ARBA process rows scored by module deployment
Generated by deploy_check.py; do not edit by hand. Per-row detail is in
results.tsv.
- ARBA biological-process rows in reviewed genes: 4058
- rows with a module whose process falls under the row term (scored): 1617
- QuickGO lookups: 12130 cached, 0 failed (failed lookups count as absent)
- taxonomy lookups: 65, 0 failed (a failed lineage keeps only taxon-free modules)
- modules with activity-typed steps: 445; 18 declare taxa only as free text (no NCBITaxon id) and are excluded, since their scope cannot be checked
- snapshot: 2026-10-17
Verdict vs. gene-review action
| verdict | ACCEPT | KEEP_AS_NON_CORE | MODIFY | MARK_AS_OVER_ANNOTATED | TOO_GENERAL | REMOVE | UNDECIDED | PENDING | (not reviewed) | total |
|---|---|---|---|---|---|---|---|---|---|---|
| ENTAILED | 376 | 236 | 124 | 125 | 1 | 7 | 6 | 0 | 0 | 875 |
| MODULE_INCOMPLETE | 41 | 26 | 9 | 4 | 0 | 0 | 1 | 0 | 0 | 81 |
| NOT_ENTAILED | 162 | 254 | 76 | 135 | 0 | 25 | 6 | 3 | 0 | 661 |
Kept and rejected, by verdict and module concept
Kept is ACCEPT or KEEP_AS_NON_CORE; rejected is REMOVE, MARK_AS_OVER_ANNOTATED or TOO_GENERAL. Shares are of reviewed rows.
| verdict | module concept | rows | kept | rejected |
|---|---|---|---|---|
| ENTAILED | exact | 220 | 93% | 4% |
| ENTAILED | ancestor of concept | 655 | 62% | 19% |
| MODULE_INCOMPLETE | exact | 26 | 92% | 4% |
| MODULE_INCOMPLETE | ancestor of concept | 55 | 78% | 5% |
| NOT_ENTAILED | exact | 119 | 80% | 10% |
| NOT_ENTAILED | ancestor of concept | 542 | 59% | 27% |
Excluded modules (taxa declared without an id): bbsome, cellulose_biosynthesis, diphthamide_biosynthesis, enterohepatic_bile_salt_cycling, erk_cascade, erythroascorbate_biosynthesis, jak_stat_signaling, lignin_monolignol_biosynthesis, nicotine_biosynthesis, oxphos, phagophore_assembly_site, phagophore_organelle_contact_site, photosynthesis, pi3k_akt_mtor, seed_triacylglycerol_biosynthesis, septal_junction, t_cell_receptor_signaling, xylan_biosynthesis
Rows where the verdict and the review disagree
Entailed by a satisfiable module, but the review rejected it (132)
| gene | term | modules | gaps / other modules | review |
|---|---|---|---|---|
| ARATH/ABI5 | GO:0007165 signal transduction | auxin_nuclear_signaling, brassinosteroid_signaling, gibberellin_della_signaling, jasmonate_coi1_jaz_signaling, phytochrome_photomorphogenesis | bacterial_recbcd_end_resection, camalexin_biosynthesis, floral_meristem_identity, floral_organ_identity_abce, plant_circadian_clock_oscillator, root_radial_patt | MARK_AS_OVER_ANNOTATED |
| ARATH/ABI5 | GO:1901701 cellular response to oxygen-containing compound | brassinosteroid_signaling, gibberellin_della_signaling, jasmonate_coi1_jaz_signaling, strigolactone_signaling_shoot_branching | auxin_nuclear_signaling, bacterial_recbcd_end_resection, camalexin_biosynthesis, floral_meristem_identity, floral_organ_identity_abce, phytochrome_photomorphoge | MARK_AS_OVER_ANNOTATED |
| ARATH/AHK4 | GO:1901701 cellular response to oxygen-containing compound | brassinosteroid_signaling, strigolactone_signaling_shoot_branching | chitin_perception, coenzyme_a_biosynthesis, cytokinin_two_component_signaling, g2_m_transition, gpi_anchor_remodeling, kinase_phosphatase_toggle, metaphase_anap | MARK_AS_OVER_ANNOTATED |
| ARATH/BRC1 | GO:0160109 plant gross anatomical part developmental process | floral_meristem_identity, floral_organ_identity_abce, root_radial_patterning_shr_scr, shoot_meristem_clv_wus_feedback, stomatal_lineage_development, trichome_initiation_mbw | auxin_nuclear_signaling, bacterial_recbcd_end_resection, brassinosteroid_signaling, camalexin_biosynthesis, gibberellin_della_signaling, jasmonate_coi1_jaz_sign | MARK_AS_OVER_ANNOTATED |
