Rv3848 Family assigned · medium auto-curated
H37Rv Rv3848 · MTBC0 mtbc0_004081 ·
302 aa · 4346436–4347344 (+) ·
RefSeq NP_218365.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane protein |
|---|---|
| MTBC0 PGAP re-annotation | TMEM165/GDT1 family protein |
| Revised (this work) | TMEM165/GDT1 family protein. Pfam: GDT1 (PF01169.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96229
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | GDT1 family protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | membrane |
| Orthologous group | COG2119 |
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 | 0.534 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.85% of strains (1232) · 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 |
|---|---|---|---|---|
GDT1 | PF01169.25 | 3.1e-21 | 107–180 | Divalent cation/proton antiporter GDT1 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: espR (ESX-1 transcriptional regulator EspR), medium confidence from genomic context alone (score 499 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3847 hyp |
hypothetical protein | 536 | 536 ctx | neighborhood:533 |
Rv3849 espR |
ESX-1 transcriptional regulator EspR | 499 | 499 ctx | neighborhood:496 |
Rv1909c furA |
ferric uptake regulation protein FurA | 499 | 79 | textmining:479 |
Rv2137c hyp |
hypothetical protein | 490 | 44 | textmining:489 |
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: TMEM165/GDT1 family protein
- Pfam (hmmscan --cut_ga): GDT1 PF01169.25 (E=3e-21)
- (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_218365.1)
- Domains: Pfam-A via hmmscan --cut_ga — GDT1 (PF01169.25)
- 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
COG2119 - Curated reference: UniProt P96229 (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 —
4 functional partner(s); context anchor
espR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004081|Rv3848| MLAATLLSLGAVFLAELGDRSQLITMTYTLRYRWWVVLTGVAIAAFTVHGVAVAIGHFLGSTVPARPAACVSAIAFLIFAVWVWREDTASDSETSPTAAEPRLALFTVVSSFALAELGDKTTLATVTLASDHHWAGVWIGTTLGMILADGLAIGAGLLLHRRLPERLLQVLTGLLFLLFGLWLLFDDALGFRSVAIAVTAAVVLAAATTAVSVRVAQTRRRRPTAAATPEDDSTRPERSSVAPGHPGSILLPLPEVSLRGRRPPSGSPDERCADPGSKGGSRRISVGCWLPGVGRIRPTRSS