generated_by: projects/RADICAL_SAM/rsam_synthesis.py
definitions:
  reviewed: gene has annotation rows and none is PENDING (ignores stale status:)
  catalysis_established: gene carries a GO:1904047 row, per the project's treatment
    rule
totals:
  genes_in_scope: 29
  resolved: 29
  missing_folder: []
  reviewed: 29
  not_reviewed: {}
  annotation_rows_in_reviewed_genes: 519
data_quality:
  reviewed_but_status_not_COMPLETE: []
actions_in_reviewed_genes:
  ACCEPT: 218
  KEEP_AS_NON_CORE: 65
  MARK_AS_OVER_ANNOTATED: 21
  MODIFY: 122
  NEW: 29
  REMOVE: 51
  TOO_GENERAL: 3
  UNDECIDED: 10
generic_row_treatment:
  GO:0003824:
    label: catalytic activity
    actions:
      KEEP_AS_NON_CORE: 5
      MODIFY: 24
  GO:0005506:
    label: iron ion binding
    actions:
      MODIFY: 3
  GO:0046872:
    label: metal ion binding
    actions:
      MODIFY: 2
  GO:0051536:
    label: iron-sulfur cluster binding
    actions:
      MODIFY: 30
  GO:0051539:
    label: 4 iron, 4 sulfur cluster binding
    actions:
      ACCEPT: 34
      KEEP_AS_NON_CORE: 12
  GO:1904047:
    label: S-adenosyl-L-methionine binding
    actions:
      ACCEPT: 2
      NEW: 19
treatment_rule_deviations: []
treatment_rule_branch_uses:
- gene: TYW1B
  organism: human
  term: GO:0003824
  label: catalytic activity
  action: KEEP_AS_NON_CORE
  expected:
  - MODIFY
  note: 'rule branch: catalysis not established'
- gene: TYW1B
  organism: human
  term: GO:0051539
  label: 4 iron, 4 sulfur cluster binding
  action: KEEP_AS_NON_CORE
  expected:
  - ACCEPT
  - NEW
  note: 'rule branch: catalysis not established'
- gene: RSAD1
  organism: human
  term: GO:0003824
  label: catalytic activity
  action: KEEP_AS_NON_CORE
  expected:
  - MODIFY
  note: 'rule branch: catalysis not established'
- gene: RSAD1
  organism: human
  term: GO:0051539
  label: 4 iron, 4 sulfur cluster binding
  action: KEEP_AS_NON_CORE
  expected:
  - ACCEPT
  - NEW
  note: 'rule branch: catalysis not established'
- gene: RSAD1
  organism: human
  term: GO:0051539
  label: 4 iron, 4 sulfur cluster binding
  action: KEEP_AS_NON_CORE
  expected:
  - ACCEPT
  - NEW
  note: 'rule branch: catalysis not established'
- gene: hemW
  organism: ECOLI
  term: GO:0003824
  label: catalytic activity
  action: KEEP_AS_NON_CORE
  expected:
  - MODIFY
  note: 'rule branch: catalysis not established'
- gene: hemW
  organism: ECOLI
  term: GO:0051539
  label: 4 iron, 4 sulfur cluster binding
  action: KEEP_AS_NON_CORE
  expected:
  - ACCEPT
  - NEW
  note: 'rule branch: catalysis not established'
- gene: hemW
  organism: ECOLI
  term: GO:0051539
  label: 4 iron, 4 sulfur cluster binding
  action: KEEP_AS_NON_CORE
  expected:
  - ACCEPT
  - NEW
  note: 'rule branch: catalysis not established'
- gene: hemW
  organism: ECOLI
  term: GO:0051539
  label: 4 iron, 4 sulfur cluster binding
  action: KEEP_AS_NON_CORE
  expected:
  - ACCEPT
  - NEW
  note: 'rule branch: catalysis not established'
- gene: hemW
  organism: ECOLI
  term: GO:0051539
  label: 4 iron, 4 sulfur cluster binding
  action: KEEP_AS_NON_CORE
  expected:
  - ACCEPT
  - NEW
  note: 'rule branch: catalysis not established'
- gene: pflC
  organism: ECOLI
  term: GO:0051539
  label: 4 iron, 4 sulfur cluster binding
  action: KEEP_AS_NON_CORE
  expected:
  - ACCEPT
  - NEW
  note: 'rule branch: catalysis not established'
- gene: ybiY
  organism: ECOLI
  term: GO:0051539
  label: 4 iron, 4 sulfur cluster binding
  action: KEEP_AS_NON_CORE
  expected:
  - ACCEPT
  - NEW
  note: 'rule branch: catalysis not established'
- gene: yjjW
  organism: ECOLI
  term: GO:0051539
  label: 4 iron, 4 sulfur cluster binding
  action: KEEP_AS_NON_CORE
  expected:
  - ACCEPT
  - NEW
  note: 'rule branch: catalysis not established'
- gene: aslB
  organism: ECOLI
  term: GO:0003824
  label: catalytic activity
  action: KEEP_AS_NON_CORE
  expected:
  - MODIFY
  note: 'rule branch: catalysis not established'
- gene: aslB
  organism: ECOLI
  term: GO:0051539
  label: 4 iron, 4 sulfur cluster binding
  action: KEEP_AS_NON_CORE
  expected:
  - ACCEPT
  - NEW
  note: 'rule branch: catalysis not established'
- gene: ydeM
  organism: ECOLI
  term: GO:0003824
  label: catalytic activity
  action: KEEP_AS_NON_CORE
  expected:
  - MODIFY
  note: 'rule branch: catalysis not established'
- gene: ydeM
  organism: ECOLI