| ARATH/CERK1 | GO:1901701 cellular response to oxygen-containing compound | brassinosteroid_signaling, strigolactone_signaling_shoot_branching | auxin_polar_transport, chitin_perception, coenzyme_a_biosynthesis, ethylene_signaling, g2_m_transition, gpcr_camp_pka_signaling, gpcr_plc_calcium_pkc_signaling, | MARK_AS_OVER_ANNOTATED |
| ARATH/CPC | GO:0009653 anatomical structure morphogenesis | floral_organ_identity_abce | auxin_nuclear_signaling, bacterial_recbcd_end_resection, brassinosteroid_signaling, camalexin_biosynthesis, floral_meristem_identity, gibberellin_della_signalin | MARK_AS_OVER_ANNOTATED |
| ARATH/CPC | GO:0048731 system development | floral_meristem_identity, floral_organ_identity_abce, root_radial_patterning_shr_scr | auxin_nuclear_signaling, bacterial_recbcd_end_resection, brassinosteroid_signaling, camalexin_biosynthesis, gibberellin_della_signaling, jasmonate_coi1_jaz_sign | MARK_AS_OVER_ANNOTATED |
| ARATH/CRY2 | GO:0009791 post-embryonic development | photoperiodic_flowering_co_ft, phytochrome_photomorphogenesis | heat_shock_response, plant_circadian_clock_oscillator, strigolactone_signaling_shoot_branching | MARK_AS_OVER_ANNOTATED |
| ARATH/CRY2 | GO:0048731 system development | photoperiodic_flowering_co_ft | heat_shock_response, phytochrome_photomorphogenesis, plant_circadian_clock_oscillator, strigolactone_signaling_shoot_branching | MARK_AS_OVER_ANNOTATED |
| ARATH/LYK4 | GO:1901701 cellular response to oxygen-containing compound | brassinosteroid_signaling | auxin_polar_transport, chitin_perception, coenzyme_a_biosynthesis, ethylene_signaling, g2_m_transition, gpcr_camp_pka_signaling, gpcr_plc_calcium_pkc_signaling, | MARK_AS_OVER_ANNOTATED |
| CUCME/A0A1S3BTE3 | GO:0007165 signal transduction | erk5_cascade, ethylene_signaling, gpcr_plc_calcium_pkc_signaling, jnk_cascade, mapk_relay, p38_cascade | coenzyme_a_biosynthesis, g2_m_transition, intraflagellar_transport, kinase_phosphatase_toggle, metaphase_anaphase_transition_and_mitotic_exit, peptidoglycan_rec | MARK_AS_OVER_ANNOTATED |
| DANRE/fgf8b | GO:0009952 anterior/posterior pattern specification | neural_ectoderm_anteroposterior_specification | egfr_signaling, erbb2_signaling, fgfr_signaling, neurexin_transsynaptic_adhesion, notch_signaling | MARK_AS_OVER_ANNOTATED |
| DANRE/rbpjb | GO:0009653 anatomical structure morphogenesis | germ_layer_specification | bacterial_recbcd_end_resection, body_axis_specification, cardiac_specification_network, cgas_sting_signaling, early_metazoan_development, er_unfolded_protein_re | MARK_AS_OVER_ANNOTATED |
| DANRE/rbpjb | GO:0048513 animal organ development | cardiac_specification_network, neural_crest_gene_regulatory_network, retinal_determination_network | bacterial_recbcd_end_resection, body_axis_specification, cgas_sting_signaling, early_metazoan_development, er_unfolded_protein_response, g1_s_transition, germ_l | MARK_AS_OVER_ANNOTATED |
| DICDI/mhcA | GO:0031152 aggregation involved in sorocarp development | dicty_allorecognition_adhesion | complex_i_assembly_factors, heat_shock_response, methylcitrate_cycle, phenylacetate_catabolism | MARK_AS_OVER_ANNOTATED |
| DROME/Acaa | GO:0006629 lipid metabolic process | fatty_acid_beta_oxidation, ketogenesis, ketone_body_oxidation, mevalonate_pathway, peroxisomal_beta_oxidation | alginate_o_acetylation, bacterial_l_carnitine_catabolism, phenylacetate_catabolism | MARK_AS_OVER_ANNOTATED |
| DROME/CG6051 | GO:0046474 glycerophospholipid biosynthetic process | gpi_anchor_remodeling | ciliary_transition_zone, kinase_phosphatase_toggle, mitophagy, peptidoglycan_recycling, phagosome_maturation, phenylacetate_catabolism | REMOVE |
