Rv3689 Resolved · medium auto-curated
H37Rv Rv3689 · MTBC0 - ·
451 aa · 4130357–4131712 (+) ·
RefSeq NP_218206.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transmembrane protein. |
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 |
I6YCR8
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Probable conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
A RNA processing and modification
|
|---|---|
| eggNOG description | pathogenesis |
| Orthologous group | COG5180 |
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 | 1.06 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 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 |
|---|---|---|---|---|
DUF7847 | PF25231.2 | 3.3e-08 | 137–410 | Domain of unknown function (DUF7847) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3690 (membrane protein), high confidence from genomic context alone (score 962 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3690 |
membrane protein | 961 | 962 ctx | neighborhood:843 cooccurence:761 |
Rv3691 hyp |
hypothetical protein | 938 | 938 ctx | neighborhood:737 cooccurence:765 |
Rv3693 |
membrane protein | 911 | 911 ctx | neighborhood:671 cooccurence:733 |
Rv3692 moxR2 |
methanol dehydrogenase transcriptional regulator MoxR | 782 | 783 ctx | neighborhood:737 |
Rv3695 |
membrane protein | 771 | 772 ctx | cooccurence:758 |
Rv3694c |
transmembrane protein | 752 | 752 ctx | cooccurence:741 |
Rv3688c hyp |
hypothetical protein | 598 | 599 ctx | neighborhood:596 |
Rv1616 hyp |
hypothetical protein | 689 | 561 ctx | cooccurence:557 |
Rv2226 hyp |
hypothetical protein | 502 | 503 ctx | cooccurence:502 |
Rv2560 hyp |
hypothetical protein | 471 | 472 ctx | cooccurence:464 |
Rv1006 hyp |
hypothetical protein | 439 | 439 ctx | cooccurence:434 |
Rv3033 hyp |
hypothetical protein | 420 | 420 ctx | cooccurence:420 |
Rv1126c hyp |
hypothetical protein | 400 | 401 | |
Rv1870c hyp |
hypothetical protein | 577 | 51 | textmining:573 |
Rv2585c |
lipoprotein | 553 | 51 | textmining:549 |
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): transmembrane protein
- Pfam (hmmscan --cut_ga): DUF7847 PF25231.2 (E=3e-08)
- (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_218206.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF7847 (PF25231.2)
- 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
COG5180 - Curated reference: UniProt I6YCR8 (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 —
16 functional partner(s); context anchor
Rv3690 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3689| MHKRYAPQRPKPDTETYIEKCTDRRQDGGHDERRQLLRPVSMLPPGYPVEPPPVAPGYAPAGYPPYPATPPGYGPPGYGAPPSYGPPPGYGPPLGYPAAPPGCGPPPGYGPPLGYGPPVAPGAVKPGIIPLRPLTLSDIFNGAVGYIRANPKATLGLTAMVVVTLQIISLVALFGPMTAFGDIVTGEPDELTGAVVGGWSASFGASLLVSWLAGVLLSGMLTVIVGRAVFGSPITVGEAWAKVRGRLLALFGLALLEAAGVVAVLGLAVVILSGVAAAANEAAAALLGFPLLLVVGVSLAYLYVVLLFAPVLIVLERLPIVEAITRSFALVRHGFWRVLGIRLLTVLVVGVVGNAIAAPFMIVGEIVTAVTASDGSVTMRLVGATLSAIGVTIGQIVTAPFSAGVVVLLYTDRRIRAEAFDLVLQTGLEAGPAGGPAPVESTDNLWLTRPF