  term: GO:0051539
  label: 4 iron, 4 sulfur cluster binding
  action: KEEP_AS_NON_CORE
  expected:
  - ACCEPT
  - NEW
  note: 'rule branch: catalysis not established'
phase3_rule_conformance:
  scope_file: projects/RADICAL_SAM/data/phase3_scope.yaml
  note: pre-existing reviews, outside the Phase 4 totals, judged by the same rule_check()
    as the genes in scope
  genes_checked: 16
  deviations: []
  branch_uses:
  - gene: PP_1969
    organism: PSEPK
    term: GO:0003824
    label: catalytic activity
    action: KEEP_AS_NON_CORE
    expected:
    - MODIFY
    note: 'rule branch: catalysis not established'
  - gene: PP_1969
    organism: PSEPK
    term: GO:0051539
    label: 4 iron, 4 sulfur cluster binding
    action: KEEP_AS_NON_CORE
    expected:
    - ACCEPT
    - NEW
    note: 'rule branch: catalysis not established'
  - gene: PP_2482
    organism: PSEPK
    term: GO:0003824
    label: catalytic activity
    action: KEEP_AS_NON_CORE
    expected:
    - MODIFY
    note: 'rule branch: catalysis not established'
  - gene: PP_2482
    organism: PSEPK
    term: GO:0051539
    label: 4 iron, 4 sulfur cluster binding
    action: KEEP_AS_NON_CORE
    expected:
    - ACCEPT
    - NEW
    note: 'rule branch: catalysis not established'
  - gene: eryCV
    organism: SACEN
    term: GO:0003824
    label: catalytic activity
    action: KEEP_AS_NON_CORE
    expected:
    - MODIFY
    note: 'rule branch: catalysis not established'
  - gene: eryCV
    organism: SACEN
    term: GO:0051539
    label: 4 iron, 4 sulfur cluster binding
    action: KEEP_AS_NON_CORE
    expected:
    - ACCEPT
    - NEW
    note: 'rule branch: catalysis not established'
  documented_exceptions_used: []
  genes:
  - gene: BACSU/lipA
    uniprot: O32129
    declared_status: IN_PROGRESS
    n_rows: 14
    pending_rows: 0
    catalysis_established: true
    sam_binding_actions:
    - NEW
    generic_rows:
      GO:0003824:
        MODIFY: 1
      GO:0046872:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        ACCEPT: 1
      GO:1904047:
        NEW: 1
  - gene: METEA/pqqE
    uniprot: P71517
    declared_status: COMPLETE
    n_rows: 9
    pending_rows: 0
    catalysis_established: true
    sam_binding_actions:
    - ACCEPT
    generic_rows:
      GO:0003824:
        MODIFY: 1
      GO:0005506:
        MODIFY: 1
      GO:0046872:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        ACCEPT: 1
      GO:1904047:
        ACCEPT: 1
  - gene: POPTR/LIP1
    uniprot: B9H5L9
    declared_status: DRAFT
    n_rows: 11
    pending_rows: 0
    catalysis_established: true
    sam_binding_actions:
    - NEW
    generic_rows:
      GO:0003824:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        ACCEPT: 1
      GO:1904047:
        NEW: 1
  - gene: POPTR/LIP1P-1
    uniprot: B9I666
    declared_status: DRAFT
    n_rows: 11
    pending_rows: 0
    catalysis_established: true
    sam_binding_actions:
    - NEW
    generic_rows:
      GO:0003824:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        ACCEPT: 1
      GO:1904047:
        NEW: 1
  - gene: POPTR/LIP1P-2
    uniprot: B9N2B0
    declared_status: DRAFT
    n_rows: 11
    pending_rows: 0
    catalysis_established: true
    sam_binding_actions:
    - NEW
    generic_rows:
      GO:0003824:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        ACCEPT: 1
      GO:1904047:
        NEW: 1
  - gene: PSEPK/PP_1969
    uniprot: Q88LG4
    declared_status: DRAFT
    n_rows: 7
    pending_rows: 0
    catalysis_established: false
    sam_binding_actions: null
    generic_rows:
      GO:0003824:
        KEEP_AS_NON_CORE: 1
      GO:0046872:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        KEEP_AS_NON_CORE: 1
  - gene: PSEPK/PP_2482
    uniprot: Q88K11
    declared_status: DRAFT
    n_rows: 7
    pending_rows: 0
    catalysis_established: false
    sam_binding_actions: null
    generic_rows:
      GO:0003824:
        KEEP_AS_NON_CORE: 1
      GO:0046872:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        KEEP_AS_NON_CORE: 1
  - gene: PSEPK/bioB
    uniprot: Q88QX2
    declared_status: DRAFT
    n_rows: 8
    pending_rows: 0
    catalysis_established: true
    sam_binding_actions:
    - NEW
    generic_rows:
      GO:0003824:
        MODIFY: 1
      GO:0005506:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        NEW: 1
