id: P72759
gene_symbol: ccmL
taxon:
  id: NCBITaxon:1111708
  label: Synechocystis sp. PCC 6803 substr. Kazusa
status: COMPLETE
locus_tag: sll1030
description: >-
  NCBI PGAP names WP_010871404.1 "beta-carboxysome shell vertex protein CcmL" from the NCBIfam
  equivalog HMM NF053795.1, which carries three GO terms: carboxysome, structural constituent of
  carboxysome shell, and carbon fixation. All three are also in GOA (from UniRule/InterPro IEA, plus an
  IPI for the shell-constituent function). The product name is accurate and more informative than the
  GO terms, since it records the vertex (pentamer) role; GO has no vertex-specific child of
  structural constituent of carboxysome shell, so the shell-constituent term is as precise as the
  ontology allows. Carboxysome and structural constituent of carboxysome shell are correct and agree
  with the main review (CNN). Carbon fixation is the same pathway-membership over-annotation that the
  main review marks as over-annotated: CcmL is a non-catalytic shell protein and RuBisCO performs the
  fixation step. These GO terms appear on the current WP_ protein record (updated 14-APR-2026) but not
  on the January 2026 genome annotation (GCF_000009725.1-RS_2026_01_07), so the genome record lags the
  WP_ records. PGAP did not pass on bacterial microcompartment from the secondary domain HMM
  NF015289, which would have been redundant with carboxysome.
source_documents:
- genes/SYNY3/ccmL/ccmL-pgap-prediction-evidence/WP_010871404.1.gp
- genes/SYNY3/ccmL/ccmL-pgap-prediction-evidence/pgap_models.yaml
- publications/PMID_18292340.md
- publications/PMID_22928045.md
references:
- id: file:SYNY3/ccmL/ccmL-pgap-prediction-evidence/WP_010871404.1.gp
  title: WP_010871404.1.gp
- id: file:SYNY3/ccmL/ccmL-pgap-prediction-evidence/pgap_models.yaml
  title: pgap_models.yaml
- id: PMID:18292340
  title: Atomic-level models of the bacterial carboxysome shell.
- id: PMID:22928045
  title: 'Structural determinants of the outer shell of β-carboxysomes in Synechococcus elongatus PCC 7942: roles for CcmK2, K3-K4, CcmO, and CcmL.'
predictions:
- source_method: NCBI PGAP
  source_version: GCF_000009725.1-RS_2026_01_07 (live); GO from WP_ record
  source_reference_id: PMID:33270901
  predicted_term:
    id: GO:0031470
    label: carboxysome
  predicted_term_type: GO_CC
  review:
    assessment: CNN
    confidence_score: 2
    summary: >-
      Correct. CcmL forms the vertices of the beta-carboxysome shell (structure of this protein,
      PMID:18292340). The same term is in GOA (GO_REF:0000120 IEA) and is ACCEPTed in the main review,
      so the prediction is correct but not novel. Not on the January 2026 genome record; present on the
      newer WP_ record.
    supported_by:
    - reference_id: file:SYNY3/ccmL/ccmL-pgap-prediction-evidence/WP_010871404.1.gp
      supporting_text: /GO_component="GO:0031470 - carboxysome [Evidence IEA]"
    - reference_id: PMID:18292340
      supporting_text: Both proteins assemble to form pentameric structures whose size and shape are compatible with formation of vertices in an icosahedral shell.
- source_method: NCBI PGAP
  source_version: GCF_000009725.1-RS_2026_01_07 (live); GO from WP_ record
  source_reference_id: PMID:33270901
  predicted_term:
    id: GO:0043886
    label: structural constituent of carboxysome shell
  predicted_term_type: GO_MF
  review:
    assessment: CNN
    confidence_score: 2
    summary: >-
      Correct. Although CcmL is a pentameric vertex protein rather than one of the hexameric CcmK
      facet proteins, the vertices are part of the shell, and GO has no vertex-specific child term, so
      this is the most specific applicable MF. The PGAP product name ("shell vertex protein") supplies
      the vertex detail. Also in GOA (IEA and IPI from PMID:18292340) and ACCEPTed in the main review:
      correct but not novel. Not on the January 2026 genome record.
    supported_by:
    - reference_id: file:SYNY3/ccmL/ccmL-pgap-prediction-evidence/WP_010871404.1.gp
      supporting_text: /product="beta-carboxysome shell vertex protein CcmL"
    - reference_id: PMID:22928045
      supporting_text: These data suggested a model for the facet structure of β-carboxysomes with CcmL forming the vertices
- source_method: NCBI PGAP
  source_version: GCF_000009725.1-RS_2026_01_07 (live); GO from WP_ record
  source_reference_id: PMID:33270901
  predicted_term:
    id: GO:0015977
    label: carbon fixation
  predicted_term_type: GO_BP
  review:
    assessment: NPI
    confidence_score: 0
    error_type: COMPLEX_ACTIVITY_TRANSFER
    summary: >-
      Over-annotation. Carbon fixation is performed by RuBisCO, the cargo of the carboxysome; CcmL is a
      non-catalytic shell vertex protein that builds the compartment. Its requirement for efficient
      fixation in vivo is necessity, not participation in the fixation step, so the organelle's process
      has been transferred to a structural subunit. The same term is in GOA via UniRule
      (GO_REF:0000104) and is MARK_AS_OVER_ANNOTATED in the main review; the comparator check found no
      experimental carbon-fixation annotation on any beta-carboxysome shell protein. Not on the January
      2026 genome record. GO lacks a carboxysome-assembly or CO2-concentrating-mechanism process term
      that would be the appropriate process for this family model.
    supported_by:
    - reference_id: file:SYNY3/ccmL/ccmL-pgap-prediction-evidence/pgap_models.yaml
      supporting_text: 'product_name: beta-carboxysome shell vertex protein CcmL'
    - reference_id: PMID:18292340
      supporting_text: The carboxysome is a bacterial microcompartment that functions as a simple organelle by sequestering enzymes involved in carbon fixation.