_conjugation`	choloyl-CoA + glycine/taurine to glyco-/tauro-cholate	UNDECIDED	`(acox2_step \| slc27a5_step)`
`branched_chain_amino_acid_biosynthesis`	Branched-chain 2-oxoacids to L-valine, L-leucine, and L-isoleucine	UNDECIDED	`(ilvD_step \| leuB_step)`
`branched_chain_amino_acid_biosynthesis`	2-Isopropylmalate to 3-isopropylmalate	UNDECIDED	`(ipm_export_step \| leuA_step)`
`c_elegans_cgmp_sensory_transduction`	TAX-4/TAX-2 heteromeric cyclic nucleotide-gated channel	UNDECIDED	`(afd_thermosensory_rgc \| daf11_gc \| o2_sensing_sgc \| odr1_gc)`
`c_elegans_lysosomal_lipid_signaling`	LBP-8 lipid chaperone shuttle	UNDECIDED	`(lipl4_lysosomal_lipolysis \| nhr_reception)`
`c_elegans_mutator_22g_rna_amplification`	RDE-3/MUT-2 poly(UG) tailing of target RNA	UNDECIDED	`(mut14_helicase \| mutator_scaffold \| rde8_endonuclease)`
`c_elegans_mutator_22g_rna_amplification`	RRF-1 RNA-dependent RNA polymerase synthesis of 22G-RNAs	UNDECIDED	`(mutator_scaffold \| pug_tailing)`
`c_elegans_mutator_22g_rna_amplification`	Mutator-dependent WAGO silencing branch	UNDECIDED	`(ego1_rdrp \| rdrp_synthesis)`
`c_elegans_p_granule_assembly_segregation`	PGL self-associating RNA-binding scaffold core	UNDECIDED	`(glh_perinuclear_layer \| meg_embryonic_shell) & !mex_gradient`
`camalexin_biosynthesis`	Indole cyanohydrin / dehydro-IAN formation	UNDECIDED	`(iaox_formation \| wrky33_activity)`
`camalexin_biosynthesis`	CYP71B15/PAD3: dihydrocamalexate synthase (no GO term yet)	UNDECIDED	`(ggp_step \| wrky33_activity)`
`cardiac_specification_network`	Cardiogenic GATA factor	UNDECIDED	`(nk2_factor \| tbox_factor)`
`cardiac_specification_network`	Hand bHLH factor	UNDECIDED	`(gata_factor \| nk2_factor)`
`cardiac_specification_network`	MEF2 myocardial differentiation factor	UNDECIDED	`(gata_factor \| nk2_factor)`
`carnitine_shuttle`	acylcarnitine (cytosolic side) / carnitine (matrix) antiport	UNDECIDED	`(cpt1_step \| cpt2_step)`
`cdp_dag_phospholipid_synthesis`	CDP-DAG-dependent cardiolipin synthase (CRD1)	UNDECIDED	`(cdp_dag_synthesis \| pgp_dephosphorylation)`
`cellulose_biosynthesis`	(1->4)-beta-D-glucan polymerization by the CSC	UNDECIDED	`(accessory_factors \| microtubule_guidance \| udp_glucose_supply)`
`cerebellum_development`	Purkinje-cell DNER contribution to Bergmann-glial maturation	UNDECIDED	`(early_purkinje_plate_formation \| gcp_smoothened_transducer \| purkinje_shh_signal)`
`cerebellum_development`	SMO transducer in granule-cell precursors	UNDECIDED	`(early_purkinje_plate_formation \| germinal_zone_lineage_specification \| purkinje_shh_signal)`
`cerebellum_development`	Granule-cell inward migration	UNDECIDED	`(early_purkinje_plate_formation \| gcp_smoothened_transducer \| purkinje_shh_signal)`
`cerebellum_development`	PTPN11-ERK Bergmann-glial specification program	UNDECIDED	`(early_purkinje_plate_formation \| gcp_smoothened_transducer \| purkinje_shh_signal)`
`cerebellum_development`	Regional cerebellar foliation	UNDECIDED	`(dner_purkinje_signal \| gcp_smoothened_transducer \| granule_cell_migration \| ptpn11_erk_bg_specification)`
`cholesterol_synthesis_post_lanosterol`	Delta24-sterol to 24,25-dihydro sterol (desmosterol to cholesterol; zymosterol to zymostenol)	UNDECIDED	`(dhcr7_step \| hsd17b7_step)`
`cholesterol_synthesis_post_lanosterol`	Delta(8)-sterol to Delta(7)-sterol	UNDECIDED	`(dhcr24_step \| hsd17b7_step)`
`ciliary_transition_zone`	MKS module	UNDECIDED	`(cep290_module \| mks5_assembly_hub)`
`coenzyme_a_biosynthesis`	Pantoate to 4-phosphopantoate	UNDECIDED	`(aminopropanal_dehydrogenase_step \| aspartate_decarboxylation_route \| ketopantoate_reductase_step)`
`coenzyme_a_biosynthesis`	(R)-pantoate and beta-alanine to pantothenate	UNDECIDED	`(aminopropanal_dehydrogenase_step \| aspartate_decarboxylation_route \| ketopantoate_reductase_step)`
`coenzyme_q10_biosynthesis`	C1 decarboxylation (COQ4) and C1 hydroxylation (COQ6)	UNDECIDED	`(c5_hydroxylation \| synthome_regulation)`
`coenzyme_q10_biosynthesis`	3-demethoxyubiquinone hydroxylase (COQ7)	UNDECIDED	`(c2_methylation \| substrate_presentation)`
`complex_i_assembly_factors`	Q-module intermediate assembly (NDUFAF3-NDUFAF4, NDUFAF6)	UNDECIDED	`(ci_membrane_arm_assembly \| ci_subunit_maturation)`
`complex_iv_assembly_factors`	incorporation of the early COX7/COX8 nuclear subunits	UNDECIDED	`(cua_metallation \| cub_metallation)`
`conidiation_regulatory_cascade`	BrlA master-switch induction	UNDECIDED	`(flbB \| flbC \| flbD \| flbE \| fluG)`