      GO:1904047:
        NEW: 1
  - gene: PSEPK/hemN
    uniprot: Q88F35
    declared_status: COMPLETE
    n_rows: 9
    pending_rows: 0
    catalysis_established: true
    sam_binding_actions:
    - NEW
    generic_rows:
      GO:0003824:
        MODIFY: 1
      GO:0046872:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        ACCEPT: 1
      GO:1904047:
        NEW: 1
  - gene: PSEPK/lipA
    uniprot: Q88DM5
    declared_status: DRAFT
    n_rows: 9
    pending_rows: 0
    catalysis_established: true
    sam_binding_actions:
    - NEW
    generic_rows:
      GO:0003824:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        ACCEPT: 1
      GO:1904047:
        NEW: 1
  - gene: PSEPK/moaA
    uniprot: Q88E69
    declared_status: COMPLETE
    n_rows: 9
    pending_rows: 0
    catalysis_established: true
    sam_binding_actions:
    - ACCEPT
    generic_rows:
      GO:0003824:
        MODIFY: 1
      GO:0046872:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        ACCEPT: 1
      GO:1904047:
        ACCEPT: 1
  - gene: PSEPK/pqqE
    uniprot: Q88QV8
    declared_status: DRAFT
    n_rows: 8
    pending_rows: 0
    catalysis_established: true
    sam_binding_actions:
    - ACCEPT
    generic_rows:
      GO:0003824:
        MODIFY: 1
      GO:0005506:
        MODIFY: 1
      GO:0046872:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        ACCEPT: 1
      GO:1904047:
        ACCEPT: 1
  - gene: SACEN/eryCV
    uniprot: A4F7N2
    declared_status: COMPLETE
    n_rows: 5
    pending_rows: 0
    catalysis_established: false
    sam_binding_actions: null
    generic_rows:
      GO:0003824:
        KEEP_AS_NON_CORE: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        KEEP_AS_NON_CORE: 1
  - gene: SCHPO/bio2
    uniprot: O59778
    declared_status: DRAFT
    n_rows: 11
    pending_rows: 0
    catalysis_established: true
    sam_binding_actions:
    - NEW
    generic_rows:
      GO:0003824:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:1904047:
        NEW: 1
  - gene: STAWA/cfr
    uniprot: A2AXI2
    declared_status: DRAFT
    n_rows: 14
    pending_rows: 0
    catalysis_established: true
    sam_binding_actions:
    - NEW
    generic_rows:
      GO:0003824:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:0051539:
        ACCEPT: 1
      GO:1904047:
        NEW: 1
  - gene: yeast/BIO2
    uniprot: P32451
    declared_status: DRAFT
    n_rows: 16
    pending_rows: 0
    catalysis_established: true
    sam_binding_actions:
    - NEW
    generic_rows:
      GO:0003824:
        MODIFY: 1
      GO:0051536:
        MODIFY: 1
      GO:1904047:
        NEW: 1
documented_rule_exceptions:
  file: projects/RADICAL_SAM/data/rule_exceptions.yaml
  declared: []
  used: []
  stale: []
sam_binding:
  scope: reviewed genes only
  new_rows_absent_from_goa:
  - CDK5RAP1
  - CDKAL1
  - ELP3
  - LIAS
  - MOCS1
  - RSAD2
  - TYW1
  - bioB
  - epmB
  - hemN
  - lipA
  - miaB
  - nrdG
  - pflA
  - rimO
  - rlmN
  - thiH
  - ygiQ
  - yhcC
  already_in_goa:
  - moaA
  - queE
  absent_catalysis_not_established:
  - RSAD1
  - TYW1B
  - aslB
  - hemW
  - pflC
  - ybiY
  - ydeM
  - yjjW
  not_reviewed_so_not_classified: []
core_function_go_terms:
  GO:0051539: 21
  GO:1904047: 21
  GO:0043364: 4
  GO:0016992: 2
  GO:0061798: 2
  GO:0035597: 2
  GO:0020037: 2
  GO:0030674: 1
  GO:0061799: 1
  GO:0035598: 1
  GO:0106261: 1
  GO:0102521: 1
  GO:0010181: 1
  GO:0004076: 1
  GO:0051537: 1
  GO:0043365: 1
  GO:0070040: 1
  GO:0002935: 1
  GO:0103039: 1
  GO:0036355: 1
  GO:0051989: 1
  GO:0030170: 1
  GO:0031419: 1
  GO:0019843: 1
  GO:0000049: 1
genes_whose_core_activity_has_no_go_term:
- RSAD2
- epmB
- hemW
- queE
- ygiQ
- yhcC
genes_with_no_core_function:
- TYW1B
- aslB
- ydeM
proposed_new_terms:
- gene: RSAD2
  organism: human
  proposed_name: S-adenosyl-L-methionine-dependent CTP dehydratase activity
- gene: nrdG
  organism: ECOLI
  proposed_name: '[anaerobic ribonucleoside-triphosphate reductase]-activating enzyme
    activity'
- gene: hemW
  organism: ECOLI
  proposed_name: heme chaperone activity
- gene: queE
  organism: ECOLI
  proposed_name: 7-carboxy-7-deazaguanine synthase activity
- gene: epmB
  organism: ECOLI
  proposed_name: L-lysine 2,3-aminomutase ((R)-beta-lysine-forming) activity
- gene: ygiQ
