Rv0856 Family assigned · medium auto-curated
H37Rv Rv0856 · MTBC0 - ·
134 aa · 952825–953229 (+) ·
RefSeq NP_215371.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Polyketide_cyc (PF03364.26) 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.
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 |
O53868
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Coenzyme Q-binding protein COQ10 START domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Polyketide cyclase / dehydrase and lipid transport |
| Orthologous group | COG3832 |
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 | 0.455 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Polyketide_cyc | PF03364.26 | 4.6e-07 | 2–116 | Polyketide cyclase / dehydrase and lipid transport |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: far (fatty-acid-CoA racemase), high confidence from genomic context alone (score 766 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) |
|---|---|---|---|---|
Rv0857 hyp |
hypothetical protein | 846 | 846 ctx | neighborhood:841 |
Rv0855 far |
fatty-acid-CoA racemase | 766 | 766 ctx | neighborhood:765 |
Rv0853c pdc |
alpha-keto-acid decarboxylase | 707 | 707 ctx | neighborhood:706 |
Rv2138 lppL |
lipoprotein LppL | 607 | 607 ctx | cooccurence:607 |
Rv0854 hyp |
hypothetical protein | 596 | 596 ctx | neighborhood:571 |
Rv2712c hyp |
hypothetical protein | 586 | 587 ctx | cooccurence:586 |
Rv3839 hyp |
hypothetical protein | 586 | 586 ctx | cooccurence:586 |
Rv0431 |
tuberculin-like peptide | 579 | 579 ctx | cooccurence:579 |
Rv3004 cfp6 |
low molecular weight protein antigen 6 | 552 | 552 ctx | cooccurence:552 |
Rv1222 rseA |
anti-sigma E factor RseA | 546 | 547 ctx | cooccurence:544 |
Rv1209 hyp |
hypothetical protein | 510 | 511 ctx | cooccurence:508 |
Rv0010c |
membrane protein | 508 | 509 ctx | cooccurence:506 |
Rv1486c hyp |
hypothetical protein | 506 | 507 ctx | cooccurence:506 |
Rv2468c hyp |
hypothetical protein | 497 | 497 ctx | cooccurence:497 |
Rv3212 hyp |
hypothetical protein | 492 | 493 ctx | cooccurence:491 |
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
- Pfam (hmmscan --cut_ga): Polyketide_cyc PF03364.26 (E=5e-07)
- (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_215371.1)
- Domains: Pfam-A via hmmscan --cut_ga — Polyketide_cyc (PF03364.26)
- 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
COG3832 - Curated reference: UniProt O53868 (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 —
23 functional partner(s); context anchor
far - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0856| MEALADVGVLASWSPLHKQVEVIDYYPDGRPHHVRATVKILGLVDKEVLEYHWGPDWVCWDADQTFQQHGQHIEYTVKPEGVDRARVRFDITVEPAGPIPGFIVKRASEHVLDAAAKGLQKLIAGAGDQGNAKS