`conidiation_regulatory_cascade`	FL fluffy master regulator	UNDECIDED	`(neu_acon2 \| neu_frq \| neu_wc1 \| neu_wc2)`
`creatine_phosphocreatine_system`	Phosphocreatine shuttle / creatine kinase system (see MODULE:phosphocreatine_shuttle)	UNDECIDED	`(biosynthesis_part \| transport_part)`
`cuproptosis`	FDX1-mediated Cu(II) reduction (master trigger)	UNDECIDED	`(atox1_copper_chaperone \| copper_exporting_atpase \| ctr1_copper_import)`
`cuproptosis`	Lipoylated pyruvate dehydrogenase complex (copper targets)	UNDECIDED	`(fdx1_trigger \| lipoylation_machinery)`
`dolichol_phosphate_sugar_donor_supply`	presentation/utilisation of Dol-P-Man and Dol-P-Glc	UNDECIDED	`(alg5_step \| dpm_complex_step)`
`emp_glycolysis`	Ferredoxin-dependent oxidation (archaeal GAPOR)	UNDECIDED	`(aldolase_step \| tpi_step)`
`emp_glycolysis`	G3P + phosphate + NAD(P)+ to 1,3-bisphospho-D-glycerate	UNDECIDED	`(aldolase_step \| tpi_step)`
`emp_glycolysis`	Non-phosphorylating NADP+ oxidation (GAPN bypass)	UNDECIDED	`(aldolase_step \| tpi_step)`
`er_unfolded_protein_response`	BiP ER HSP70 chaperones	UNDECIDED	`(atf6_arm \| hac1_transcription_factor \| xbp1_transcription_factor)`
`ergosterol_biosynthesis`	lanosterol to 4,4-dimethylcholesta-8,14,24-trienol + formate	UNDECIDED	`(erg7_step \| ncp1_activity)`
`ergosterol_biosynthesis`	squalene + O2 + reduced P450 reductase to (S)-2,3-epoxysqualene	UNDECIDED	`(erg9_step \| ncp1_activity)`
`ergosterol_biosynthesis`	4-methyl sterol to 4-carboxy sterol (three successive oxidations; twice per sterol)	UNDECIDED	`(cyb5_activity \| erg24_step)`
`ergosterol_biosynthesis`	episterol to ergosta-5,7,24(28)-trienol	UNDECIDED	`(cyb5_activity \| erg2_step)`
`ergosterol_biosynthesis`	ergosta-5,7,24(28)-trienol to ergosta-5,7,22,24(28)-tetraenol	UNDECIDED	`(erg3_step \| ncp1_activity)`
`ergosterol_biosynthesis`	(S)-2,3-epoxysqualene to lanosterol	UNDECIDED	`(erg1_step \| erg27_activity)`
`erythromycin_biosynthesis`	EryBV attaches L-mycarose to erythronolide B	UNDECIDED	`(eryF_step \| mycarose_pathway)`
`erythromycin_biosynthesis`	EryCIII (activated by EryCII) attaches D-desosamine, forming erythromycin D	UNDECIDED	`(desosamine_pathway \| eryBV_step)`
`ether_lipid_plasmalogen_biosynthesis`	Alkyldihydroxyacetone-phosphate synthase (AGPS)	UNDECIDED	`(dhap_acylation \| fatty_alcohol_synthesis)`
`eukaryotic_thiamine_biosynthesis`	HMP-P to HMP-PP	UNDECIDED	`(hmp_kinase_step \| thi5_hmpp_synthase_step)`
`eukaryotic_thiamine_biosynthesis`	Thiazole phosphate + HMP-PP to thiamine monophosphate (THI6)	UNDECIDED	`(adt_processing_step \| het_kinase_step \| hmpp_kinase_step)`
`ferroptosis`	Ferroptosis execution	UNDECIDED	`(labile_iron_supply \| pufa_phospholipid_supply) & !(dhodh_coq_defense \| fsp1_coq_defense \| gch1_bh4_defense \| gpx4_gsh_defense)`
`ferroptosis`	GPX4-glutathione defense	UNDECIDED	`(atf4_isr_inducer \| nrf2_master_antioxidant) & !tp53_context_regulator`
`floral_meristem_identity`	AP1/CAL/FUL establish floral fate	UNDECIDED	`(integrator_input \| lfy_program) & !tfl1_inflorescence_maintenance`
`floral_meristem_identity`	LEAFY floral meristem identity program	UNDECIDED	`(ap1_floral_fate \| integrator_input) & !tfl1_inflorescence_maintenance`
`floral_organ_identity_abce`	Whorl-specific floral quartet complexes	UNDECIDED	`(b_function \| e_function)`
`folate_one_carbon_interconversion`	5,10-methenyl-THF to 10-formyl-THF hydrolysis	UNDECIDED	`(formyl_folate_salvage \| methylene_methenyl_redox)`
`g1_s_transition`	Activator E2F transcription factor	UNDECIDED	`(g1_cdk_priming \| g1s_cdk_activation) & !rb_corepressor`
`g1_s_transition`	Fission-yeast MBF (Cdc10-Res1-Res2)	UNDECIDED	`(g1_cdk_priming \| g1s_cdk_activation)`
`g1_s_transition`	G1/S cyclin-CDK activation	UNDECIDED	`(e2f_activator \| fission_yeast_mbf \| sbf_mbf \| scf_ligase)`
`g1_s_transition`	SBF/MBF transcription factor	UNDECIDED	`(g1_cdk_priming \| g1s_cdk_activation) & !whi5_corepressor`
`g2_m_transition`	Cdc25 dephosphorylation of CDK1 Tyr15/Thr14	UNDECIDED	`(cdk1_cyclinb_assembly \| polo_reinforcement \| wee1_inhibition) & !checkpoint_restraint`
`g2_m_transition`	Cyclin B-CDK1 assembly and CAK phosphorylation	UNDECIDED	`(cdc25_activation \| endosulfine \| pp2a_b55)`
`g2_m_transition`	Inhibitory Tyr15/Thr14 phosphorylation by Wee1/Myt1	UNDECIDED	`(cdk1_cyclinb_assembly \| checkpoint_restraint) & !(cdk1_cyclinb_assembly \| polo_reinforcement)`
`galactose_leloir_pathway`	alpha-D-galactose 1-phosphate + UDP-glucose to glucose-1-phosphate + UDP-galactose	UNDECIDED	`(gale_step \| galk1_step)`