  organism: ECOLI
  proposed_name: 23S rRNA (dihydrouridine(2449)/cytidine(2498)-ribose-5'-C)-methyltransferase
    activity
- gene: yhcC
  organism: ECOLI
  proposed_name: tRNA 5-carboxymethylaminomethyl-2-thiouridine(34) demodifying activity
source_defects:
- gene: nrdG
  organism: ECOLI
  defect_type: WRONG_GENE_PRODUCT
  resource: OTHER
  record: null
  requested_change: REPOINT
  asserted_value: UniProtKB:P0A9N8
  corrected_value: UniProtKB:P28903
  confidence: PROBABLE
- gene: nrdG
  organism: ECOLI
  defect_type: WRONG_TERM
  resource: INTERPRO
  record: InterPro:IPR012837
  requested_change: REPOINT
  asserted_value: GO:0043365
  corrected_value: GO:0043364
  confidence: CONFIRMED
- gene: hemN
  organism: ECOLI
  defect_type: WRONG_TERM
  resource: INTERPRO
  record: InterPro:IPR004558
  requested_change: REPOINT
  asserted_value: GO:0004109
  corrected_value: GO:0051989
  confidence: CONFIRMED
- gene: hemW
  organism: ECOLI
  defect_type: WRONG_TERM
  resource: INTERPRO
  record: InterPro:IPR004559
  requested_change: DELETE_VALUE
  asserted_value: GO:0004109
  corrected_value: null
  confidence: CONFIRMED
- gene: hemW
  organism: ECOLI
  defect_type: WRONG_TERM
  resource: INTERPRO
  record: InterPro:IPR004559
  requested_change: DELETE_VALUE
  asserted_value: GO:0006779
  corrected_value: null
  confidence: CONFIRMED
- gene: hemW
  organism: ECOLI
  defect_type: WRONG_TERM
  resource: UNIPROT
  record: UniProtKB:Q9CGF7
  requested_change: CHECK
  asserted_value: GO:0006779
  corrected_value: null
  confidence: SUSPECTED
- gene: pflC
  organism: ECOLI
  defect_type: WRONG_TERM
  resource: UNIPROT
  record: UniProtKB:P32675
  requested_change: REPOINT
  asserted_value: RHEA:19225
  corrected_value: RHEA:61976
  confidence: PROBABLE
- gene: pflC
  organism: ECOLI
  defect_type: WRONG_TERM
  resource: UNIPROT
  record: UniProtKB:P32675
  requested_change: DELETE_VALUE
  asserted_value: EC:1.97.1.4
  corrected_value: null
  confidence: PROBABLE
- gene: ybiY
  organism: ECOLI
  defect_type: WRONG_TERM
  resource: UNIPROT
  record: UniProtKB:P75794
  requested_change: REPOINT
  asserted_value: RHEA:19225
  corrected_value: RHEA:61976
  confidence: PROBABLE
- gene: ybiY
  organism: ECOLI
  defect_type: WRONG_TERM
  resource: UNIPROT
  record: UniProtKB:P75794
  requested_change: DELETE_VALUE
  asserted_value: EC:1.97.1.4
  corrected_value: null
  confidence: PROBABLE
remove_breakdown:
  uninformative_protein_binding: 36
  asserted_row_rejected_on_biology: 3
  propagated_mapping_or_inference: 12
remove_non_protein_binding_by_evidence:
  IBA: 3
  IEA: 8
  IMP: 1
  ISS: 1
  NAS: 2
source_defect_summary:
  total: 10
  by_resource:
    INTERPRO: 4
    OTHER: 1
    UNIPROT: 5
  interpro_defects: 4
  distinct_interpro_entries:
  - InterPro:IPR004558
  - InterPro:IPR004559
  - InterPro:IPR012837
  pflb_substrate_pushes:
  - nrdG:GO:0043365
  - pflC:RHEA:19225
  - pflC:EC:1.97.1.4
  - ybiY:RHEA:19225
  - ybiY:EC:1.97.1.4
ibas_whose_node_placement_was_argued:
- gene: LIAS
  organism: human
  term: GO:0009107
  label: obsolete lipoate biosynthetic process
  action: MODIFY
  root_cause: TERM_SCOPING_PROBLEM
  failure_modes: []
  sources:
  - id: PANTHER:PTN000101947
    status: SOURCE_STALE_OR_MISSING
- gene: RSAD2
  organism: human
  term: GO:0005739
  label: mitochondrion
  action: KEEP_AS_NON_CORE
  root_cause: NO_FAILURE_NON_CORE
  failure_modes: []
  sources:
  - id: PANTHER:PTN002724426
    status: SUPPORTS_TRANSFER
- gene: RSAD2
  organism: human
  term: GO:0005783
  label: endoplasmic reticulum
  action: ACCEPT
  root_cause: NO_FAILURE_CORE
  failure_modes: []
  sources:
  - id: PANTHER:PTN002724426
    status: SUPPORTS_TRANSFER
- gene: RSAD2
  organism: human
  term: GO:0050778
  label: positive regulation of immune response
  action: TOO_GENERAL
  root_cause: TERM_SCOPING_PROBLEM
  failure_modes: []
  sources:
  - id: PANTHER:PTN002724426
    status: SUPPORTS_TRANSFER
- gene: RSAD2
  organism: human
  term: GO:0051539
  label: 4 iron, 4 sulfur cluster binding
  action: ACCEPT
  root_cause: NO_FAILURE_CORE
  failure_modes: []
  sources:
  - id: PANTHER:PTN000481986
    status: SUPPORTS_TRANSFER
- gene: RSAD2
  organism: human
  term: GO:0051607
  label: defense response to virus
  action: ACCEPT
  root_cause: NO_FAILURE_CORE
  failure_modes: []
