Rv3850 Family assigned · low auto-curated
H37Rv Rv3850 · MTBC0 mtbc0_004083 ·
218 aa · 4348125–4348781 (+) ·
RefSeq NP_218367.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | DUF6474 family protein |
| Revised (this work) | DUF6474 family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96227
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Conserved protein |
UniProt still lists this protein as Conserved protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2E45H |
|---|
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 | 0.631 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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 |
|---|---|---|---|---|
DUF6474 | PF20079.5 | 8.5e-79 | 1–217 | Family of unknown function (DUF6474) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3851 (membrane protein), high confidence from genomic context alone (score 960 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3851 |
membrane protein | 960 | 960 ctx | neighborhood:847 coexpression:751 |
Rv3849 espR |
ESX-1 transcriptional regulator EspR | 854 | 813 ctx | neighborhood:712 |
Rv3438 hyp |
hypothetical protein | 777 | 777 ctx | cooccurence:774 |
Rv1109c hyp |
hypothetical protein | 775 | 775 ctx | cooccurence:772 |
Rv2732c |
transmembrane protein | 775 | 775 ctx | cooccurence:772 |
Rv0556 |
transmembrane protein | 774 | 775 ctx | cooccurence:774 |
Rv3205c hyp |
hypothetical protein | 773 | 773 ctx | cooccurence:772 |
Rv2446c |
integral membrane protein | 772 | 772 ctx | cooccurence:771 |
Rv0358 hyp |
hypothetical protein | 772 | 772 ctx | cooccurence:771 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 770 | 770 ctx | cooccurence:768 |
Rv1166 lpqW |
monoacyl phosphatidylinositol tetramannoside-binding protein LpqW | 769 | 769 ctx | cooccurence:767 |
Rv0383c ttfA hyp |
hypothetical protein | 767 | 767 ctx | cooccurence:767 |
Rv3212 hyp |
hypothetical protein | 765 | 765 ctx | cooccurence:764 |
Rv3852 hns |
histone-like protein Hns | 764 | 764 ctx | neighborhood:763 |
Rv0996 |
transmembrane protein | 763 | 764 ctx | cooccurence:763 |
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: hypothetical protein
- MTBC0 PGAP product: DUF6474 family protein
- Pfam (hmmscan --cut_ga): DUF6474 PF20079.5 (E=9e-79)
- (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_218367.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF6474 (PF20079.5)
- 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
2E45H - Curated reference: UniProt P96227 (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 —
138 functional partner(s); context anchor
Rv3851 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004083|Rv3850| MGLFGKRKSRATRRAEARAIKARAKLEAKLSAKNEARRIKAAQRAESKALKAQLKARRDSDRAALKVAEAELKVAREGKLLSPTRIRRLLTVSRLLAPILTPVIYRAAMAARGLIDQRRADQLGVPLAQIGRFSGHGARLSARVGGAERSLRMVQEKKPKDVETKQFVSAVTNRLTDLSAAVAAAEHMPAKRRRTAHSAISSQLDGIEADLMARLGLT