Rv2084 Still unknown · low auto-curated
H37Rv Rv2084 · MTBC0 mtbc0_002220 ·
331 aa · 2370421–2371568 (+) ·
RefSeq NP_216600.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 1l7c-assembly1_A alpha-catenin fragment, residues 385-651 (prob 0.21, TM 0.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLK1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2084 |
UniProt still lists this protein as Uncharacterized protein Rv2084; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2B714 |
|---|---|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 | 0.466 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 5 missense, 0 nonsense, 4 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 60.94% of strains (88485) · reference-fixed |
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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 60.3 (low). Low-confidence model: the fold may be unreliable, so treat these structural hits with caution.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
1l7c-assembly1_A |
0.21 | 0.26 | 7.3e-01 | 1l7c-assembly1_A alpha-catenin fragment, residues 385-651 |
3o43-assembly1_A |
0.18 | 0.35 | 1.5e+00 | 3o43-assembly1_A Complex of an alpha/beta-peptide based on the gp41 CHR domain bound to gp41-5 |
5xfl-assembly2_B |
0.18 | 0.29 | 1.6e+00 | 5xfl-assembly2_B Crystal structure of the force-sensing device region of alpha N-catenin |
5v54-assembly1_B |
0.18 | 0.23 | 4.0e-01 | 5v54-assembly1_B Crystal structure of 5-HT1B receptor in complex with methiothepin |
4dzv-assembly1_A |
0.16 | 0.31 | 1.3e+00 | 4dzv-assembly1_A Complex of 4-alpha/beta bound to gp41-5 |
4p9t-assembly1_C |
0.15 | 0.36 | 3.9e+00 | 4p9t-assembly1_C Structure of the free form of the N-terminal VH1 domain of monomeric alpha-catenin |
4dzu-assembly1_A |
0.13 | 0.34 | 2.9e+00 | 4dzu-assembly1_A Complex of 3-alpha bound to gp41-5 |
6rz5-assembly2_B |
0.12 | 0.19 | 5.1e-01 | 6rz5-assembly2_B XFEL crystal structure of the human cysteinyl leukotriene receptor 1 in complex with zafirlukast |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2081c (transmembrane protein), medium confidence from genomic context alone (score 494 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2083 hyp |
hypothetical protein | 853 | 853 ctx | neighborhood:801 |
Rv2082 hyp |
hypothetical protein | 807 | 807 ctx | neighborhood:801 |
Rv2085 hyp |
hypothetical protein | 572 | 572 ctx | neighborhood:552 |
Rv2086 hyp |
hypothetical protein | 562 | 563 ctx | neighborhood:552 |
Rv2081c |
transmembrane protein | 494 | 494 ctx | neighborhood:491 |
Rv2087 |
Rv2087, (MTCY49.27), len: 76 aa. Conserved hypothetical protein, similar to but shorter than transposases, but we can find no sequence error | 413 | 412 ctx | neighborhood:410 |
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: hypothetical protein
- Foldseek best: 1l7c-assembly1_A alpha-catenin fragment, residues 385-651 (prob 0.21, E=7e-01, TM=0.26)
- (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_216600.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
2B714 - Curated reference: UniProt P9WLK1 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 60.3, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
6 functional partner(s); context anchor
Rv2081c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002220|Rv2084| MSDDSSSAFDLICAEIERQLRGGELLMDAAAASELLLTVRYQLDTQPRPLVIVHGPLFQAVKAARAQVYGRLIQLRHARCEVLDERWQLRPTGQRDVRALLIDVLNVLLAAITAAGVERAYACAERRAMAAAVVAKNYRDALGVELQCNSVCRAAAEAIHALAHRTGATEDADCLPPVDVIHADVTRRMHGEVATDVVAAGELVIAARHLLDPMPRGELSYGPLHEGGNAARKSVYRRLVQLWQARRAVTDGDVDLRDARTLLTDLDSILREMRTAATIQQAYTRAERRAMAAAVVAKIRGDAMGLDAQRDAVHRAAADALHALQSVGIHQ