  sources:
  - id: PANTHER:PTN002724426
    status: SUPPORTS_TRANSFER
- gene: CDKAL1
  organism: human
  term: GO:0005783
  label: endoplasmic reticulum
  action: MODIFY
  root_cause: TERM_SCOPING_PROBLEM
  failure_modes:
  - GRANULARITY_MISMATCH
  sources:
  - id: PANTHER:PTN000228711
    status: SUPPORTS_TRANSFER
- gene: CDK5RAP1
  organism: human
  term: GO:0005829
  label: cytosol
  action: MARK_AS_OVER_ANNOTATED
  root_cause: PROPAGATION_BAD
  failure_modes:
  - COMPARTMENT_OR_COMPLEX_MISMATCH
  sources:
  - id: PANTHER:PTN000228824
    status: SUPPORTS_SOURCE_BUT_NOT_TARGET
  - id: UniProtKB:P0AEI1
    status: SUPPORTS_SOURCE_BUT_NOT_TARGET
  - id: UniProtKB:Q96SZ6
    status: SOURCE_WEAK_OR_INFERRED
- gene: ELP3
  organism: human
  term: GO:0005737
  label: cytoplasm
  action: MODIFY
  root_cause: TERM_SCOPING_PROBLEM
  failure_modes:
  - GRANULARITY_MISMATCH
  sources:
  - id: PANTHER:PTN000123913
    status: SUPPORTS_TRANSFER
- gene: TYW1B
  organism: human
  term: GO:0031591
  label: wybutosine biosynthetic process
  action: UNDECIDED
  root_cause: UNRESOLVED
  failure_modes:
  - PSEUDO_OR_SUBACTIVITY_LOSS
  sources:
  - id: PANTHER:PTN000358104
    status: SUPPORTS_SOURCE_BUT_NOT_TARGET
  - id: SGD:S000006128
    status: SUPPORTS_SOURCE_BUT_NOT_TARGET
- gene: RSAD1
  organism: human
  term: GO:0005737
  label: cytoplasm
  action: MODIFY
  root_cause: TERM_SCOPING_PROBLEM
  failure_modes:
  - GRANULARITY_MISMATCH
  sources:
  - id: PANTHER:PTN000358281
    status: SUPPORTS_TRANSFER
- gene: RSAD1
  organism: human
  term: GO:0006779
  label: porphyrin-containing compound biosynthetic process
  action: REMOVE
  root_cause: PROPAGATION_BAD
  failure_modes:
  - PSEUDO_OR_SUBACTIVITY_LOSS
  - FUNCTIONAL_DIVERGENCE
  sources:
  - id: PANTHER:PTN000358281
    status: SUPPORTS_SOURCE_BUT_NOT_TARGET
- gene: moaA
  organism: ECOLI
  term: GO:0061799
  label: cyclic pyranopterin monophosphate synthase activity
  action: REMOVE
  root_cause: PROPAGATION_BAD
  failure_modes:
  - ROLE_CONFLATION
  sources:
  - id: PANTHER:PTN000539172
    status: SUPPORTS_SOURCE_BUT_NOT_TARGET
  - id: UniProtKB:Q9NZB8
    status: SUPPORTS_SOURCE_BUT_NOT_TARGET
- gene: nrdG
  organism: ECOLI
  term: GO:0015949
  label: nucleobase-containing small molecule interconversion
  action: MARK_AS_OVER_ANNOTATED
  root_cause: TERM_SCOPING_PROBLEM
  failure_modes:
  - ROLE_CONFLATION
  sources:
  - id: PANTHER:PTN001576428
    status: SOURCE_WEAK_OR_INFERRED
  - id: UniProtKB:P0A9N8
    status: SOURCE_WEAK_OR_INFERRED
- gene: hemN
  organism: ECOLI
  term: GO:0006779
  label: porphyrin-containing compound biosynthetic process
  action: MODIFY
  root_cause: TERM_SCOPING_PROBLEM
  failure_modes:
  - GRANULARITY_MISMATCH
  sources:
  - id: PANTHER:PTN000358281
    status: SUPPORTS_TRANSFER
- gene: hemW
  organism: ECOLI
  term: GO:0006779
  label: porphyrin-containing compound biosynthetic process
  action: REMOVE
  root_cause: PROPAGATION_BAD
  failure_modes:
  - PSEUDO_OR_SUBACTIVITY_LOSS
  - FUNCTIONAL_DIVERGENCE
  sources:
  - id: PANTHER:PTN000358281
    status: SUPPORTS_SOURCE_BUT_NOT_TARGET
- gene: queE
  organism: ECOLI
  term: GO:0008616
  label: tRNA queuosine(34) biosynthetic process
  action: MODIFY
  root_cause: TERM_SCOPING_PROBLEM
  failure_modes:
  - GRANULARITY_MISMATCH
  sources:
  - id: PANTHER:PTN000881343
    status: SUPPORTS_TRANSFER
- gene: queE
  organism: ECOLI
  term: GO:0016840
  label: carbon-nitrogen lyase activity
  action: MODIFY
  root_cause: TERM_SCOPING_PROBLEM
  failure_modes:
  - GRANULARITY_MISMATCH
  sources:
  - id: PANTHER:PTN000881343
    status: SUPPORTS_TRANSFER
- gene: epmB
  organism: ECOLI
  term: GO:0016869
  label: intramolecular aminotransferase activity
  action: MODIFY
  root_cause: TERM_SCOPING_PROBLEM
  failure_modes:
  - GRANULARITY_MISMATCH
  sources:
  - id: PANTHER:PTN000776770
    status: SUPPORTS_TRANSFER
  - id: UniProtKB:P39280
    status: SUPPORTS_TRANSFER
iba_root_causes:
  NO_FAILURE_CORE: 3
  NO_FAILURE_NON_CORE: 1
  PROPAGATION_BAD: 4
  TERM_SCOPING_PROBLEM: 10
  UNRESOLVED: 1
genes:
  LIAS:
    organism: human
    uniprot: O43766
    declared_status: COMPLETE
    reviewed: true
    n_rows: 21
    pending_rows: 0
    actions:
      ACCEPT: 11
      MARK_AS_OVER_ANNOTATED: 3
      MODIFY: 6
      NEW: 1