`gibberellin_della_signaling`	PIF-driven growth transcription	UNDECIDED	`(della_degradation \| della_recognition)`
`glutathione_synthesis_gamma_glutamyl_cycle`	Cys-Gly dipeptidase (DUG1/CNDP2 M20A family)	UNDECIDED	`(dug2_dug3_gsh_cleavage \| extracellular_gsh_breakdown \| intracellular_gsh_degradation)`
`glutathione_synthesis_gamma_glutamyl_cycle`	gamma-glutamyl transpeptidase (GGT)	UNDECIDED	`(glutathione_recycling \| glutathione_synthesis)`
`glutathione_synthesis_gamma_glutamyl_cycle`	5-oxoprolinase (OPLAH)	UNDECIDED	`(gamma_glutamyl_cyclization \| intracellular_gsh_degradation)`
`glutathione_thioredoxin_redox_systems`	Thioredoxin-dependent thiol peroxidases	UNDECIDED	`(sod_step \| trx_step)`
`glycogen_biosynthesis`	glycogen(n) + UDP-glucose to glycogen(n+1) + UDP	UNDECIDED	`(gbe1_step \| gyg1_step \| ugp2_step)`
`glycogen_synthesis_and_mobilization`	GlgP-dependent glycogen phosphorolysis	UNDECIDED	`(glgb_branch_formation \| glgx_branch_removal)`
`glycolate_glyoxylate_assimilation`	Tartronate semialdehyde to glycerate	UNDECIDED	`(glyoxylate_carboligase \| hydroxypyruvate_isomerization)`
`glycosphingolipid_biosynthesis`	GM2/GD2 synthase (B4GALNT1)	UNDECIDED	`(ganglio_gd3 \| ganglio_gm3)`
`glycosphingolipid_lysosomal_degradation`	ceramide to sphingosine + fatty acid	UNDECIDED	`(galc_step \| gba_step \| smpd1_step)`
`heat_shock_response`	Cytosolic Hsp70 folding cycle with J-domain, HSP110 and BAG cofactors	UNDECIDED	`(hsf_activation \| shsp_holdase)`
`hedgehog_signaling`	Slimb/beta-TrCP SCF substrate adaptor	UNDECIDED	`(ck1_processive_kinase \| gsk3_processive_kinase)`
`hedgehog_signaling`	SUFU release and Fused-family phosphorylation of Ci/GLI	UNDECIDED	`(smo_pka_inhibition \| smo_transducer)`
`hedgehog_signaling`	Smoothened pseudosubstrate inhibition of protein kinase A	UNDECIDED	`(hh_coreceptor \| hspg_ligand_distribution \| patched_receptor \| vertebrate_secreted_accessories)`
`hedgehog_signaling`	Smoothened transducer	UNDECIDED	`(hh_coreceptor \| hspg_ligand_distribution \| patched_receptor \| vertebrate_secreted_accessories) & !patched_receptor`
`hexosamine_biosynthesis`	Phosphoacetylglucosamine mutase (PGM3)	UNDECIDED	`(glcn6p_acetylation \| glcnac_salvage)`
`homocysteine_metabolism`	L-homocysteine + 5-methyl-THF to L-methionine + THF	UNDECIDED	`(cobalamin_support \| mthfr_step)`
`intraflagellar_transport`	Accessory homodimeric kinesin-2 transport	UNDECIDED	`(dyf5_regulation \| kinesin_ii_import)`
`intraflagellar_transport`	Heterotrimeric kinesin-II transport of IFT trains	UNDECIDED	`(ift_a_complex \| ift_b_complex) & !dyf5_regulation`
`jak_stat_signaling`	STAT recruitment and phosphorylation	UNDECIDED	`(alt_stat_inputs \| receptor_phosphorylation)`
`lignin_monolignol_biosynthesis`	Monolignol transport across the plasma membrane	UNDECIDED	`(c3h_step \| cad_step \| ccoaomt_step \| comt_step \| hct_step)`
`lipid_a_raetz_biosynthesis`	Lipid A disaccharide synthesis	UNDECIDED	`(lpxD_step \| lpxH_step)`
`malate_aspartate_shuttle`	Inner-membrane carriers (SLC25A11 OGC, SLC25A12 AGC1)	UNDECIDED	`(mas_cytosolic_arm \| mas_matrix_arm)`
`metaphase_anaphase_transition_and_mitotic_exit`	Cdh1/Hct1/Ste9 coactivator	UNDECIDED	`(apc_c \| cdc14_scer \| clp1_spom \| cohesin_kleisin \| metazoan_pp2a_b55_reactivation)`
`metazoan_autophagosome_biogenesis`	LC3-subfamily Atg8 in phagophore elongation	UNDECIDED	`(atg8_conjugation \| cargo_recruitment)`
`metazoan_autophagosome_biogenesis`	GABARAP-type LGG-1 in autophagosome formation	UNDECIDED	`(atg8_conjugation \| cargo_recruitment)`
`methionine_cycle`	S-adenosyl-L-homocysteine -> L-homocysteine	UNDECIDED	`(gnmt_activity \| meth_activity)`
`methionine_cycle`	Cystathionine beta-synthase activity	UNDECIDED	`(ahc_step \| amet_pool)`
`methionine_cycle`	Glycine N-methyltransferase activity	UNDECIDED	`(amet_pool \| mat1_activity \| mat3_activity) & !(ahcys_pool \| mlthf_pool)`
`methionine_cycle`	MAT-III methionine adenosyltransferase activity	UNDECIDED	`(amet_pool \| bhmt_route \| met_pool \| mete_route \| ms_route)`
`methionine_cycle`	Folate-dependent remethylation, cobalamin-independent (MetE-type methionine synthase)	UNDECIDED	`(ahc_step \| mthfr_activity)`
`methionine_cycle`	Folate-dependent remethylation, cobalamin-dependent (MetH/MTR-type methionine synthase)	UNDECIDED	`(ahc_step \| mthfr_activity)`
`mitochondrial_complex_v`	F1 sector (alpha3-beta3 catalytic head + central stalk)	UNDECIDED	`(complex_v_assembly \| complex_v_fo)`
