Rv3785 Family assigned · medium auto-curated
H37Rv Rv3785 · MTBC0 mtbc0_004013 ·
357 aa · 4255441–4256514 (+) ·
RefSeq NP_218302.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains Rv3785_N (PF27209.1) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKX1
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv3785 |
UniProt still lists this protein as Uncharacterized protein Rv3785; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2E5IU |
|---|---|
| Gene Ontology (8) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0044424, GO:0044444, GO:0044464
|
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 | 0.256 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 7 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 2.01% of strains (2915) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Rv3785_N | PF27209.1 | 4.0e-19 | 18–119 | Rv3785 N-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3784 (dTDP-glucose 4,6-dehydratase), medium confidence from genomic context alone (score 575 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) |
|---|---|---|---|---|
Rv3784 |
dTDP-glucose 4,6-dehydratase | 942 | 575 ctx | neighborhood:548 textmining:870 |
Rv1759c wag22 |
PE-PGRS family protein Wag22 | 754 | 41 | textmining:754 |
Rv3367 PE_PGRS51 |
PE-PGRS family protein PE_PGRS51 | 528 | 41 | textmining:528 |
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
- Pfam (hmmscan --cut_ga): Rv3785_N PF27209.1 (E=4e-19)
- (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_218302.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv3785_N (PF27209.1)
- 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
2E5IU - Curated reference: UniProt P9WKX1 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
3 functional partner(s); context anchor
Rv3784 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004013|Rv3785| MVTVARRPVCPVTLTPGDPALASVRDLVDAWSAHDALAELVTMFGGAFPQTDHLEARLASLDKFSTAWDYRARARAARALHGEPVRCQDSGGGARWLIPRLDLPAKKRDAIVGLAQQLGLTLESTPQGTTFDHVLVIGTGRHSNLIRARWARELAKGRQVGHIVLAAASRRLLPSEDDAVAVCAPGARTEFELLAAAARDAFGLDVHPAVRYVRQRDDNPHRDSMVWRFAADTNDLGVPITLLEAPSPEPDSSRATSADTFTFTAHTLGMQDSTCLLVTGQPFVPYQNFDALRTLALPFGIQVETVGFGIDRYDGLGELDQQHPAKLLQEVRSTIRAARALLERIEAGERMATDPRR