Rv3694c Resolved · high auto-curated
H37Rv Rv3694c · MTBC0 mtbc0_003915 ·
330 aa · 4160070–4161062 (-) ·
RefSeq NP_218211.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | stage II sporulation protein M |
| Revised (this work) | Stage II sporulation protein M. Pfam: DUF8413 (PF28475.1), SpoIIM (PF01944.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O69662
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible conserved transmembrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | membrane |
| Orthologous group | COG1300 |
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 | 0.182 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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 |
|---|---|---|---|---|
DUF8413 | PF28475.1 | 6.2e-22 | 4–75 | Domain of unknown function (DUF8413) |
SpoIIM | PF01944.23 | 7.6e-44 | 107–281 | Stage II sporulation protein M |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3695 (membrane protein), high confidence from genomic context alone (score 966 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3695 |
membrane protein | 965 | 966 ctx | neighborhood:782 cooccurence:774 |
Rv3693 |
membrane protein | 838 | 807 ctx | cooccurence:774 |
Rv3691 hyp |
hypothetical protein | 791 | 792 ctx | cooccurence:774 |
Rv3690 |
membrane protein | 789 | 790 ctx | cooccurence:773 |
Rv3689 |
transmembrane protein | 752 | 752 ctx | cooccurence:741 |
Rv3692 moxR2 |
methanol dehydrogenase transcriptional regulator MoxR | 476 | 476 ctx | cooccurence:431 |
Rv1078 pra hyp |
hypothetical protein | 472 | 472 | |
Rv0176 |
Mce associated transmembrane protein | 458 | 458 |
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: transmembrane protein
- MTBC0 PGAP product: stage II sporulation protein M
- Pfam (hmmscan --cut_ga): DUF8413 PF28475.1 (E=6e-22), SpoIIM PF01944.23 (E=8e-44)
- (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_218211.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF8413 (PF28475.1), SpoIIM (PF01944.23)
- 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
COG1300 - Curated reference: UniProt O69662 (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 —
8 functional partner(s); context anchor
Rv3695 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003915|Rv3694c| MDVDAFLLTNRGTWDRLDHLIKKRHSLSGAEIDELVELYQRVSTHLSMLRSASSDQLMTGRLSSLVARARSAVTGAHAPLTRTFIRFWTVSFPVVAYRTWRWWLATAVAFFAVVVLIGFWVAGSHEVQSAIGTPTEIDELVSHDVQSYYSEHPAASFALQVWVNNSWVATTCIAMSVVLGLPIPLVLFDNAANVGLIAGLMFQAGKGDFLLGLLLPHGLLELTAVFLAAAIGMRLGWSVISAGNRPRGQVLAEQGRGVVSVAVGLVGVFLVAGLIEAVVTPSPLPTFVRIAVGIIAEAVFLSYIGYFGRRAAQAGETGDMEDAPDVVPTG