| DROME/Doc1 | GO:0160108 animal gross anatomical part developmental process | cardiac_specification_network, retinal_determination_network | bacterial_recbcd_end_resection, body_axis_specification, cgas_sting_signaling, early_metazoan_development, er_unfolded_protein_response, g1_s_transition, germ_l | MARK_AS_OVER_ANNOTATED |
| DROME/Rel | GO:0048468 cell development | primordial_germ_cell_specification | bacterial_recbcd_end_resection, body_axis_specification, cardiac_specification_network, cgas_sting_signaling, early_metazoan_development, er_unfolded_protein_re | MARK_AS_OVER_ANNOTATED |
| DROME/Rel | GO:0048731 system development | cardiac_specification_network, retinal_determination_network | bacterial_recbcd_end_resection, body_axis_specification, cgas_sting_signaling, early_metazoan_development, er_unfolded_protein_response, fgfr_signaling, g1_s_tr | MARK_AS_OVER_ANNOTATED |
| DROME/Rel | GO:0160108 animal gross anatomical part developmental process | cardiac_specification_network, retinal_determination_network | bacterial_recbcd_end_resection, body_axis_specification, cgas_sting_signaling, early_metazoan_development, er_unfolded_protein_response, fgfr_signaling, g1_s_tr | MARK_AS_OVER_ANNOTATED |
| DROME/drk | GO:0160108 animal gross anatomical part developmental process | nucleokinesis | cgas_sting_signaling, ciliary_transition_zone, egfr_signaling, erbb2_signaling, hedgehog_signaling, metaphase_anaphase_transition_and_mitotic_exit, metazoan_aut | MARK_AS_OVER_ANNOTATED |
| DROME/toy | GO:0030154 cell differentiation | cardiac_specification_network, primordial_germ_cell_specification | bacterial_recbcd_end_resection, body_axis_specification, cgas_sting_signaling, early_metazoan_development, er_unfolded_protein_response, g1_s_transition, germ_l | MARK_AS_OVER_ANNOTATED |
| DROME/toy | GO:0048731 system development | cardiac_specification_network, retinal_determination_network | bacterial_recbcd_end_resection, body_axis_specification, cgas_sting_signaling, early_metazoan_development, er_unfolded_protein_response, g1_s_transition, germ_l | MARK_AS_OVER_ANNOTATED |
| PSEAE/ubiE | GO:0042181 ketone biosynthetic process | ubiquinone_biosynthesis | methionine_cycle | MARK_AS_OVER_ANNOTATED |
| PSEPK/carB | GO:0006520 amino acid metabolic process | arginine_biosynthesis | de_novo_pyrimidine_synthesis, urea_cycle | MARK_AS_OVER_ANNOTATED |
| PSEPK/dinB | GO:0006259 DNA metabolic process | bacterial_imuabc_damage_induced_mutagenesis, bacterial_nonhomologous_end_joining, bacterial_nucleotide_excision_repair, bacterial_recbcd_end_resection | bacterial_nitrogen_regulatory_pts, sphingolipid_de_novo_synthesis | MARK_AS_OVER_ANNOTATED |
| PSEPK/galC | GO:0019336 phenol-containing compound catabolic process | bacterial_gallate_catabolism | MARK_AS_OVER_ANNOTATED | |
| PSEPK/galC | GO:0042537 benzene-containing compound metabolic process | bacterial_gallate_catabolism | MARK_AS_OVER_ANNOTATED | |
| PSEPK/galC | GO:0072329 monocarboxylic acid catabolic process | bacterial_gallate_catabolism | MARK_AS_OVER_ANNOTATED | |
| PSEPK/glgB | GO:0044042 glucan metabolic process | tres_mak_glge_branched_alpha_glucan_biosynthesis | phenylacetate_catabolism | MARK_AS_OVER_ANNOTATED |
| PSEPK/kdsA1 | GO:0046394 carboxylic acid biosynthetic process | kdo_biosynthesis, methionine_biosynthesis | MARK_AS_OVER_ANNOTATED | |
| PSEPK/leuC | GO:0043436 oxoacid metabolic process | branched_chain_amino_acid_biosynthesis, methylcitrate_cycle | bacterial_sulfoquinovose_catabolism, mitochondrial_complex_i_core | MARK_AS_OVER_ANNOTATED |