    core_functions:
    - kind: GO
      id: GO:0016992
      label: lipoate synthase activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  RSAD2:
    organism: human
    uniprot: Q8WXG1
    declared_status: COMPLETE
    reviewed: true
    n_rows: 59
    pending_rows: 0
    actions:
      ACCEPT: 26
      KEEP_AS_NON_CORE: 17
      MARK_AS_OVER_ANNOTATED: 1
      MODIFY: 2
      NEW: 2
      REMOVE: 8
      TOO_GENERAL: 3
    core_functions:
    - kind: PROPOSED
      name: S-adenosyl-L-methionine-dependent CTP dehydratase activity
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    - kind: GO
      id: GO:0030674
      label: protein-macromolecule adaptor activity
      slot: molecular_function
    n_core_proposed: 1
    sam_binding_actions:
    - NEW
    catalysis_established: true
  MOCS1:
    organism: human
    uniprot: Q9NZB8
    declared_status: COMPLETE
    reviewed: true
    n_rows: 30
    pending_rows: 0
    actions:
      ACCEPT: 19
      KEEP_AS_NON_CORE: 7
      MODIFY: 3
      NEW: 1
    core_functions:
    - kind: GO
      id: GO:0061798
      label: GTP 3',8'-cyclase activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    - kind: GO
      id: GO:0061799
      label: cyclic pyranopterin monophosphate synthase activity
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  CDKAL1:
    organism: human
    uniprot: Q5VV42
    declared_status: COMPLETE
    reviewed: true
    n_rows: 23
    pending_rows: 0
    actions:
      ACCEPT: 8
      KEEP_AS_NON_CORE: 2
      MODIFY: 9
      NEW: 1
      REMOVE: 3
    core_functions:
    - kind: GO
      id: GO:0035598
      label: tRNA (N(6)-L-threonylcarbamoyladenosine(37)-C(2))-methylthiotransferase
        activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  CDK5RAP1:
    organism: human
    uniprot: Q96SZ6
    declared_status: COMPLETE
    reviewed: true
    n_rows: 28
    pending_rows: 0
    actions:
      ACCEPT: 12
      KEEP_AS_NON_CORE: 2
      MARK_AS_OVER_ANNOTATED: 4
      MODIFY: 6
      NEW: 1
      REMOVE: 2
      UNDECIDED: 1
    core_functions:
    - kind: GO
      id: GO:0035597
      label: tRNA-2-methylthio-N(6)-dimethylallyladenosine(37) synthase activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  ELP3:
    organism: human
    uniprot: Q9H9T3
    declared_status: COMPLETE
    reviewed: true
    n_rows: 42
    pending_rows: 0
    actions:
      ACCEPT: 10
      KEEP_AS_NON_CORE: 11
      MARK_AS_OVER_ANNOTATED: 3
      MODIFY: 12
      NEW: 1
      REMOVE: 4
      UNDECIDED: 1
    core_functions:
    - kind: GO
      id: GO:0106261
      label: tRNA uridine(34) acetyltransferase activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  TYW1:
    organism: human
    uniprot: Q9NV66
    declared_status: COMPLETE
    reviewed: true
    n_rows: 9
    pending_rows: 0
    actions:
      ACCEPT: 4
      MODIFY: 3
      NEW: 2
    core_functions:
    - kind: GO
      id: GO:0102521
      label: tRNA-4-demethylwyosine synthase activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    - kind: GO
      id: GO:0010181
      label: FMN binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  TYW1B:
    organism: human
    uniprot: Q6NUM6
    declared_status: COMPLETE
    reviewed: true
    n_rows: 8
    pending_rows: 0
    actions:
      KEEP_AS_NON_CORE: 2
      MODIFY: 1
      REMOVE: 1
      UNDECIDED: 4
    core_functions: []
    n_core_proposed: 0
    sam_binding_actions: null
    catalysis_established: false
  RSAD1:
    organism: human
    uniprot: Q9HA92
    declared_status: COMPLETE
    reviewed: true
    n_rows: 12
    pending_rows: 0
    actions:
      ACCEPT: 3
      KEEP_AS_NON_CORE: 3
      MODIFY: 3
      REMOVE: 3
    core_functions:
    - kind: GO
      id: GO:0020037
      label: heme binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions: null
    catalysis_established: false
  bioB:
    organism: ECOLI
    uniprot: P12996
    declared_status: COMPLETE
    reviewed: true
    n_rows: 16
    pending_rows: 0
    actions:
      ACCEPT: 9
      KEEP_AS_NON_CORE: 1
      MODIFY: 3
      NEW: 1
      REMOVE: 2
    core_functions:
    - kind: GO
      id: GO:0004076
      label: biotin synthase activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:0051537
      label: 2 iron, 2 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  lipA:
