Rv3847 Resolved · medium auto-curated
H37Rv Rv3847 · MTBC0 mtbc0_004080 ·
177 aa · 4345648–4346181 (+) ·
RefSeq NP_218364.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | peptidase |
| Revised (this work) | Peptidase. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96230
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Peptidase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2AXA6 |
|---|
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) pseudogene candidate
| pN/pS | 0.372 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 32.30% of strains (46908) · 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: sodA (superoxide dismutase), high confidence from genomic context alone (score 745 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) |
|---|---|---|---|---|
Rv3846 sodA |
superoxide dismutase | 745 | 745 ctx | neighborhood:733 |
Rv2525c hyp |
hypothetical protein | 729 | 730 ctx | cooccurence:728 |
Rv1275 lprC |
lipoprotein LprC | 709 | 710 ctx | cooccurence:708 |
Rv1274 lprB |
lipoprotein LprB | 707 | 707 ctx | cooccurence:704 |
Rv1171 hyp |
hypothetical protein | 693 | 694 ctx | cooccurence:692 |
Rv0822c hyp |
hypothetical protein | 672 | 672 ctx | cooccurence:671 |
Rv1776c |
transcriptional regulator | 634 | 634 ctx | cooccurence:634 |
Rv0185 hyp |
hypothetical protein | 566 | 566 ctx | cooccurence:566 |
Rv0048c |
membrane protein | 562 | 562 ctx | cooccurence:562 |
Rv3163c hyp |
hypothetical protein | 556 | 556 ctx | cooccurence:556 |
Rv2001 hyp |
hypothetical protein | 552 | 552 ctx | cooccurence:551 |
Rv3166c hyp |
hypothetical protein | 537 | 537 ctx | cooccurence:537 |
Rv3848 |
transmembrane protein | 536 | 536 ctx | neighborhood:533 |
Rv0358 hyp |
hypothetical protein | 532 | 532 ctx | cooccurence:531 |
Rv2585c |
lipoprotein | 531 | 531 ctx | cooccurence:531 |
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: peptidase
- (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_218364.1)
- 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
2AXA6 - Curated reference: UniProt P96230 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
35 functional partner(s); context anchor
sodA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004080|Rv3847| MGTGSGGPIGVSPFHSRGALKGFVISGRWPDSTKEWAQLLMVAVRVASLPGLLSTTTVFGAREELPDEPEPGTVGLVLAEGTVFGESAIQPGYFADHQPPALLMLHPPSETTPSLPECTGAASGCVLLPGLPYLGLEHRAAWVEAEADGTITSMVSRVGVDPISHPDTAILAMLLAA