| PSEPK/lpd | GO:0045333 cellular respiration | tca_cycle | bacterial_pyruvate_metabolism, branched_chain_amino_acid_catabolism, complex_i_assembly_factors, glycine_cleavage_system, lysine_catabolism, pyruvate_metabolism | MARK_AS_OVER_ANNOTATED |
| PSEPK/murG | GO:1901137 carbohydrate derivative biosynthetic process | peptidoglycan_precursor_biosynthesis | tres_mak_glge_branched_alpha_glucan_biosynthesis | MARK_AS_OVER_ANNOTATED |
| PSEPK/mutL | GO:0006259 DNA metabolic process | bacterial_imuabc_damage_induced_mutagenesis, bacterial_nonhomologous_end_joining, bacterial_nucleotide_excision_repair, bacterial_recbcd_end_resection | bacterial_cytochrome_c_maturation_system_i, bacterial_lps_transport, bacterial_pst_phosphate_uptake, bacterial_type_ii_secretion, bacterial_type_iii_secretion_i | MARK_AS_OVER_ANNOTATED |
| PSEPK/paaH | GO:0032787 monocarboxylic acid metabolic process | bacterial_fatty_acid_beta_oxidation, fatty_acid_beta_oxidation, phenylacetate_catabolism | bacterial_beta_aryl_ether_dimer_cleavage, bacterial_sulfoquinovose_catabolism, complex_i_assembly_factors | MARK_AS_OVER_ANNOTATED |
| PSEPK/pcaF | GO:0006629 lipid metabolic process | bacterial_fatty_acid_beta_oxidation, fatty_acid_beta_oxidation | alginate_o_acetylation, bacterial_l_carnitine_catabolism, bacterial_lipoprotein_maturation, bacterial_mcl_pha_synthesis_and_mobilization, beta_ketoadipate_lower | REMOVE |
| PSEPK/pgsA | GO:0019637 organophosphate metabolic process | bacterial_phosphatidylglycerol_cardiolipin_biosynthesis | bacterial_nitrogen_regulatory_pts, sphingolipid_de_novo_synthesis | MARK_AS_OVER_ANNOTATED |
| PSEPK/pvdD | GO:0072330 monocarboxylic acid biosynthetic process | coenzyme_a_biosynthesis | REMOVE | |
| … 92 more in results.tsv |
Accepted by the review, but the protein fills no step of a module under the term (162)
| gene | term | modules | gaps / other modules | review |
|---|---|---|---|---|
| 9POAL/NCGR_LOCUS29329 | GO:0006531 aspartate metabolic process | aspartate_asparagine_metabolism | aspartate_family_threonine_biosynthesis, coenzyme_a_biosynthesis, complex_i_assembly_factors, sphingolipid_de_novo_synthesis | ACCEPT |
| ARATH/AT1G74310 | GO:0009408 response to heat | heat_shock_response | bacterial_nucleotide_excision_repair, coenzyme_q10_biosynthesis, linc_complex, muth_independent_mismatch_repair, peroxisome-lifecycle, phenylacetate_catabolism | ACCEPT |
| ARATH/EBF1 | GO:0009723 response to ethylene | ethylene_signaling | ACCEPT | |
| ARATH/EBF2 | GO:0009723 response to ethylene | ethylene_signaling | ACCEPT | |
| ARATH/EIL1 | GO:0009873 ethylene-activated signaling pathway | ethylene_signaling | auxin_nuclear_signaling, bacterial_recbcd_end_resection, brassinosteroid_signaling, camalexin_biosynthesis, floral_meristem_identity, floral_organ_identity_abce | ACCEPT |
| ARATH/ESP | GO:0019762 glucosinolate catabolic process | aliphatic_glucosinolate_myrosinase_defense | heat_shock_response, sphingolipid_de_novo_synthesis | ACCEPT |
| ARATH/FIE | GO:0040029 epigenetic regulation of gene expression | autonomous_flowering_pathway, vernalization_flc_silencing | auxin_nuclear_signaling, brassinosteroid_signaling, complex_i_assembly_factors, floral_meristem_identity, floral_organ_identity_abce, gibberellin_della_signalin | ACCEPT |
| ARATH/HSP17.7 | GO:0006950 response to stress | bacterial_nucleotide_excision_repair, bacterial_recbcd_end_resection, bacterial_ruvabc_holliday_junction_processing, heat_shock_response, jnk_cascade | ACCEPT | |
