Rv2808 Still unknown · low auto-curated
H37Rv Rv2808 · MTBC0 mtbc0_002988 ·
85 aa · 3137461–3137718 (+) ·
RefSeq NP_217324.1
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: 6fnd-assembly1_B Crystal structure of Toxoplasma gondii AKMT (prob 0.16, TM 0.54). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P71643
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 291GV |
|---|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 0 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 90.8 (very high). 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 |
|---|---|---|---|---|
6fnd-assembly1_B |
0.16 | 0.54 | 4.4e+00 | 6fnd-assembly1_B Crystal structure of Toxoplasma gondii AKMT |
5mq1-assembly1_A |
0.10 | 0.43 | 4.0e+00 | 5mq1-assembly1_A Crystal structure of the BRD7 bromodomain in complex with BI-9564 |
4hwd-assembly3_B |
0.09 | 0.39 | 4.4e+00 | 4hwd-assembly3_B Crystal structure of ATBAG2 |
8y3y-assembly1_D |
0.09 | 0.45 | 4.7e+00 | 8y3y-assembly1_D The Cryo-EM structure of anti-phage defense associated DSR2 tetramer bound with two DSAD1 inhibitors (opposite side) |
1xg2-assembly1_B |
0.08 | 0.41 | 6.2e+00 | 1xg2-assembly1_B Crystal structure of the complex between pectin methylesterase and its inhibitor protein |
3kav-assembly1_A |
0.07 | 0.39 | 6.6e+00 | 3kav-assembly1_A Crystal Structure of THE MUTANT (L80M) PA2107 PROTEIN from Pseudomonas aeruginosa, Northeast Structural Genomics Consortium Target PaR198 |
8y3m-assembly1_B |
0.07 | 0.51 | 9.2e+00 | 8y3m-assembly1_B Cryo-EM structure of DSR2-DSAD1 complex (cross-linked) |
8zak-assembly1_A |
0.06 | 0.30 | 3.5e+00 | 8zak-assembly1_A Crystal structure of the channel protein CorA from Campylobacter jejuni in complex with Ni2+ |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2809 hyp |
hypothetical protein | 576 | 576 ctx | neighborhood:561 |
Rv2807 hyp |
hypothetical protein | 428 | 428 ctx | neighborhood:428 |
Rv3766 hyp |
hypothetical protein | 660 | 47 | textmining:658 |
Rv2004c hyp |
hypothetical protein | 441 | 47 | textmining:438 |
Rv2003c hyp |
hypothetical protein | 545 | 46 | textmining:543 |
Rv3459c rpsK |
30S ribosomal protein S11 | 433 | 46 | textmining:431 |
Rv2283 hyp |
hypothetical protein | 804 | 41 | textmining:804 |
Rv2402 |
trehalase | 547 | 41 | textmining:547 |
Rv3128c |
Rv3128c, (MTCY164.38c), len: 337 aa. Conserved hypothetical protein, similar to other conserved hypothetical proteins. This ORF corresponds | 426 | 41 | textmining:427 |
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: 6fnd-assembly1_B Crystal structure of Toxoplasma gondii AKMT (prob 0.16, E=4e+00, TM=0.54)
- (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_217324.1)
- 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
291GV - Curated reference: UniProt P71643 (TrEMBL, unreviewed; 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 90.8, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 9 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002988|Rv2808| MSNVLDAISTEHRPVIEQELENRNPALFDELRRTEKPTNEQSDAVIDVLSDALMKTFGPDWVPNDYGLKIERAIDAYLETWPIYR