Rv2083 Still unknown · low auto-curated
H37Rv Rv2083 · MTBC0 mtbc0_002219 ·
314 aa · 2369484–2370428 (+) ·
RefSeq NP_216599.1
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. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLK3
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv2083 |
UniProt still lists this protein as Uncharacterized protein Rv2083; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2BK8T |
|---|---|
| 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 | 0.61 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.36% of strains (518) · 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2081c (transmembrane protein), medium confidence from genomic context alone (score 496 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) |
|---|---|---|---|---|
Rv2084 hyp |
hypothetical protein | 853 | 853 ctx | neighborhood:801 |
Rv2082 hyp |
hypothetical protein | 827 | 827 ctx | neighborhood:785 |
Rv2085 hyp |
hypothetical protein | 571 | 572 ctx | neighborhood:552 |
Rv2086 hyp |
hypothetical protein | 556 | 556 ctx | neighborhood:552 |
Rv1617 pykA |
pyruvate kinase | 513 | 513 | coexpression:513 |
Rv2081c |
transmembrane protein | 496 | 496 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 |
Rv0291 mycP3 |
membrane-anchored mycosin MycP | 591 | 97 | textmining:566 |
Rv0284 eccC3 |
ESX-3 secretion system protein EccC3 | 559 | 70 | textmining:546 |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 648 | 61 | textmining:641 |
Rv0292 eccE3 |
ESX-3 secretion system protein EccE | 556 | 54 | textmining:550 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 633 | 51 | textmining:630 |
Rv0282 eccA3 |
ESX-3 secretion system protein EccA | 549 | 46 | textmining:547 |
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
- (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_216599.1)
- 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
2BK8T - Curated reference: UniProt P9WLK3 (SwissProt, reviewed; Predicted)
- 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 81.8, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
13 functional partner(s); context anchor
Rv2081c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002219|Rv2083| MTSIESHPEQYWAAAGRPGPVPLALGPVHPGGPTLIDLLMALFGLSTNADLGGTNADIEGDDTDRRAHAADAARKFSANEANAAEQMQGVGAQGMAQMASGIGGALSGALGGVMGPLTQLPQQAMQAGQGAMQPLMSAMQQAQGADGLAAVDGARLLDSIGGEPGLGSGAGGGDVGGGGAGGTTPTGYLGPPPVPTSSPPTTPAGAPTKSATMPPPGGASPASAHMGAAGMPMVPPGAMGARGEGSGQEKPVEKRVTAPAVPNGQPVKGRLTVPPSAPTTKPTDGKPVVRRRILLPEHKDFGRIAPDEKTDAGE