| ARATH/LYK4 | GO:0045087 innate immune response | plant_nlr_resistosome_signaling | auxin_polar_transport, brassinosteroid_signaling, chitin_perception, coenzyme_a_biosynthesis, ethylene_signaling, g2_m_transition, gpcr_camp_pka_signaling, gpcr | ACCEPT |
| ARATH/LYK5 | GO:0045087 innate immune response | plant_nlr_resistosome_signaling | chitin_perception, heat_shock_response | ACCEPT |
| ARATH/MKK4 | GO:0098542 defense response to other organism | plant_nlr_resistosome_signaling | auxin_polar_transport, brassinosteroid_signaling, chitin_perception, coenzyme_a_biosynthesis, erk5_cascade, ethylene_signaling, g2_m_transition, gpcr_camp_pka_s | ACCEPT |
| ARATH/MKK5 | GO:0098542 defense response to other organism | plant_nlr_resistosome_signaling | auxin_polar_transport, brassinosteroid_signaling, chitin_perception, coenzyme_a_biosynthesis, erk5_cascade, ethylene_signaling, g2_m_transition, gpcr_camp_pka_s | ACCEPT |
| ARATH/NPR1 | GO:0031347 regulation of defense response | chitin_perception, plant_nlr_resistosome_signaling | gibberellin_della_signaling, root_radial_patterning_shr_scr, trichome_initiation_mbw | ACCEPT |
| ARATH/NPR1 | GO:0045087 innate immune response | plant_nlr_resistosome_signaling | gibberellin_della_signaling, root_radial_patterning_shr_scr, trichome_initiation_mbw | ACCEPT |
| ARATH/RBOHD | GO:0006952 defense response | plant_nlr_resistosome_signaling | complex_i_assembly_factors, gpcr_plc_calcium_pkc_signaling | ACCEPT |
| ARATH/RPM1 | GO:0009626 plant-type hypersensitive response | plant_nlr_resistosome_signaling | ACCEPT | |
| BACSU/minD | GO:0032506 cytokinetic process | bacterial_divisome_peptidoglycan_transpeptidation | bacterial_cytochrome_c_maturation_system_i, bacterial_lps_transport, bacterial_nucleotide_excision_repair, bacterial_pst_phosphate_uptake, bacterial_type_ii_sec | ACCEPT |
| CANAL/HSP104 | GO:0034605 cellular response to heat | heat_shock_response | bacterial_nucleotide_excision_repair, coenzyme_q10_biosynthesis, linc_complex, mitochondrial_complex_ii, muth_independent_mismatch_repair, peroxisome-lifecycle, | ACCEPT |
| DANRE/asah2 | GO:0006672 ceramide metabolic process | glycosphingolipid_biosynthesis, sphingolipid_de_novo_synthesis | glycosphingolipid_lysosomal_degradation, gpcr_plc_calcium_pkc_signaling, phenylacetate_catabolism, sphingosine_1_phosphate_rheostat | ACCEPT |
| DANRE/sult1st2 | GO:0006805 xenobiotic metabolic process | phenylacetate_catabolism | ACCEPT | |
| DICDI/cotB | GO:0030435 sporulation resulting in formation of a cellular spore | dicty_sdf2_encapsulation_relay | bacterial_recbcd_end_resection | ACCEPT |
| DROME/18w | GO:0009653 anatomical structure morphogenesis | germ_layer_specification | notch_signaling | ACCEPT |
| DROME/CycA | GO:0000278 mitotic cell cycle | cell_cycle_progression, g1_s_transition, g2_m_transition, metaphase_anaphase_transition_and_mitotic_exit | ACCEPT | |
| DROME/Pde4 | GO:0007268 chemical synaptic transmission | synaptic_vesicle_exocytosis | gpi_anchor_remodeling, phenylacetate_catabolism | ACCEPT |
| DROME/klg | GO:0009653 anatomical structure morphogenesis | germ_layer_specification | notch_signaling | ACCEPT |
| DROME/klg | GO:0030154 cell differentiation | cardiac_specification_network, nucleokinesis, primordial_germ_cell_specification | notch_signaling | ACCEPT |
| DROME/klg | GO:0160108 animal gross anatomical part developmental process | cardiac_specification_network, nucleokinesis, retinal_determination_network | notch_signaling | ACCEPT |
| DROME/loqs | GO:0010468 regulation of gene expression | maternal_to_zygotic_transition, pirna_mediated_germline_silencing, selenocysteine_biosynthesis_incorporation | cgas_sting_signaling | ACCEPT |
