Rv3629c Family assigned · medium auto-curated
H37Rv Rv3629c · MTBC0 mtbc0_003846 ·
365 aa · 4091661–4092758 (-) ·
RefSeq NP_218146.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF475 domain-containing protein |
| Revised (this work) | DUF475 domain-containing protein. Pfam: TerC (PF03741.23), DUF475 (PF04332.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06378
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved integral membrane protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Protein of unknown function (DUF475) |
| Orthologous group | COG2899 |
| KEGG orthology |
K09799
|
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 | 0.09 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.34% of strains (495) · 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 |
|---|---|---|---|---|
TerC | PF03741.23 | 4.5e-14 | 36–321 | Integral membrane protein TerC family |
DUF475 | PF04332.22 | 1.9e-143 | 45–355 | Protein of unknown function (DUF475) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3630 (integral membrane protein), high confidence from genomic context alone (score 708 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3630 |
integral membrane protein | 960 | 708 ctx | neighborhood:704 textmining:870 |
Rv3631 |
transferase | 956 | 677 ctx | neighborhood:674 textmining:870 |
Rv3632 |
membrane protein | 952 | 651 ctx | neighborhood:646 textmining:870 |
Rv0180c |
transmembrane protein | 579 | 579 ctx | cooccurence:578 |
Rv0824c desA1 |
acyl-ACP desaturase DesA | 427 | 427 ctx | cooccurence:402 |
Rv3718c hyp |
hypothetical protein | 418 | 418 ctx | cooccurence:417 |
Rv0090 |
membrane protein | 416 | 416 ctx | cooccurence:416 |
Rv3633 hyp |
hypothetical protein | 903 | 286 | textmining:870 |
Rv3623 lpqG |
lipoprotein LpqG | 512 | 167 | textmining:439 |
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: integral membrane protein
- MTBC0 PGAP product: DUF475 domain-containing protein
- Pfam (hmmscan --cut_ga): TerC PF03741.23 (E=4e-14), DUF475 PF04332.22 (E=2e-143)
- (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_218146.1)
- Domains: Pfam-A via hmmscan --cut_ga — TerC (PF03741.23), DUF475 (PF04332.22)
- 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
COG2899 - Curated reference: UniProt O06378 (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 —
9 functional partner(s); context anchor
Rv3630 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003846|Rv3629c| MSTFRIFGFSLLMTVVALVTGYLHGGPTALFLLAVLALLEVSLSFDNAIINAAILQRMSPFWQRMFLTIGILIAVFGMRLVFPLAIIWTTAGLDPVRAMELALRPPAHGALEFADGSPSYEKLITAAHPQIAAFGGMFLLMLFLDFVVHDRDIKWLKWIEVPFARIGRLGQVPVIVASVGLVLAGALLTHSSDQRGTVLIAGLLGMVTYLVVNGISRAFRPAGLGEATPGVQARQAAGKAGCALFLYLEVLDAAFSFDGVTGAFAITTDPIIIALGLGVVGAMFVRSITIYLVRQDTLDRYVYLEHGAHWAIGALAIILLLSIDHRFAVPEWVTASVGVVFIGAAFTESVRRNRLTVRSPTKFGS