`mitochondrial_upr`	HSP60 and mtHSP70 matrix chaperone output	UNDECIDED	`(dve1_activator \| jmjd31_demethylase \| lin65_cofactor \| ubl5_coactivator \| uprmt_transcription_factor)`
`mitochondrial_upr`	ATFS-1/ATF5 nuclear transcriptional activation	UNDECIDED	`(atf4_isr_activation \| atfs1_import_checkpoint \| dve1_activator \| hri_eif2a_phosphorylation \| jmjd31_demethylase \| lin65_cofactor \| ubl5_coactivator) & !atfs1_import_checkpoint`
`muth_independent_mismatch_repair`	DNA polymerase-dependent gap filling	UNDECIDED	`(excision_nuclease_choice \| ssb_excision_scaffold)`
`neural_crest_gene_regulatory_network`	FoxD3 crest specifier	UNDECIDED	`(id3_competence \| myc_competence \| pax3_border \| pax7_border \| pou5f3_competence \| tfap2c_border \| zic1_border)`
`neural_crest_gene_regulatory_network`	Neural crest delamination and migration	UNDECIDED	`(foxd3_spec \| snai2_spec \| sox10_variant \| sox8_spec \| sox9_variant \| tfap2a_spec \| tfap2b_spec)`
`neural_crest_gene_regulatory_network`	Pax3 border specifier	UNDECIDED	`(gbx2_border \| msx1_border \| pou5f3_competence \| tfap2a_border)`
`neural_crest_gene_regulatory_network`	Snail1 early crest specifier	UNDECIDED	`(id3_competence \| myc_competence \| pax3_border \| pax7_border \| pou5f3_competence \| tfap2c_border \| zic1_border)`
`neural_crest_gene_regulatory_network`	Snai2 crest specifier	UNDECIDED	`(pax3_border \| snai1_spec) & !twist1_snai2_inhibition`
`neural_crest_gene_regulatory_network`	Sox10	UNDECIDED	`(id3_competence \| myc_competence \| pax3_border \| pax7_border \| pou5f3_competence \| tfap2c_border \| zic1_border)`
`neural_crest_gene_regulatory_network`	Sox8 crest specifier	UNDECIDED	`(id3_competence \| myc_competence \| pax3_border \| pax7_border \| pou5f3_competence \| tfap2c_border \| zic1_border)`
`neural_crest_gene_regulatory_network`	Sox9	UNDECIDED	`(id3_competence \| myc_competence \| pax3_border \| pax7_border \| pou5f3_competence \| tfap2c_border \| zic1_border)`
`neural_crest_gene_regulatory_network`	AP-2alpha crest specifier	UNDECIDED	`(id3_competence \| myc_competence \| pax3_border \| pax7_border \| pou5f3_competence \| tfap2c_border \| zic1_border)`
`neural_crest_gene_regulatory_network`	AP-2beta (TFAP2A–TFAP2B) crest specifier	UNDECIDED	`(id3_competence \| myc_competence \| pax3_border \| pax7_border \| pou5f3_competence \| tfap2c_border \| zic1_border)`
`neural_crest_gene_regulatory_network`	Twist1 ectomesenchyme driver	UNDECIDED	`(neural_crest_emigration \| pax3_border)`
`nicotine_biosynthesis`	nicotinic acid N-glucoside reduction (A622 / NaGR)	UNDECIDED	`(mpo_step \| ugt_step)`
`nitrogen_assimilation_glutamate_glutamine`	L-glutamate + ammonium + ATP to L-glutamine	UNDECIDED	`(glutamate_deamination_step \| gs_gogat_route \| nadp_gdh_route)`
`nitrogen_cycle`	Ammonia assimilation (GS/GOGAT cycle)	UNDECIDED	`(assim_nitrite_reduction \| nitrogen_fixation)`
`notch_signaling`	Notch receptor binds ligand in trans	UNDECIDED	`(notch_fringe_elongation \| notch_ligand_presentation) & !notch_cis_inhibition`
`notch_signaling`	Notch target gene output	UNDECIDED	`(csl_dna_binding \| mastermind_coactivation)`
`nucleokinesis`	Dynein-dynactin-LIS1-NDEL1 nuclear motor	UNDECIDED	`(nuclear_envelope_motor_coupling \| perinuclear_microtubule_track)`
`oxphos`	F1 catalytic head	UNDECIDED	`(complex_IV \| respiratory_chain_variants)`
`oxphos`	Fo proton-translocating sector	UNDECIDED	`(complex_IV \| respiratory_chain_variants)`
`oxphos`	Proton-motive-force-driven ATP synthesis (rotational)	UNDECIDED	`(complex_IV \| respiratory_chain_variants) & !if1_inhibitor`
`oxphos`	Quinone pool (ubiquinone/menaquinone)	UNDECIDED	`(auxiliary_quinone_dehydrogenases \| complex_I \| complex_II)`
`pentose_phosphate_nonoxidative_branch`	D-xylulose-5-P + D-ribose-5-P to sedoheptulose-7-P + D-glyceraldehyde-3-P	UNDECIDED	`(rpe_step \| rpia_step)`
`pentose_phosphate_pathway`	Transketolase: xylulose 5-phosphate plus ribose 5-phosphate	UNDECIDED	`(ribose_5_phosphate_isomerase_step \| ribulose_phosphate_epimerase_step)`
`pentose_phosphate_pathway`	Transketolase: xylulose 5-phosphate plus erythrose 4-phosphate	UNDECIDED	`(ribulose_phosphate_epimerase_step \| transaldolase_step)`
`peptidoglycan_precursor_biosynthesis`	MurF pentapeptide ligation	UNDECIDED	`(ddl_dipeptide_synthesis \| murE_third_residue_ligation)`
`peptidoglycan_recycling`	AnmK formation of MurNAc-6-phosphate	UNDECIDED	`(ampD_peptide_release_step \| nagZ_glycan_processing_step)`
