MTBC Gene Atlas

Rv1439c Family assigned · medium auto-curated

H37Rv Rv1439c · MTBC0 mtbc0_001540 · 141 aa · 1626326–1626751 (-) · RefSeq NP_215955.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationnuclear transport factor 2 family protein
Revised (this work)Nuclear transport factor 2 family protein. Pfam: SnoaL_2 (PF12680.14).

Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.

Curated reference (UniProt)

UniProt O06820 TrEMBL · unreviewed · Evidence at protein level
UniProt nameSnoaL-like domain-containing protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category S Function unknown
eggNOG descriptionSnoaL-like domain
Orthologous groupCOG3631

Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.

Conservation & selection (intra-MTBC, 145 209 strains)

pN/pS 0.846 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 2 synonymous, 5 missense, 0 nonsense, 1 frameshift
Disruption 1 distinct premature-stop/frameshift site(s); most common in 0.10% of strains (151) · clonal

pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.

Domains (Pfam, hmmscan --cut_ga)

PfamAccessioni-EvalueResiduesDescription
SnoaL_2PF12680.14 2.1e-1310–109 SnoaL-like domain

Evidence

  • Legacy H37Rv annotation: hypothetical protein
  • MTBC0 PGAP product: nuclear transport factor 2 family protein
  • Pfam (hmmscan --cut_ga): SnoaL_2 PF12680.14 (E=2e-13)
  • (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)

Sources

  • Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
  • Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215955.1)
  • Domains: Pfam-A via hmmscan --cut_ga — SnoaL_2 (PF12680.14)
  • Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
  • Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021, doi:10.1093/molbev/msab293), eggNOG 5.0 DB (Huerta-Cepas et al. 2019) — OG COG3631
  • Curated reference: UniProt O06820 (TrEMBL, unreviewed; Evidence at protein level)
  • Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001540|Rv1439c|
MQMSASNAFVEGFADFWKAPSPDRLTDHLHPDVVLVRPLSPPRHGLGAAQREFTRILGLLPDLHGEVDRWSQAGDVVFIEFRLIARLGSEVVEWPVVDRFLLRGDKAVERVSYFDSLPLLIKVVKHPSAWRGWLTTMRSRA