Rv2085 Still unknown · low auto-curated
H37Rv Rv2085 · MTBC0 - ·
101 aa · 2343027–2343332 (+) ·
RefSeq NP_216601.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| 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.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WLJ9
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv2085 |
UniProt still lists this protein as Uncharacterized protein Rv2085; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | transposase activity |
| Orthologous group | COG2963 |
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 | 0.334 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (188) · 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: Rv2087 (Rv2087, (MTCY49.27), len: 76 aa. Conserved hypothetical protein, similar to but shorter than transposases, but we can find no sequence error), high confidence from genomic context alone (score 834 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) |
|---|---|---|---|---|
Rv2086 hyp |
hypothetical protein | 945 | 942 ctx | neighborhood:781 cooccurence:716 |
Rv2087 |
Rv2087, (MTCY49.27), len: 76 aa. Conserved hypothetical protein, similar to but shorter than transposases, but we can find no sequence error | 834 | 834 ctx | neighborhood:584 cooccurence:588 |
Rv2082 hyp |
hypothetical protein | 795 | 796 ctx | neighborhood:552 cooccurence:559 |
Rv2084 hyp |
hypothetical protein | 572 | 572 ctx | neighborhood:552 |
Rv2083 hyp |
hypothetical protein | 571 | 572 ctx | neighborhood:552 |
Rv2942 mmpL7 |
transmembrane transport protein MmpL7 | 512 | 513 ctx | cooccurence:507 |
Rv3899c hyp |
hypothetical protein | 506 | 506 ctx | cooccurence:502 |
Rv3350c PPE56 |
PPE family protein PPE56 | 480 | 480 ctx | cooccurence:477 |
Rv3347c PPE55 |
PPE family protein PPE55 | 469 | 469 ctx | cooccurence:466 |
Rv0355c PPE8 |
PPE family protein PPE8 | 466 | 466 ctx | cooccurence:463 |
Rv3349c |
transposase | 461 | 462 ctx | cooccurence:452 |
Rv1749c |
integral membrane protein | 457 | 457 ctx | cooccurence:457 |
Rv3343c PPE54 |
PPE family protein PPE54 | 456 | 457 ctx | cooccurence:454 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 453 | 453 ctx | cooccurence:453 |
Rv1885c |
chorismate mutase | 449 | 449 ctx | cooccurence:446 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): 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_216601.1)
- 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
COG2963 - Curated reference: UniProt P9WLJ9 (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 45.7, very low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
27 functional partner(s); context anchor
Rv2087 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2085| MSDMCDVVSFVGAAERVLRARFRPSPESGPPVHARRCGWSLGISAETLRRWAGQAEVDSGVVAGVSASRSGSVKTSELEQTIEILKVATSFFARKCDPRHR