MTBC Gene Atlas

Rv1996 Resolved · high auto-curated

H37Rv Rv1996 · MTBC0 mtbc0_002123 · 317 aa · 2262617–2263570 (+) · RefSeq NP_216512.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)universal stress protein
MTBC0 PGAP re-annotationuniversal stress protein
Revised (this work)Universal stress protein. Pfam: Usp (PF00582.33).

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

Curated reference (UniProt)

UniProt P9WLP1 SwissProt · reviewed · Evidence at protein level
UniProt nameUniversal stress protein Rv1996

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category T Signal transduction mechanisms
eggNOG descriptionUniversal stress protein
Orthologous groupCOG0589
Gene Ontology (8) GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944

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 0.576 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 3 synonymous, 5 missense, 0 nonsense, 2 frameshift
Disruption 2 distinct premature-stop/frameshift site(s); most common in 0.68% of strains (981) · 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
UspPF00582.33 3.8e-2510–159 Universal stress protein family

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv3127 hyp hypothetical protein 916 913 coexpression:860
Rv2032 acg NAD(P)H nitroreductase 911 908 coexpression:859
Rv1738 hyp hypothetical protein 922 906 coexpression:861
Rv0079 hyp hypothetical protein 927 903 coexpression:903
Rv2031c hspX alpha-crystallin 916 893 coexpression:864
Rv3131 NAD(P)H nitroreductase 918 890 coexpression:860
Rv3134c universal stress protein 894 887 coexpression:850
Rv0080 hyp hypothetical protein 887 883 coexpression:854
Rv2007c fdxA ferredoxin 902 881 coexpression:860
Rv2623 TB31.7 universal stress protein 869 865 coexpression:853
Rv3130c tgs1 diacyglycerol O-acyltransferase 878 860 coexpression:860
Rv2626c hrp1 hypoxic response protein 870 856 coexpression:853
Rv2627c hyp hypothetical protein 846 846 coexpression:824
Rv1733c transmembrane protein 870 843 coexpression:822
Rv2030c hyp hypothetical protein 852 836 coexpression:802

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: universal stress protein
  • MTBC0 PGAP product: universal stress protein
  • Pfam (hmmscan --cut_ga): Usp PF00582.33 (E=4e-25)
  • (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_216512.1)
  • Domains: Pfam-A via hmmscan --cut_ga — Usp (PF00582.33)
  • 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 COG0589
  • Curated reference: UniProt P9WLP1 (SwissProt, reviewed; 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 — 37 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_002123|Rv1996|
MSAQQTNLGIVVGVDGSPCSHTAVEWAARDAQMRNVALRVVQVVPPVITAPEGWAFEYSRFQEAQKREIVEHSYLVAQAHQIVEQAHKVALEASSSGRAAQITGEVLHGQIVPTLANISRQVAMVVLGYRGQGAVAGALLGSVSSSLVRHAHGPVAVIPEEPRPARPPHAPVVVGIDGSPTSGLAAEIAFDEASRRGVDLVALHAWSDMGPLDFPRLNWAPIEWRNLEDEQEKMLARRLSGWQDRYPDVVVHKVVVCDRPAPRLLELAQTAQLVVVGSHGRGGFPGMHLGSVSRAVVNSGQAPVIVARIPQDPAVPA