Rv2086 Still unknown · low auto-curated
H37Rv Rv2086 · MTBC0 - ·
201 aa · 2343311–2343916 (+) ·
RefSeq NP_216602.2
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. Foldseek best (non-significant) hit: 8i0p-assembly1_u The cryo-EM structure of human pre-Bact complex (prob 0.01, TM 0.14). |
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 |
P64937
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv2086 |
UniProt still lists this protein as Uncharacterized protein Rv2086; 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 | transposition |
| Orthologous group | COG2801 |
| KEGG orthology |
K07497
|
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 | 1.814 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 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)
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 77.2 (confident). A confident model makes the fold comparison meaningful.
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 |
|---|---|---|---|---|
8i0p-assembly1_u |
0.01 | 0.14 | 8.2e+00 | 8i0p-assembly1_u The cryo-EM structure of human pre-Bact complex |
8g3d-assembly1_5F |
0.01 | 0.16 | 9.8e+00 | 8g3d-assembly1_5F 48-nm doublet microtubule from Tetrahymena thermophila strain K40R |
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 769 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) |
|---|---|---|---|---|
Rv2085 hyp |
hypothetical protein | 945 | 942 ctx | neighborhood:781 cooccurence:716 |
Rv2082 hyp |
hypothetical protein | 841 | 840 ctx | neighborhood:552 cooccurence:655 |
Rv2087 |
Rv2087, (MTCY49.27), len: 76 aa. Conserved hypothetical protein, similar to but shorter than transposases, but we can find no sequence error | 769 | 769 ctx | neighborhood:571 cooccurence:480 |
Rv3349c |
transposase | 622 | 623 ctx | cooccurence:617 |
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 578 | 578 ctx | cooccurence:572 |
Rv3350c PPE56 |
PPE family protein PPE56 | 573 | 574 ctx | cooccurence:571 |
Rv0355c PPE8 |
PPE family protein PPE8 | 565 | 565 ctx | cooccurence:562 |
Rv2084 hyp |
hypothetical protein | 562 | 563 ctx | neighborhood:552 |
Rv2961 |
transposase | 560 | 561 ctx | cooccurence:555 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 559 | 559 ctx | cooccurence:559 |
Rv2083 hyp |
hypothetical protein | 556 | 556 ctx | neighborhood:552 |
Rv3347c PPE55 |
PPE family protein PPE55 | 554 | 555 ctx | cooccurence:552 |
Rv3343c PPE54 |
PPE family protein PPE54 | 541 | 542 ctx | cooccurence:539 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 539 | 539 ctx | cooccurence:539 |
Rv3899c hyp |
hypothetical protein | 537 | 535 ctx | cooccurence:529 |
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
- Foldseek best: 8i0p-assembly1_u The cryo-EM structure of human pre-Bact complex (prob 0.01, E=8e+00, TM=0.14)
- (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_216602.2)
- 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
COG2801 - Curated reference: UniProt P64937 (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 77.2, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
49 functional partner(s); context anchor
Rv2087 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2086| MRPATPLICAFGDKHKHTYGVTPICRALAVHGVQIASRTYFADRAAAPSKRALWDTTITEILAGYYEPDAEGKRPPECLYGSLKMWAHLQRQGFRWPSATVKTIMRANGWRGVPLAAHITHHRTRPGRGPGPRPGGSAMAGFSNEPAGSGRLHLRADDVEFRLHRVRGRRLRRCDRGLGMLADQRRSVRRTRITPRPSRLT