`peptidoglycan_recycling`	Mpl ligation of the recovered tripeptide to UDP-MurNAc	UNDECIDED	`(ampD_peptide_release_step \| murU_step)`
`peroxisomal_beta_oxidation`	Acyl-CoA oxidases	UNDECIDED	`(intraperoxisomal_activation \| thiolytic_cleavage)`
`peroxisomal_beta_oxidation`	Multifunctional proteins (D-specific MFE-2; L-specific bifunctional protein)	UNDECIDED	`(acyl_coa_oxidation \| enoyl_coa_isomerisation)`
`phagophore_assembly_site`	Atg1-dependent Atg13 phosphorylation and Atg1 complex dissociation	UNDECIDED	`(pas_atg2_atg18 \| pas_atg8_conjugation \| pas_membrane_component \| pas_pi3k_complex_i)`
`phagophore_organelle_contact_site`	ATG2-family ER-phagophore membrane tether	UNDECIDED	`(atg9_rim_scramblase \| wipi4_atg18_clamp)`
`phagophore_organelle_contact_site`	Lipid flux through the contact site	UNDECIDED	`(atg2_clr_rim_anchor \| atg2_tether \| donor_membrane_face) & !escrt_iii_rim_sealing`
`phenylalanine_tyrosine_biosynthesis`	phenylpyruvate / 4-hydroxyphenylpyruvate to L-phenylalanine / L-tyrosine	UNDECIDED	`(pdh_step \| pdt_step)`
`photosynthesis`	NADP-dependent glyceraldehyde-3-phosphate dehydrogenase	UNDECIDED	`(atp_synthase \| light_harvesting) & !cp12_scaffold`
`photosynthesis`	Phosphoribulokinase	UNDECIDED	`(atp_synthase \| light_harvesting) & !cp12_scaffold`
`photosynthesis`	Bisphosphatase regeneration steps (FBPase, SBPase)	UNDECIDED	`(atp_synthase \| light_harvesting)`
`photosynthesis`	Rubisco activase and inhibitor removal	UNDECIDED	`(atp_synthase \| light_harvesting)`
`photosynthesis`	Rubisco carboxylation of RuBP	UNDECIDED	`(atp_synthase \| carbon_concentrating_mechanism \| light_harvesting)`
`polyamine_metabolism`	FAD-dependent polyamine oxidation	UNDECIDED	`(polyamine_acetylation \| spermidine_to_spermine)`
`polyamine_metabolism`	Spermidine synthase	UNDECIDED	`(ornithine_to_putrescine \| sam_decarboxylation)`
`polyamine_metabolism`	Spermine synthase	UNDECIDED	`(putrescine_to_spermidine \| sam_decarboxylation)`
`pqq_biosynthesis`	PqqC terminal PQQ formation	UNDECIDED	`(pqqa_proteolysis \| pqqb_oxygenation)`
`primary_cilium_life_cycle`	ARL13B activates ARL3	UNDECIDED	`(ift81_ift74_tubulin \| ift_a_complex \| ift_b_scaffold)`
`primary_cilium_life_cycle`	ARL3 releases lipidated cargo	UNDECIDED	`(arl13b_arl3_gef \| pde6d_prenyl_carrier \| unc119b_myristoyl_carrier) & !rp2_arl3_gap`
`primary_cilium_life_cycle`	Aurora A drives disassembly	UNDECIDED	`(nedd9_aurka_activation \| pitchfork_aurka_activation)`
`primary_cilium_life_cycle`	Dynein-2	UNDECIDED	`(cep290_tz_scaffold \| mks_module \| nphp_module) & !cilium_length_control`
`primary_cilium_life_cycle`	IFT81-IFT74 tubulin module	UNDECIDED	`(cep290_tz_scaffold \| mks_module \| nphp_module) & !cilium_length_control`
`primary_cilium_life_cycle`	INPP5E sets ciliary phosphoinositides	UNDECIDED	`(ift81_ift74_tubulin \| ift_a_complex \| ift_b_scaffold)`
`primary_cilium_life_cycle`	Heterotrimeric kinesin-2	UNDECIDED	`(cep290_tz_scaffold \| mks_module \| nphp_module) & !cilium_length_control`
`primary_cilium_life_cycle`	Myosin-Va preciliary vesicle delivery	UNDECIDED	`(cp110_cep97_cap \| ttbk2_cap_removal)`
`primary_cilium_life_cycle`	NEDD9 activates Aurora A	UNDECIDED	`(arl3_cargo_release \| inpp5e_pip2_hydrolysis \| tulp3_gpcr_import)`
`primary_cilium_life_cycle`	PDE6D carries farnesylated cargo	UNDECIDED	`(ift81_ift74_tubulin \| ift_a_complex \| ift_b_scaffold)`
`primary_cilium_life_cycle`	Pitchfork activates Aurora A	UNDECIDED	`(arl3_cargo_release \| inpp5e_pip2_hydrolysis \| tulp3_gpcr_import)`
`primary_cilium_life_cycle`	PLK1 activates KIF2A	UNDECIDED	`(arl3_cargo_release \| inpp5e_pip2_hydrolysis \| tulp3_gpcr_import)`
`primary_cilium_life_cycle`	Phosphorylated Tctex-1 promotes resorption	UNDECIDED	`(arl3_cargo_release \| inpp5e_pip2_hydrolysis \| tulp3_gpcr_import)`
`primary_cilium_life_cycle`	TULP3 links IFT-A to membrane cargo	UNDECIDED	`(ift81_ift74_tubulin \| ift_a_complex \| ift_b_scaffold)`
`primary_cilium_life_cycle`	UNC119B carries myristoylated cargo	UNDECIDED	`(ift81_ift74_tubulin \| ift_a_complex \| ift_b_scaffold)`
`proline_metabolism`	P5C dehydrogenase completion of proline catabolism	UNDECIDED	`(oat_p5c_supply \| prodh_p5c_formation)`
`proline_metabolism`	P5C reductase-dependent L-proline formation	UNDECIDED	`(aldh18a1_semialdehyde_formation \| oat_p5c_supply \| split_semialdehyde_formation)`
`propionyl_coa_catabolism`	(R)-methylmalonyl-CoA to succinyl-CoA	UNDECIDED	`(adocbl_supply \| mcee_step)`
