{
  "abstract": "Background: EndoMS/NucS mediates non-canonical mismatch repair in several archaeal and actinobacterial lineages. A 2017 phylogenomic survey found that NucS and canonical MutS-MutL were largely mutually exclusive, with coexistence concentrated in Halobacteria and Deinococcus-Thermus. This study reassessed this pattern in an expanded prokaryotic reference collection and tested how annotation wording relates to complete multidomain protein architecture.\n\nResults: GFF3 annotations from 23,435 NCBI reference genomes (22,606 Bacteria and 829 Archaea) were screened and annotation-positive candidates were evaluated with Pfam profile HMMs. Complete NucS required NucS_N (PF21003) and NucS_C (PF01939) on the same protein; canonical MutS required five defined MutS profiles on one protein without a same-protein PF01713 warning; and MutL required PF01119 plus PF08676. Annotation screening yielded 1,145 apparent coexistence genomes, whereas 470 met all three profile criteria: 421 Halobacteria, 48 Deinococcota and one highly contaminated Lysobacter korlensis assembly. Across 6,270 unique NucS candidate proteins, 5,189 carried both NucS profiles, 111 were NucS_N-only, 901 were NucS_C-only and 69 matched neither. The 682-genome generic “NucS domain-containing” tier contained 680 testable genomes and 717 unique proteins; 685 were NucS_C-only, eight NucS_N-only, five carried both profiles and 19 carried neither. At genome level, 663/680 testable generic-tier genomes (97.50%) contained at least one NucS-associated domain, but only five contained a same-protein two-domain NucS candidate. Explicit nucS annotations showed 99.63% two-domain concordance; canonical MutS and MutL annotation-positive genomes met strong profile criteria in 96.78% and 97.14%, respectively. The Jaccard overlap between two-domain NucS and strong MutS-MutL positives was 2.18%.\n\nConclusions: The contemporary collection confirms the lineage concentration reported in 2017 rather than identifying a new coexistence lineage. The main advance is an architecture-aware audit showing that broad “NucS domain-containing” annotations are usually valid at the domain level but are poor proxies for complete two-domain NucS. Because annotation-negative genomes were not exhaustively searched, the reported counts are validated positives from an annotation-first workflow, not exhaustive prevalence or gene-loss estimates.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 1,
  "authors": [
    {
      "name": "Kiarash Sadeghian Esfahani"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/f8zavp6x0fe2r.bib",
  "cited_by": 0,
  "doi": "10.1186/s12864-026-13470-8",
  "fulltext_url": null,
  "id": "f8zavp6x0fe2r",
  "issns": [
    "1471-2164"
  ],
  "landing_url": "https://link.springer.com/article/10.1186/s12864-026-13470-8",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Genomics and Phylogenetic Studies"
    ]
  ],
  "openalex": "W7204898840",
  "pdf_url": null,
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-15",
  "publisher": "Springer Science and Business Media LLC",
  "ris": "https://research.draconitic.com/paper/f8zavp6x0fe2r.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:08Z",
      "native_id": "10.1186/s12864-026-13470-8",
      "source": "crossref",
      "url": "https://link.springer.com/article/10.1186/s12864-026-13470-8"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Genomics and Phylogenetic Studies",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Annotation-aware multidomain validation of NucS and MutS-MutL across 23,435 prokaryotic reference genomes",
  "title_text": "Annotation-aware multidomain validation of NucS and MutS-MutL across 23,435 prokaryotic reference genomes",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:08Z",
  "url": "https://research.draconitic.com/paper/f8zavp6x0fe2r",
  "venue": "BMC Genomics",
  "versions": []
}