MTBC Gene Atlas

Rv1976c Family assigned · medium auto-curated

H37Rv Rv1976c · MTBC0 mtbc0_002092 · 135 aa · 2237961–2238368 (-) · RefSeq NP_216492.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationNYN domain-containing protein
Revised (this work)NYN domain-containing protein. Pfam: NYN_YacP (PF05991.18).

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

Curated reference (UniProt)

UniProt O53977 TrEMBL · unreviewed · Evidence at protein level
UniProt nameRNA-binding protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category S Function unknown
eggNOG descriptionYacP-like NYN domain
Orthologous groupCOG3688

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 0.35 · purifying
Polymorphic sites (≥ 0.1% of strains) 2 synonymous, 2 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
NYN_YacPPF05991.18 6.7e-094–125 YacP-like NYN domain

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv2130c mshC cysteine:1D-myo-inosityl 2-amino-2-deoxy--D-glucopyranoside ligase 706 700 coexpression:683
Rv3580c cysS1 cysteine--tRNA ligase 702 696 coexpression:679
Rv3579c rlmB 23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB 519 497 coexpression:480
Rv0881 tRNA/rRNA methyltransferase 516 494 coexpression:477
Rv1644 tsnR 23S rRNA methyltransferase TsnR 516 494 coexpression:477
Rv0380c RNA methyltransferase 516 494 coexpression:477
Rv3577 hyp hypothetical protein 468 469 ctx cooccurence:467
Rv0182c sigG ECF RNA polymerase sigma factor SigG 409 410
Rv3223c sigH ECF RNA polymerase sigma factor SigH 409 410
Rv3681c whiB4 transcriptional regulator WhiB4 409 409
Rv3328c sigJ ECF RNA polymerase sigma factor SigJ 409 409
Rv1221 sigE ECF RNA polymerase sigma factor SigE 409 409
Rv1189 sigI ECF RNA polymerase sigma factor SigI 408 408
Rv1322 hyp hypothetical protein 408 408
Rv3911 sigM ECF RNA polymerase sigma factor SigM 406 407

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: NYN domain-containing protein
  • Pfam (hmmscan --cut_ga): NYN_YacP PF05991.18 (E=7e-09)
  • (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_216492.1)
  • Domains: Pfam-A via hmmscan --cut_ga — NYN_YacP (PF05991.18)
  • 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 COG3688
  • Curated reference: UniProt O53977 (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 — 24 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_002092|Rv1976c|
MRWIVDGMNVIGSRPDGWWRDRHRAMVMLVERLEGWAITKARGDDVTVVFERPPSTAIPSSVVEVAHAPKAAANSADDEIVRLVRSGAQPQEIRVVTSDKALTDRVRDLGAAVYPAERFRDLIDPRGSNAARRTQ