    organism: ECOLI
    uniprot: P60716
    declared_status: COMPLETE
    reviewed: true
    n_rows: 19
    pending_rows: 0
    actions:
      ACCEPT: 8
      MARK_AS_OVER_ANNOTATED: 1
      MODIFY: 7
      NEW: 1
      REMOVE: 2
    core_functions:
    - kind: GO
      id: GO:0016992
      label: lipoate synthase activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  moaA:
    organism: ECOLI
    uniprot: P30745
    declared_status: COMPLETE
    reviewed: true
    n_rows: 17
    pending_rows: 0
    actions:
      ACCEPT: 11
      KEEP_AS_NON_CORE: 1
      MARK_AS_OVER_ANNOTATED: 1
      MODIFY: 3
      REMOVE: 1
    core_functions:
    - kind: GO
      id: GO:0061798
      label: GTP 3',8'-cyclase activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - ACCEPT
    catalysis_established: true
  nrdG:
    organism: ECOLI
    uniprot: P0A9N8
    declared_status: COMPLETE
    reviewed: true
    n_rows: 23
    pending_rows: 0
    actions:
      ACCEPT: 8
      MARK_AS_OVER_ANNOTATED: 4
      MODIFY: 4
      NEW: 3
      REMOVE: 4
    core_functions:
    - kind: GO
      id: GO:0043364
      label: glycyl-radical enzyme activating activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  pflA:
    organism: ECOLI
    uniprot: P0A9N4
    declared_status: COMPLETE
    reviewed: true
    n_rows: 22
    pending_rows: 0
    actions:
      ACCEPT: 11
      KEEP_AS_NON_CORE: 1
      MARK_AS_OVER_ANNOTATED: 1
      MODIFY: 6
      NEW: 1
      REMOVE: 2
    core_functions:
    - kind: GO
      id: GO:0043365
      label: '[formate-C-acetyltransferase]-activating enzyme activity'
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  rlmN:
    organism: ECOLI
    uniprot: P36979
    declared_status: COMPLETE
    reviewed: true
    n_rows: 32
    pending_rows: 0
    actions:
      ACCEPT: 16
      KEEP_AS_NON_CORE: 3
      MODIFY: 5
      NEW: 1
      REMOVE: 7
    core_functions:
    - kind: GO
      id: GO:0070040
      label: rRNA (adenine(2503)-C2-)-methyltransferase activity
      slot: molecular_function
    - kind: GO
      id: GO:0002935
      label: tRNA (adenine(37)-C2)-methyltransferase activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  miaB:
    organism: ECOLI
    uniprot: P0AEI1
    declared_status: COMPLETE
    reviewed: true
    n_rows: 19
    pending_rows: 0
    actions:
      ACCEPT: 10
      MODIFY: 7
      NEW: 1
      REMOVE: 1
    core_functions:
    - kind: GO
      id: GO:0035597
      label: tRNA-2-methylthio-N(6)-dimethylallyladenosine(37) synthase activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  rimO:
    organism: ECOLI
    uniprot: P0AEI4
    declared_status: COMPLETE
    reviewed: true
    n_rows: 17
    pending_rows: 0
    actions:
      ACCEPT: 10
      MODIFY: 5
      NEW: 1
      REMOVE: 1
    core_functions:
    - kind: GO
      id: GO:0103039
      label: protein methylthiotransferase activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  thiH:
    organism: ECOLI
    uniprot: P30140
    declared_status: COMPLETE
    reviewed: true
    n_rows: 19
    pending_rows: 0
    actions:
      ACCEPT: 13
      MARK_AS_OVER_ANNOTATED: 1
      MODIFY: 3
      NEW: 1
      REMOVE: 1
    core_functions:
    - kind: GO
      id: GO:0036355
      label: 2-iminoacetate synthase activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  hemN:
    organism: ECOLI
    uniprot: P32131
    declared_status: COMPLETE
    reviewed: true
    n_rows: 14
    pending_rows: 0
    actions:
      ACCEPT: 8
      MODIFY: 5
      NEW: 1
    core_functions:
    - kind: GO
      id: GO:0051989
      label: coproporphyrinogen dehydrogenase activity
      slot: molecular_function
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions:
    - NEW
    catalysis_established: true
  hemW:
    organism: ECOLI
    uniprot: P52062
    declared_status: COMPLETE
    reviewed: true
    n_rows: 15
    pending_rows: 0
    actions:
      ACCEPT: 4
      KEEP_AS_NON_CORE: 6
      MODIFY: 1
      REMOVE: 4
    core_functions:
    - kind: PROPOSED
      name: heme chaperone activity
    - kind: GO
      id: GO:0020037
      label: heme binding
      slot: molecular_function
    n_core_proposed: 1
    sam_binding_actions: null
    catalysis_established: false
  queE:
    organism: ECOLI
    uniprot: P64554
