MTBC Gene Atlas

Rv1487 Family assigned · medium auto-curated

H37Rv Rv1487 · MTBC0 mtbc0_001590 · 144 aa · 1686746–1687180 (+) · RefSeq NP_216003.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationNfeD family protein
Revised (this work)NfeD family protein. Pfam: NfeD (PF01957.26).

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

Curated reference (UniProt)

UniProt P71767 TrEMBL · unreviewed · Evidence at protein level
UniProt nameConserved membrane protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category O Post-translational modification, protein turnover, chaperones
U Intracellular trafficking, secretion and vesicular transport
eggNOG descriptionMembrane protein implicated in regulation of membrane protease activity
Orthologous groupCOG1585

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 0.186 · strong purifying
Polymorphic sites (≥ 0.1% of strains) 2 synonymous, 1 missense, 0 nonsense, 0 frameshift

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
NfeDPF01957.26 8.8e-1484–140 NfeD-like C-terminal, partner-binding domain

Functional interaction network (STRING v12, guilt-by-association)

PartnerProductScoreNo text-miningChannels (≥400)
Rv1488 hyp hypothetical protein 973 971 ctx neighborhood:851 cooccurence:750
Rv1489 hyp hypothetical protein 853 854 ctx neighborhood:847
Rv2066 cobIJ bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase 756 757 coexpression:726
Rv2208 cobS adenosylcobinamide-GDP ribazoletransferase 749 750 coexpression:749
Rv0870c integral membrane protein 733 734 coexpression:733
Rv1486c hyp hypothetical protein 833 692 ctx neighborhood:644 textmining:479
Rv1489A hyp hypothetical protein 665 665 ctx neighborhood:608
Rv2070c cobK precorrin-6A reductase 441 441 coexpression:423
Rv2881c cdsA phosphatidate cytidylyltransferase 436 436 coexpression:436
Rv0255c cobQ1 cobyric acid synthase 436 436 coexpression:436
Rv2065 cobH precorrin-8X methylmutase 418 419 coexpression:402
Rv2030c hyp hypothetical protein 402 403 coexpression:403
Rv2071c cobM precorrin-4 C(11)-methyltransferase 472 266

STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.

Evidence

  • Legacy H37Rv annotation: hypothetical protein
  • MTBC0 PGAP product: NfeD family protein
  • Pfam (hmmscan --cut_ga): NfeD PF01957.26 (E=9e-14)
  • (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_216003.1)
  • Domains: Pfam-A via hmmscan --cut_ga — NfeD (PF01957.26)
  • 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 COG1585
  • Curated reference: UniProt P71767 (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)
  • Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 13 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001590|Rv1487|
MPVALIWLIAALVLVGAEALTGDMFLLMLGGGALAASVSSWLLAWPMWADGAVFLLVSVLLLVLVRPAVRRRLTQTKGVQLGIEALEGKKAVVLGRVARDGGQVKLDGQVWTARPLNDGDVFEPGDSVTVVQIDGATAVVFKDV