`protein_prenylation_caax_processing`	CAAX endoprotease (RCE1)	UNDECIDED	`(farnesylation \| geranylgeranylation_I)`
`purine_nucleotide_catabolism`	Adenosine deaminase (ADA)	UNDECIDED	`(cyto_amp_5nt \| ecto_amp_5nt)`
`purine_nucleotide_catabolism`	Purine-nucleoside phosphorylase (PNP)	UNDECIDED	`(adenosine_deamination \| imp_gmp_5nt)`
`purine_nucleotide_catabolism`	Xanthine dehydrogenase/oxidase (XDH)	UNDECIDED	`(guanine_deamination \| nucleoside_phosphorolysis)`
`purine_nucleotide_interconversion`	IMP + L-aspartate + GTP to adenylosuccinate + GDP + Pi	UNDECIDED	`(ampd_step \| ndp_kinase_step)`
`purine_salvage_and_catabolism`	hypoxanthine/guanine + PRPP to IMP/GMP + PPi	UNDECIDED	`(adenine_moiety_deamination \| pnp_step)`
`purine_salvage_and_catabolism`	hypoxanthine to xanthine to urate	UNDECIDED	`(guanine_deamination_step \| pnp_step)`
`pyrenoid_ccm`	Lumenal bicarbonate dehydration (CAH3)	UNDECIDED	`(pyrenoid_tubule_biogenesis \| thylakoid_bicarbonate_entry)`
`pyrenoid_ccm`	Rubisco carboxylation in the pyrenoid matrix	UNDECIDED	`(lumenal_co2_release \| starch_sheath_barrier)`
`pyrenoid_ccm`	Thylakoid bicarbonate entry (bestrophin-like channels)	UNDECIDED	`(ccm_induction \| ci_uptake \| stromal_co2_recapture)`
`pyrimidine_nucleotide_catabolism`	Dihydropyrimidine dehydrogenase (DPYD)	UNDECIDED	`(thymidine_phosphorolysis \| uridine_phosphorolysis)`
`pyrimidine_nucleotide_catabolism`	Uridine phosphorylase (UPP1 / UPP2)	UNDECIDED	`(cytidine_deamination \| pyrimidine_5nt)`
`pyrimidine_salvage`	uracil + PRPP to UMP + PPi	UNDECIDED	`(cytosine_deamination_step \| nucleoside_cleavage)`
`retinal_determination_network`	Eyes absent transcriptional coactivator-phosphatase	UNDECIDED	`(dach_cofactor \| pax6_selector)`
`retinal_determination_network`	Six-family homeodomain transcription factor	UNDECIDED	`(eya_cofactor \| pax6_selector)`
`retinoid_visual_cycle`	11-cis retinol dehydrogenase (RDH5)	UNDECIDED	`(cralbp_carrier \| isomerohydrolysis \| photoisomerase)`
`riboflavin_biosynthesis`	6,7-dimethyl-8-ribityllumazine formation	UNDECIDED	`(dhbp_branch \| phosphoribitylaminouracil_phosphatase_step)`
`root_radial_patterning_shr_scr`	Nuclear capture of SHR by SCR and BIRD/IDD proteins	UNDECIDED	`(shr_mobile_signal \| shr_scr_bird_activation)`
`root_radial_patterning_shr_scr`	SHR-SCR-BIRD activation of SCR, MGP and CYCD6;1	UNDECIDED	`(cycd6_formative_division \| shr_nuclear_capture)`
`scer_hog1_cascade`	Ssk2/Ssk22 MAP kinase kinase kinase activation	UNDECIDED	`(ssk1_rr \| ste50_ste11_activation)`
`selenocysteine_biosynthesis_incorporation`	SelA-dependent Sec-tRNA(Sec) synthesis	UNDECIDED	`(selenophosphate_synthesis \| ser_trna_sec_synthesis)`
`selenocysteine_biosynthesis_incorporation`	EEFSEC-dependent Sec-tRNA(Sec) delivery	UNDECIDED	`(secisbp2_recognition \| sepsecs_sec_trna_formation)`
`selenocysteine_biosynthesis_incorporation`	PSTK-dependent phosphoseryl-tRNA(Sec) formation	UNDECIDED	`(selenophosphate_synthesis \| ser_trna_sec_synthesis)`
`selenocysteine_biosynthesis_incorporation`	SECISBP2-dependent SECIS recognition	UNDECIDED	`(selenophosphate_synthesis \| ser_trna_sec_synthesis)`
`sialic_acid_metabolism`	CMP-N-acetylneuraminate synthetase (CMAS)	UNDECIDED	`(lysosomal_sialic_acid_export \| neu5ac9p_to_neu5ac)`
`spytag_spycatcher`	FbaB fibronectin binding and host-cell adhesion/invasion	UNDECIDED	`(fbab_cell_wall_anchoring \| fbab_cnab2_isopeptide \| fbab_thioester_host_capture)`
`synaptic_vesicle_exocytosis`	NSF / alpha-SNAP disassembly of the cis-SNARE complex	UNDECIDED	`(presynaptic_calcium_influx \| vesicle_priming)`
`taurine_biosynthesis_and_transport`	Taurine transporter TauT (SLC6A6)	UNDECIDED	`(cysteamine_dioxygenation \| cysteinesulfinate_decarboxylation)`
`tetrahydrobiopterin_metabolism`	aromatic amino acid hydroxylation consumes BH4, producing pterin-4a-carbinolamine	UNDECIDED	`(qdpr_step \| spr_step)`
`tetrahydrofolate_biosynthesis`	7,8-dihydroneopterin to 7,8-dihydropteroate	UNDECIDED	`(adc_lyase_step \| dihydroneopterin_dephosphorylation_step)`
`thiamine_diphosphate_biosynthesis`	HMP diphosphate plus thiazole phosphate to thiamine phosphate	UNDECIDED	`(thiD_step \| thiG_step)`
`thiamine_diphosphate_biosynthesis`	Thiazole phosphate synthesis	UNDECIDED	`(dehydroglycine_supply \| dxs_step \| thiS_sulfur_carrier_role)`
`thiamine_diphosphate_biosynthesis`	ThiI: sulfur transfer to ThiS	UNDECIDED	`(cysteine_desulfurase_activity \| thiF_this_adenylylation_activity)`