| ECOLI/SlyD | GO:0042026 protein refolding | bacterial_dnak_dnaj_refolding_cycle, bacterial_groel_groes_chaperonin_folding | methylcitrate_cycle, phenylacetate_catabolism, retinoid_visual_cycle, urease_biogenesis_urea_hydrolysis | ACCEPT |
| ECOLI/degP | GO:0030163 protein catabolic process | heparan_sulfate_lysosomal_degradation, keratan_chondroitin_sulfate_lysosomal_degradation | gram_negative_omp_biogenesis, phenylacetate_catabolism, pqq_biosynthesis, protease_activation_cascade | ACCEPT |
| EMENI/wA | GO:0046148 pigment biosynthetic process | carotene_backbone_biosynthesis, heme_biosynthesis, siroheme_biosynthesis | alginate_o_acetylation, bacterial_l_carnitine_catabolism, bacterial_unsaturated_fatty_acid_biosynthesis, complex_i_assembly_factors, conidiation_regulatory_casc | ACCEPT |
| EMENI/yA | GO:0042440 pigment metabolic process | carotene_backbone_biosynthesis, heme_biosynthesis, heme_degradation, siroheme_biosynthesis | complex_i_assembly_factors, conidiation_regulatory_cascade | ACCEPT |
| HORVU/MLA10 | GO:0002758 innate immune response-activating signaling pathway | chitin_perception, plant_nlr_resistosome_signaling | ACCEPT | |
| NEUCR/hsp98 | GO:0034605 cellular response to heat | heat_shock_response | bacterial_nucleotide_excision_repair, coenzyme_q10_biosynthesis, linc_complex, mitochondrial_complex_ii, muth_independent_mismatch_repair, peroxisome-lifecycle, | ACCEPT |
| ORYSJ/RGA4 | GO:0002758 innate immune response-activating signaling pathway | chitin_perception, plant_nlr_resistosome_signaling | ACCEPT | |
| ORYSJ/RGA4 | GO:0009626 plant-type hypersensitive response | plant_nlr_resistosome_signaling | ACCEPT | |
| PANAN/crtI | GO:0016120 carotene biosynthetic process | carotene_backbone_biosynthesis | complex_i_assembly_factors | ACCEPT |
| POPTR/WIN6.2C | GO:0098542 defense response to other organism | plant_nlr_resistosome_signaling | chitin_perception, phenylacetate_catabolism | ACCEPT |
| PSEPK/PP_1451 | GO:0000270 peptidoglycan metabolic process | bacterial_divisome_peptidoglycan_transpeptidation, bacterial_rod_complex_peptidoglycan_transpeptidation, d_amino_acid_cell_wall_precursor_supply, gram_negative_lipoprotein_peptidoglycan_tether_remodeling, low_molecular_mass_pbp_peptidoglycan_hydrolysis | phenylacetate_catabolism, pqq_biosynthesis, protease_activation_cascade | ACCEPT |
| PSEPK/fabG | GO:0030497 fatty acid elongation | fatty_acid_elongation_cycle | bacterial_beta_aryl_ether_dimer_cleavage, bacterial_sulfoquinovose_catabolism, complex_i_assembly_factors, type_ii_fatty_acid_synthesis | ACCEPT |
| … 122 more in results.tsv |
Protein fills a step, but the module has an unfilled step in this organism (81)
| gene | term | modules | gaps / other modules | review |
|---|---|---|---|---|
| ARATH/CLF | GO:0050793 regulation of developmental process | autonomous_flowering_pathway | autonomous_flowering_pathway:coolair_proximal_polyadenylation | ACCEPT |
| ARATH/FVE | GO:0010629 negative regulation of gene expression | autonomous_flowering_pathway | autonomous_flowering_pathway:coolair_proximal_polyadenylation | ACCEPT |
| ARATH/FVE | GO:0040029 epigenetic regulation of gene expression | autonomous_flowering_pathway | autonomous_flowering_pathway:coolair_proximal_polyadenylation | ACCEPT |
| ARATH/SWN | GO:0050793 regulation of developmental process | autonomous_flowering_pathway | autonomous_flowering_pathway:coolair_proximal_polyadenylation | ACCEPT |
| DANRE/polb | GO:0006259 DNA metabolic process | bacterial_nucleotide_excision_repair, bacterial_recbcd_end_resection, muth_independent_mismatch_repair | bacterial_nucleotide_excision_repair:liga_sealing, bacterial_recbcd_end_resection:recb_resection, muth_independent_mismatch_repair:repair_synthesis_and_sealing | MODIFY |
