Rv3690 Still unknown · low auto-curated
H37Rv Rv3690 · MTBC0 mtbc0_003911 ·
217 aa · 4155687–4156340 (+) ·
RefSeq NP_218207.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF4129 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF4129. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O69658
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Domain of unknown function (DUF4129) |
| Orthologous group | 2CT9V |
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
DUF4129 | PF13559.12 | 5.8e-11 | 122–188 | Domain of unknown function (DUF4129) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3689 (transmembrane protein), high confidence from genomic context alone (score 962 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3691 hyp |
hypothetical protein | 986 | 986 ctx | neighborhood:760 cooccurence:774 coexpression:767 |
Rv3689 |
transmembrane protein | 961 | 962 ctx | neighborhood:843 cooccurence:761 |
Rv3693 |
membrane protein | 949 | 947 ctx | neighborhood:684 cooccurence:772 |
Rv3692 moxR2 |
methanol dehydrogenase transcriptional regulator MoxR | 803 | 804 ctx | neighborhood:760 |
Rv3694c |
transmembrane protein | 789 | 790 ctx | cooccurence:773 |
Rv3695 |
membrane protein | 785 | 785 ctx | cooccurence:773 |
Rv3688c hyp |
hypothetical protein | 770 | 769 ctx | neighborhood:766 |
Rv2226 hyp |
hypothetical protein | 462 | 441 ctx | cooccurence:412 |
Rv0518 hyp |
hypothetical protein | 432 | 433 ctx | cooccurence:426 |
Rv2332 mez |
malate oxidoreductase | 428 | 428 | coexpression:418 |
Rv2531c |
amino acid decarboxylase | 436 | 412 | experimental:405 |
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: membrane protein
- MTBC0 PGAP product: DUF4129 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF4129 PF13559.12 (E=6e-11)
- (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_218207.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF4129 (PF13559.12)
- 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
2CT9V - Curated reference: UniProt O69658 (TrEMBL, unreviewed; Evidence at protein level)
- 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 —
11 functional partner(s); context anchor
Rv3689 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003911|Rv3690| MPSIDIDREAAHQAAQRELDKPIYPKDSLTKELTDWIDEQLYRILEKGSSIPGGWFTITVLLILLMIAVTAAVQIARRTMRTNRGGDYQLFDAGQLTAAQHRSTAESYAAEGNWAAAIRHRLQAVARELEETGMLNPAAGRTANELASDAGEVLPHLAGELTQAATAFNDVTYGERPGTQGAYQMIADLDDHLRSRSPAVVSAVQHPAVFDSWAQVR