`thiamine_uptake_and_activation`	Mitochondrial thiamine pyrophosphate carrier (SLC25A19)	UNDECIDED	`(thiamine_activation \| thtp_homeostasis)`
`type_ii_fatty_acid_synthesis`	FabD malonyl-ACP loading	UNDECIDED	`(acetyl_coa_carboxylation \| acp_carrier_role)`
`ubiquinone_biosynthesis`	4-Hydroxy-3-polyprenylbenzoate to 3,4-dihydroxy-5-polyprenylbenzoate	UNDECIDED	`(hydroxybenzoate_prenylation \| ubiquinone_biosynthesis_accessory_system)`
`ubiquinone_biosynthesis`	UbiX: flavin prenyltransferase	UNDECIDED	`(hydroxybenzoate_prenylation \| ubiquinone_biosynthesis_accessory_system)`
`ubiquinone_biosynthesis`	Polyprenylation of 4-hydroxybenzoate	UNDECIDED	`(chorismate_lyase_route \| hydroxybenzaldehyde_oxidation_step \| polyprenyl_diphosphate_tail_synthesis)`
`urea_cycle`	L-citrulline + L-aspartate + ATP to argininosuccinate + AMP + PPi	UNDECIDED	`(citrin_aspartate_supply \| ornithine_citrulline_transport)`
`urea_cycle`	citrulline export / ornithine import across the inner membrane (SLC25A15)	UNDECIDED	`(arg1_step \| otc_step)`
`ureide_urea_catabolism`	urea + HCO3- + ATP to allophanate + ADP + Pi	UNDECIDED	`(allantoicase_route \| ureidoglycine_aminohydrolase_step \| ureidoglycolate_breakdown_step)`
`ureide_urea_catabolism`	Nickel urease (one step; most fungi, plants, many bacteria)	UNDECIDED	`(allantoicase_route \| ureidoglycine_aminohydrolase_step \| ureidoglycolate_breakdown_step)`
`wnt_signaling`	Wnt-Frizzled-co-receptor engagement	UNDECIDED	`(rspo_lgr_potentiation \| wnt_ligand_biogenesis) & !(rnf43_znrf3_receptor_turnover \| secreted_antagonists)`
`aps_dependent_assimilatory_sulfate_reduction`	Assimilatory reduction of sulfite to sulfide	ALTERNATIVE_VARIANTS	`(direct_aps_reduction_route \| paps_reductase_activity)`
`bacterial_alkanesulfonate_uptake_desulfonation`	SsuD alkanesulfonate monooxygenation	DECLARED	`(ssuabc_import \| ssue_fmn_reduction)`	`ssuabc_import & ssue_fmn_reduction`
`bacterial_isc_iron_sulfur_cluster_assembly`	IscU scaffold assembly	DECLARED	`(fdx_electron_delivery \| isc_sulfur_mobilization)`	`isc_sulfur_mobilization & fdx_electron_delivery`
`bacterial_methionine_cycle`	Folate-dependent methionine regeneration	ALTERNATIVE_VARIANTS	`(ahcy_route \| luxs_step)`
`bacterial_nonhomologous_end_joining`	LigD-mediated DNA-end sealing	DECLARED	`(ku_end_recognition \| ligd_end_processing)`	`ku_end_recognition`
`bacterial_pst_phosphate_uptake`	PstSACB phosphate translocation	DECLARED	`(pstb_energy_coupling \| psts_phosphate_capture)`	`psts_phosphate_capture & pstb_energy_coupling`
`bacterial_purine_base_oxidation_to_urate`	XdhAB-dependent xanthine oxidation to urate	ALTERNATIVE_VARIANTS	`(guanine_deamination_route \| hypoxanthine_oxidation_route)`
`bacterial_sec_posttranslational_protein_export`	SecYEG protein-conducting channel	DECLARED	`(seca_atpase_motor \| secdf_yajc_accessory_complex)`	`seca_atpase_motor`
`bacterial_shikimate_chorismate_biosynthesis`	EPSP to chorismate	ALTERNATIVE_VARIANTS	`(arom_epsps_step \| discrete_epsps_step)`
`bacterial_type_iv_secretion_apparatus`	Type IV secretion pilus	DECLARED	`(envelope_core_complex \| mating_pair_stabilization \| virb4_family_atpase)`	`envelope_core_complex & virb4_family_atpase`
`biotin_biosynthesis`	Pimelate thioester to 8-amino-7-oxononanoate (KAPA)	ALTERNATIVE_VARIANTS	`(bioH_step \| fungal_peroxisomal_beta_oxidation_variant \| saccharomyces_bio1_variant)`
`c_elegans_dbl1_body_size_signaling`	SMA-6/DAF-4 receptor activation	DECLARED	`(dbl1_ligand \| sma10_lrig)`	`dbl1_ligand`
`carotene_backbone_biosynthesis`	Epsilon cyclization (lycopene -> delta-carotene)	ALTERNATIVE_VARIANTS	`(crti_type_desaturation \| crtiso_step)`
`chitin_perception`	BIK1 phosphorylation of RBOHD	ALTERNATIVE_VARIANTS	`(atcerk1_kinase \| oscerk1_kinase)`
`chitin_perception`	PBL27/OsRLCK185 RLCK phosphorylation of the MAP3K	ALTERNATIVE_VARIANTS	`(atcerk1_kinase \| oscerk1_kinase)`
`coenzyme_a_biosynthesis`	4'-phosphopantothenate to phosphopantothenoylcysteine	ALTERNATIVE_VARIANTS	`(pantothenate_kinase_step \| phosphopantothenate_synthetase_step)`
`de_novo_purine_synthesis`	SAICAR synthetase	ALTERNATIVE_VARIANTS	`(ade2_purE_domain_substep \| direct_air_carboxylase_route \| purE_substep)`
`emp_glycolysis`	D-glucose 6-phosphate to D-fructose 6-phosphate	ALTERNATIVE_VARIANTS	`(adp_kinase_entry_variant \| atp_kinase_entry_variant \| glucan_entry_variant \| pts_entry_variant)`
`emp_glycolysis`	3-phospho-D-glycerate to 2-phospho-D-glycerate	ALTERNATIVE_VARIANTS	`(ferredoxin_oxidation_variant \| nonphosphorylating_nadp_variant \| pgk_step)`