| DESRO/K9J287 | GO:0006259 DNA metabolic process | bacterial_nucleotide_excision_repair, bacterial_recbcd_end_resection | bacterial_nucleotide_excision_repair:liga_sealing, bacterial_recbcd_end_resection:recb_resection | MODIFY |
| DORPE/AP180 | GO:0048488 synaptic vesicle endocytosis | synaptic_vesicle_endocytosis | synaptic_vesicle_endocytosis:adaptor_and_coat_assembly, synaptic_vesicle_endocytosis:coat_disassembly | ACCEPT |
| DORPE/P21613 | GO:0007097 nuclear migration | nucleokinesis | nucleokinesis:nuclear_envelope_motor_coupling, nucleokinesis:dynein_lis1_nude_motor | MARK_AS_OVER_ANNOTATED |
| DORPE/TDO | GO:0006569 L-tryptophan catabolic process | kynurenine_nad_de_novo | kynurenine_nad_de_novo:trp_to_kynurenine, kynurenine_nad_de_novo:kynurenine_to_3haa, kynurenine_nad_de_novo:three_haa_to_nad | ACCEPT |
| DROME/Ass | GO:0008652 amino acid biosynthetic process | arginine_biosynthesis | arginine_biosynthesis:glutamate_acetylation_step, arginine_biosynthesis:acetylglutamate_kinase_step, arginine_biosynthesis:acetylglutamyl_phosphate_reductase_st | MODIFY |
| DROME/CG8142 | GO:0006281 DNA repair | bacterial_nucleotide_excision_repair, bacterial_recbcd_end_resection, muth_independent_mismatch_repair | bacterial_nucleotide_excision_repair:liga_sealing, bacterial_recbcd_end_resection:recb_resection, muth_independent_mismatch_repair:repair_synthesis_and_sealing | KEEP_AS_NON_CORE |
| DROME/CG8353 | GO:0055086 nucleobase-containing small molecule metabolic process | pyrimidine_nucleotide_catabolism | pyrimidine_nucleotide_catabolism:thymidine_phosphorolysis | KEEP_AS_NON_CORE |
| DROME/CG8353 | GO:0072527 pyrimidine-containing compound metabolic process | pyrimidine_nucleotide_catabolism | pyrimidine_nucleotide_catabolism:thymidine_phosphorolysis | KEEP_AS_NON_CORE |
| DROME/PolG1 | GO:0006281 DNA repair | bacterial_nucleotide_excision_repair, bacterial_recbcd_end_resection, muth_independent_mismatch_repair | bacterial_nucleotide_excision_repair:liga_sealing, bacterial_recbcd_end_resection:recb_resection, muth_independent_mismatch_repair:repair_synthesis_and_sealing | KEEP_AS_NON_CORE |
| DROME/Prx4 | GO:0019725 cellular homeostasis | glutathione_thioredoxin_redox_systems | glutathione_thioredoxin_redox_systems:glutathione_glutaredoxin_system | MODIFY |
| DROME/RfC38 | GO:0006281 DNA repair | bacterial_recbcd_end_resection | bacterial_recbcd_end_resection:recb_resection | KEEP_AS_NON_CORE |
| ECOLI/SecA | GO:0043952 protein transport by the Sec complex | bacterial_sec_posttranslational_protein_export | bacterial_sec_posttranslational_protein_export:secb_precursor_carriage | ACCEPT |
| GADMO/A0A8C5FPT8 | GO:0016192 vesicle-mediated transport | synaptic_vesicle_exocytosis | synaptic_vesicle_exocytosis:vesicle_priming, synaptic_vesicle_exocytosis:presynaptic_calcium_influx | ACCEPT |
| PANAN/crtB | GO:0016117 carotenoid biosynthetic process | carotene_backbone_biosynthesis | carotene_backbone_biosynthesis:phytoene_desaturation_to_lycopene | ACCEPT |
| PSEPK/efp | GO:0006417 regulation of translation | selenocysteine_biosynthesis_incorporation | selenocysteine_biosynthesis_incorporation:lineage_specific_sec_route | KEEP_AS_NON_CORE |
| PSEPK/moaE | GO:0032324 molybdopterin cofactor biosynthetic process | molybdenum_cofactor_biosynthesis | molybdenum_cofactor_biosynthesis:mo_mpt_formation | MARK_AS_OVER_ANNOTATED |
| SCHJY/shc1 | GO:0006629 lipid metabolic process | methylcitrate_cycle | methylcitrate_cycle:propionate_activation, methylcitrate_cycle:methylcitrate_synthesis, methylcitrate_cycle:methylisocitrate_formation, methylcitrate_cycle:meth | MODIFY |
