Rv2660c Still unknown · low auto-curated
H37Rv Rv2660c · MTBC0 mtbc0_002834 ·
75 aa · 3003166–3003393 (-) ·
RefSeq NP_217176.1
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: 8pui-assembly1_A human PHOX2B C-terminal domain including the polyA fr (prob 0.02, TM 0.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6Y1F5
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.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 3 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 40.3 (very 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 |
|---|---|---|---|---|
8pui-assembly1_A |
0.02 | 0.30 | 8.2e+00 | 8pui-assembly1_A human PHOX2B C-terminal domain including the polyA fragment at 298K |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2659c (prophage integrase), medium confidence from genomic context alone (score 486 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) |
|---|---|---|---|---|
Rv2661c hyp |
hypothetical protein | 776 | 775 ctx | neighborhood:773 |
Rv2662 hyp |
hypothetical protein | 577 | 577 ctx | neighborhood:572 |
Rv2659c |
prophage integrase | 486 | 486 ctx | neighborhood:481 |
Rv2658c |
prophage protein | 485 | 484 ctx | neighborhood:481 |
Rv2656c |
prophage protein | 476 | 476 ctx | neighborhood:461 |
Rv2654c |
antitoxin | 476 | 476 ctx | neighborhood:461 |
Rv2655c |
prophage protein | 469 | 469 ctx | neighborhood:461 |
Rv2657c |
prophage protein | 511 | 464 ctx | neighborhood:461 |
Rv2663 hyp |
hypothetical protein | 406 | 406 ctx | neighborhood:403 |
Rv1954c hyp |
hypothetical protein | 641 | 70 | textmining:630 |
Rv3288c usfY hyp |
hypothetical protein | 664 | 53 | textmining:660 |
Rv1374c hyp |
hypothetical protein | 562 | 50 | textmining:558 |
Rv1168c PPE17 |
PPE family protein PPE17 | 514 | 50 | textmining:510 |
Rv2558 hyp |
hypothetical protein | 731 | 47 | textmining:730 |
Rv2557 hyp |
hypothetical protein | 515 | 47 | textmining:512 |
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: 8pui-assembly1_A human PHOX2B C-terminal domain including the polyA fragment at (prob 0.02, E=8e+00, TM=0.30)
- (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_217176.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Curated reference: UniProt I6Y1F5 (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 40.3, very low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
22 functional partner(s); context anchor
Rv2659c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002834|Rv2660c| MIAGVDQALAATGQASQRAAGASGGVTVGVGVGTEQRNLSVVAPSQFTFSSRSPDFVDETAGQSWCAILGLNQFH