`glucarate_galactarate_catabolism`	5-dehydro-4-deoxyglucarate to 2,5-dioxopentanoate	ALTERNATIVE_VARIANTS	`(galactarate_entry \| glucarate_entry)`
`glycogen_synthesis_and_mobilization`	GlgB-dependent glycogen branching	ALTERNATIVE_VARIANTS	`(glga_adp_chain_extension \| glga_udp_chain_extension)`
`heme_biosynthesis`	ALA condensation	ALTERNATIVE_VARIANTS	`(c4_alas_step \| c5_heml_activity)`
`jak_stat_signaling`	STAT-dependent transcription	DECLARED	`(mapk_branch_interface \| stat_dimerization_import) & !(pias_restraint \| ptp_dephosphorylation)`	`stat_dimerization_import & !(ptp_dephosphorylation \| pias_restraint)`
`metazoan_autophagosome_biogenesis`	EPG5-dependent autophagosome-lysosome fusion	ALTERNATIVE_VARIANTS	`(gabarap_fusion \| lgg2_late)`
`methionine_biosynthesis`	Direct sulfhydrylation of O-acetylhomoserine (metY)	ALTERNATIVE_VARIANTS	`(o_acetyl_activation \| o_succinyl_activation)`
`methionine_biosynthesis`	Direct sulfhydrylation of O-succinylhomoserine (metZ)	ALTERNATIVE_VARIANTS	`(o_acetyl_activation \| o_succinyl_activation)`
`methionine_biosynthesis`	Cystathionine gamma-synthase	ALTERNATIVE_VARIANTS	`(o_acetyl_activation \| o_succinyl_activation)`
`methionine_biosynthesis`	Homocysteine methylation to methionine	ALTERNATIVE_VARIANTS	`(direct_sulfhydrylation \| direct_sulfhydrylation_metZ \| metC_node)`
`methionine_cycle`	MAT-I methionine adenosyltransferase activity	ALTERNATIVE_VARIANTS	`(bhmt_route \| mete_route \| ms_route) & !amet_pool`
`methionine_cycle`	Methionine adenosyltransferase (MAT2A/MetK/SAM1-type)	ALTERNATIVE_VARIANTS	`(bhmt_route \| mete_route \| ms_route)`
`methionine_cycle`	SAM-dependent methyltransferase activity (general)	ALTERNATIVE_VARIANTS	`(mat1_activity \| mat3_activity \| mat_single_chain_activity) & !ahcys_pool`
`methionine_salvage_mta_cycle`	acireductone + O2 to 4-methylthio-2-oxobutanoate + formate	ALTERNATIVE_VARIANTS	`(bifunctional_e1_variant \| hkmtp_phosphatase_step)`
`methionine_salvage_mta_cycle`	MTR-1-P to S-methyl-5-thio-D-ribulose 1-phosphate	ALTERNATIVE_VARIANTS	`(mta_phosphorylase_route \| mtr_kinase_step)`
`methylcitrate_cycle`	2-methyl-cis-aconitate hydration	ALTERNATIVE_VARIANTS	`(prpD_direct_route \| prpF_isomerization)`
`mitophagy`	Atg8-family docking of mitophagy receptors on the phagophore	ALTERNATIVE_VARIANTS	`(allo1_receptor \| bnip3_nix_receptor \| fundc1_receptor \| ubiquitin_binding_receptors)`
`nad_biosynthesis_salvage`	NaMN adenylylation alternatives	ALTERNATIVE_VARIANTS	`(nadc_step \| nicotinate_preiss_handler_route \| nmn_deamidating_route \| pncb_after_pnca_step)`
`nad_de_novo_and_salvage_fungal`	NaMN to nicotinate adenine dinucleotide (NaAD)	ALTERNATIVE_VARIANTS	`(nicotinate_phosphoribosyltransferase_step \| nrk1_nicotinate_riboside_kinase_activity \| quinolinate_phosphoribosyltransferase_step)`
`peroxisome-lifecycle`	Matrix protein cargo targeting	ALTERNATIVE_VARIANTS	`(pex16_supported_pmp_route \| pex3_family_membrane_docking \| rrbp1_supported_er_biogenesis_route)`
`pirna_mediated_germline_silencing`	HRDE-1 nuclear 22G-RNA Argonaute	ALTERNATIVE_VARIANTS	`(piwil2_slicer \| wago1_cytoplasmic_effector)`
`pirna_mediated_germline_silencing`	Piwi-directed H3K9me3 heterochromatin (Drosophila)	ALTERNATIVE_VARIANTS	`(piwil2_slicer \| wago1_cytoplasmic_effector)`
`pirna_mediated_germline_silencing`	PIWIL4/MIWI2 nuclear piRNA effector	ALTERNATIVE_VARIANTS	`(piwil2_slicer \| wago1_cytoplasmic_effector)`
`pirna_mediated_germline_silencing`	WAGO-4 Z granule 22G-RNA Argonaute	ALTERNATIVE_VARIANTS	`(piwil2_slicer \| wago1_cytoplasmic_effector)`
`primordial_germ_cell_specification`	piRNA-guided transposon silencing in the germline	ALTERNATIVE_VARIANTS	`(pgc_tripartite_network \| preformation)`
`riboflavin_biosynthesis`	Pyrimidine-intermediate dephosphorylation	ALTERNATIVE_VARIANTS	`(rib2_deaminase_step \| ribd_reductase_step)`
`triacylglycerol_biosynthesis`	1-Acylglycerol-3-phosphate O-acyltransferases (AGPAT/SLC1, MBOAT ALE1, LOA1)	ALTERNATIVE_VARIANTS	`(acyl_dhap_reduction \| g3p_route)`
`type_ii_fatty_acid_synthesis`	Four-reaction FAS-II elongation cycle	ALTERNATIVE_VARIANTS	`(kasIII_route \| mad_route_first_condensation)`
`ureide_urea_catabolism`	(S)-ureidoglycolate to glyoxylate	ALTERNATIVE_VARIANTS	`(allantoicase_route \| ureidoglycine_aminohydrolase_step)`
`vitamin_b6_plp_metabolism`	PLP homeostasis (PDXP)	ALTERNATIVE_VARIANTS	`(pdxs_pdxt_de_novo_variant \| pnpo_step)`