| SCHPO/SPAC17A5.13 | GO:0009396 folic acid-containing compound biosynthetic process | tetrahydrofolate_biosynthesis | tetrahydrofolate_biosynthesis:dihydroneopterin_dephosphorylation_step | ACCEPT |
| SCHPO/SPAC1B3.01c | GO:0008655 pyrimidine-containing compound salvage | pyrimidine_salvage | pyrimidine_salvage:cmp_kinase_step | KEEP_AS_NON_CORE |
| SCHPO/SPAC3A11.07 | GO:0015980 energy derivation by oxidation of organic compounds | mitochondrial_complex_i_core | mitochondrial_complex_i_core:complex_i_q_module | KEEP_AS_NON_CORE |
| SCHPO/asp1 | GO:0032958 inositol phosphate biosynthetic process | myo_inositol_and_inositol_phosphate_biosynthesis | myo_inositol_and_inositol_phosphate_biosynthesis:myo_inositol_synthesis | ACCEPT |
| SCHPO/caa1 | GO:0043490 malate-aspartate shuttle | malate_aspartate_shuttle | malate_aspartate_shuttle:mas_carriers | KEEP_AS_NON_CORE |
| SCHPO/cut1 | GO:0000280 nuclear division | metaphase_anaphase_transition_and_mitotic_exit | metaphase_anaphase_transition_and_mitotic_exit:securin_separase_cohesin | MARK_AS_OVER_ANNOTATED |
| SCHPO/ecm31 | GO:0072330 monocarboxylic acid biosynthetic process | coenzyme_a_biosynthesis | coenzyme_a_biosynthesis:phosphopantetheine_adenylyltransferase_step | MODIFY |
| SCHPO/maa1 | GO:0043490 malate-aspartate shuttle | malate_aspartate_shuttle | malate_aspartate_shuttle:mas_carriers | KEEP_AS_NON_CORE |
| SCHPO/mus81 | GO:0000724 double-strand break repair via homologous recombination | bacterial_recbcd_end_resection | bacterial_recbcd_end_resection:recb_resection | ACCEPT |
| SCHPO/pcd1 | GO:0055086 nucleobase-containing small molecule metabolic process | pyrimidine_nucleotide_catabolism | pyrimidine_nucleotide_catabolism:uridine_phosphorolysis, pyrimidine_nucleotide_catabolism:thymidine_phosphorolysis, pyrimidine_nucleotide_catabolism:dihydropyri | KEEP_AS_NON_CORE |
| SCHPO/pcd1 | GO:0072527 pyrimidine-containing compound metabolic process | pyrimidine_nucleotide_catabolism, pyrimidine_salvage | pyrimidine_nucleotide_catabolism:uridine_phosphorolysis, pyrimidine_nucleotide_catabolism:thymidine_phosphorolysis, pyrimidine_nucleotide_catabolism:dihydropyri | KEEP_AS_NON_CORE |
| SCHPO/ppc1 | GO:0015937 coenzyme A biosynthetic process | coenzyme_a_biosynthesis | coenzyme_a_biosynthesis:phosphopantetheine_adenylyltransferase_step | ACCEPT |
| SCHPO/rqh1 | GO:0000724 double-strand break repair via homologous recombination | bacterial_recbcd_end_resection | bacterial_recbcd_end_resection:recb_resection | ACCEPT |
| SCHPO/sid2 | GO:0010564 regulation of cell cycle process | metaphase_anaphase_transition_and_mitotic_exit | metaphase_anaphase_transition_and_mitotic_exit:securin_separase_cohesin | KEEP_AS_NON_CORE |
| human/ABCC6 | GO:0009410 response to xenobiotic stimulus | phenylacetate_catabolism | phenylacetate_catabolism:phenylacetate_activation, phenylacetate_catabolism:phenylacetyl_coa_epoxidation, phenylacetate_catabolism:paaJ_thiolysis | KEEP_AS_NON_CORE |
| human/BCAT2 | GO:0009082 branched-chain amino acid biosynthetic process | branched_chain_amino_acid_biosynthesis | branched_chain_amino_acid_biosynthesis:ilvIH_step, branched_chain_amino_acid_biosynthesis:ilvC_step, branched_chain_amino_acid_biosynthesis:ilvD_step, branched_ | KEEP_AS_NON_CORE |
| human/BLM | GO:0000724 double-strand break repair via homologous recombination | bacterial_recbcd_end_resection | bacterial_recbcd_end_resection:recb_resection | ACCEPT |
| human/ENO3 | GO:0006094 gluconeogenesis | entner_doudoroff_and_gluconeogenesis | entner_doudoroff_and_gluconeogenesis:entner_doudoroff_branch | ACCEPT |
| … 41 more in results.tsv |