    declared_status: COMPLETE
    reviewed: true
    n_rows: 14
    pending_rows: 0
    actions:
      ACCEPT: 4
      KEEP_AS_NON_CORE: 2
      MODIFY: 8
    core_functions:
    - kind: PROPOSED
      name: 7-carboxy-7-deazaguanine synthase activity
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    n_core_proposed: 1
    sam_binding_actions:
    - ACCEPT
    catalysis_established: true
  epmB:
    organism: ECOLI
    uniprot: P39280
    declared_status: COMPLETE
    reviewed: true
    n_rows: 9
    pending_rows: 0
    actions:
      ACCEPT: 2
      MARK_AS_OVER_ANNOTATED: 1
      MODIFY: 4
      NEW: 2
    core_functions:
    - kind: PROPOSED
      name: L-lysine 2,3-aminomutase ((R)-beta-lysine-forming) activity
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    - kind: GO
      id: GO:0030170
      label: pyridoxal phosphate binding
      slot: molecular_function
    n_core_proposed: 1
    sam_binding_actions:
    - NEW
    catalysis_established: true
  pflC:
    organism: ECOLI
    uniprot: P32675
    declared_status: COMPLETE
    reviewed: true
    n_rows: 8
    pending_rows: 0
    actions:
      ACCEPT: 3
      KEEP_AS_NON_CORE: 1
      MODIFY: 3
      REMOVE: 1
    core_functions:
    - kind: GO
      id: GO:0043364
      label: glycyl-radical enzyme activating activity
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions: null
    catalysis_established: false
  ybiY:
    organism: ECOLI
    uniprot: P75794
    declared_status: COMPLETE
    reviewed: true
    n_rows: 8
    pending_rows: 0
    actions:
      ACCEPT: 3
      KEEP_AS_NON_CORE: 1
      MODIFY: 3
      REMOVE: 1
    core_functions:
    - kind: GO
      id: GO:0043364
      label: glycyl-radical enzyme activating activity
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions: null
    catalysis_established: false
  yjjW:
    organism: ECOLI
    uniprot: P39409
    declared_status: COMPLETE
    reviewed: true
    n_rows: 10
    pending_rows: 0
    actions:
      ACCEPT: 3
      KEEP_AS_NON_CORE: 1
      MODIFY: 3
      REMOVE: 3
    core_functions:
    - kind: GO
      id: GO:0043364
      label: glycyl-radical enzyme activating activity
      slot: molecular_function
    n_core_proposed: 0
    sam_binding_actions: null
    catalysis_established: false
  aslB:
    organism: ECOLI
    uniprot: P25550
    declared_status: COMPLETE
    reviewed: true
    n_rows: 5
    pending_rows: 0
    actions:
      KEEP_AS_NON_CORE: 2
      MODIFY: 1
      UNDECIDED: 2
    core_functions: []
    n_core_proposed: 0
    sam_binding_actions: null
    catalysis_established: false
  ydeM:
    organism: ECOLI
    uniprot: P76134
    declared_status: COMPLETE
    reviewed: true
    n_rows: 6
    pending_rows: 0
    actions:
      KEEP_AS_NON_CORE: 2
      MARK_AS_OVER_ANNOTATED: 1
      MODIFY: 1
      UNDECIDED: 2
    core_functions: []
    n_core_proposed: 0
    sam_binding_actions: null
    catalysis_established: false
  ygiQ:
    organism: ECOLI
    uniprot: Q46861
    declared_status: COMPLETE
    reviewed: true
    n_rows: 8
    pending_rows: 0
    actions:
      ACCEPT: 1
      MODIFY: 3
      NEW: 4
    core_functions:
    - kind: PROPOSED
      name: 23S rRNA (dihydrouridine(2449)/cytidine(2498)-ribose-5'-C)-methyltransferase
        activity
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    - kind: GO
      id: GO:0031419
      label: cobalamin binding
      slot: molecular_function
    - kind: GO
      id: GO:0019843
      label: rRNA binding
      slot: molecular_function
    n_core_proposed: 1
    sam_binding_actions:
    - NEW
    catalysis_established: true
  yhcC:
    organism: ECOLI
    uniprot: P0ADW6
    declared_status: COMPLETE
    reviewed: true
    n_rows: 6
    pending_rows: 0
    actions:
      ACCEPT: 1
      MODIFY: 2
      NEW: 3
    core_functions:
    - kind: PROPOSED
      name: tRNA 5-carboxymethylaminomethyl-2-thiouridine(34) demodifying activity
    - kind: GO
      id: GO:0051539
      label: 4 iron, 4 sulfur cluster binding
      slot: molecular_function
    - kind: GO
      id: GO:1904047
      label: S-adenosyl-L-methionine binding
      slot: molecular_function
    - kind: GO
      id: GO:0000049
      label: tRNA binding
      slot: molecular_function
    n_core_proposed: 1
    sam_binding_actions:
    - NEW
    catalysis_established: true