These computational predictions are reviewed separately from the GOA annotation set used for this review. The assessments below are from this project and do not constitute official GO annotations or endorsement by GO/UniProt. They are not included in the existing annotation review above.
NCBI PGAP External predictions
View prediction review YAML · imuB-pgap-predictions-review.yaml · Review status: COMPLETE
NCBI PGAP names WP_010954010.1 "Y-family DNA polymerase" from the SPARCLE CDD domain architecture 10131054 (a single PolY_like domain, cd03468) and passes on EC 2.7.7.7 and five GO terms: damaged DNA binding, DNA-directed DNA polymerase activity, metal ion binding, DNA replication and DNA repair. ImuB keeps the Y-family polymerase fold but has lost the active-site carboxylates; in the characterized mycobacterial system it is a polymerase-inactive adaptor that links ImuA and the catalytic DnaE2/ImuC to the beta clamp. In the KT2440 sequence every CDD-annotated active-site position carries a non-acidic residue except one. The polymerase activity, the EC number and the metal ion binding are therefore wrong (pseudoenzyme over-annotation). DNA replication and DNA repair are broad processes that the main review refines to translesion synthesis, and damaged DNA binding is unverified for ImuB. The error lies on the architecture: a bare PolY_like architecture cannot distinguish active Y-family polymerases from ImuB, so the product name and GO reach every ImuB with it.
Source documents: genes/PSEPK/imuB/imuB-pgap-prediction-evidence/WP_010954010.1.gp · genes/PSEPK/imuB/imuB-pgap-prediction-evidence/pgap_models.yaml
Review score: 2 = concordant with evidence; 1 = uncertain; 0 = discordant with evidence. This is an assessment score, not a model probability.
Prediction method: NCBI PGAP · Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record ·
PMID:33270901 Review rationale: Uncertain. The term is inherited from active Y-family polymerases, which bind lesion-containing primer-template DNA in their catalytic cleft. The CDD annotation maps a DNA-binding site onto ImuB, but no study has shown that ImuB binds DNA, damaged or otherwise; the characterized interactions are protein-protein (ImuA, DnaE2 and the beta clamp). In the mycobacterial mutasome the predicted DNA-binding component is ImuA', not ImuB. Neither in GOA nor proposed in the main review.
Supporting Evidence: - PMID:20615954: "a putative polymerase-inactive Y-family homolog that binds β as well as the other cassette components, and a predicted DNA-binding protein"
Prediction method: NCBI PGAP · Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record ·
PMID:33270901 PSEUDOENZYME OVERANNOTATION
Review rationale: Wrong. ImuB homologs keep the Y-family fold but lack the active-site carboxylates that coordinate the catalytic metals. In the GenPept record, the CDD active-site positions (7-8, 11-12, 44, 47, 101-102, 154) carry L, L, L, A, P, A, R, A and D in the KT2440 sequence: only one acidic residue remains and the two-metal palm carboxylates are gone. In the ImuA-ImuB-DnaE2 cassette, DNA synthesis is done by DnaE2/ImuC, and ImuB is the polymerase-inactive adaptor (main review core function: protein-macromolecule adaptor activity). The SPARCLE architecture is a single PolY_like domain shared with active polymerases, so it cannot separate ImuB from them.
Supporting Evidence: - PMID:20615954: "Despite retaining structural features characteristic of Y-family members, ImuB homologs lack conserved active-site amino acids required for polymerase activity."
- PMID:20615954: "However, the absence of active-site carboxylates appears incompatible with catalytic function in ImuB"
- PMID:28118378: "ImuB lacks catalytic residues essential for polymerase activities, but possesses β-clamp-binding motif."
Prediction method: NCBI PGAP · Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record ·
PMID:33270901 PSEUDOENZYME OVERANNOTATION
Review rationale: Not supported. In Y-family polymerases, metal ion binding is the coordination of the two catalytic Mg2+/Mn2+ ions by the active-site carboxylates. ImuB has lost those carboxylates, so the basis for the prediction is absent; no other metal site is known in ImuB. The term follows from the same pseudoenzyme over-annotation as the polymerase activity.
Supporting Evidence: - PMID:20615954: "However, the absence of active-site carboxylates appears incompatible with catalytic function in ImuB"
Prediction method: NCBI PGAP · Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record ·
PMID:33270901 Review rationale: Broadly true but less precise. ImuB takes part in damage-induced, DnaE2-dependent translesion synthesis, which the main review proposes as GO:0019985; in GO, translesion synthesis is part of DNA replication, so this term is an ancestor of the specific process. It is not in GOA. ImuB takes part in replication only through lesion bypass, not in normal replicative synthesis.
Supporting Evidence: - PMID:28118378: "Therefore, the study in Mycobacterium tuberculosis suggested that ImuB mediates the access of the cassette components to the replication fork through interaction with the β-clamp [46]."
- PMID:17331811: "accumulation of stationary-phase mutants up to two-fold."
Prediction method: NCBI PGAP · Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record ·
PMID:33270901 Review rationale: In GOA (InterPro IEA), where the main review MODIFIES it to translesion synthesis (GO:0019985) on the grounds that ImuB is an accessory of error-prone lesion bypass rather than a repair enzyme. Scored as less precise for consistency with that action. Strictly, the refinement is lateral rather than a descendant: in GO, translesion synthesis falls under DNA damage tolerance and DNA replication, not DNA repair, because bypass tolerates the lesion rather than removing it. The damage-response context is right; ImuB contributes to alkylation damage tolerance in P. putida.
Supporting Evidence: - PMID:28118378: "This cassette encodes an in silico predicted SulA/RecA like DNA-binding protein ImuA, a nonfunctional homolog of Y-family DNA polymerases ImuB and an error-prone TLS DNA polymerase DnaE2 (later ImuC) [42–45]."
Prediction method: NCBI PGAP · Version: GCF_000007565.2-RS_2026_02_04 (live); GO from WP_ record ·
PMID:33270901 PSEUDOENZYME OVERANNOTATION
Review rationale: Wrong, for the same reason as GO:0003887: EC 2.7.7.7 (DNA-directed DNA polymerase) requires the catalytic carboxylates that ImuB lacks. The UniProt entry carries no EC number.
Supporting Evidence: - PMID:20615954: "Despite retaining structural features characteristic of Y-family members, ImuB homologs lack conserved active-site amino acids required for polymerase activity."