Rv3819 Still unknown · low auto-curated
H37Rv Rv3819 · MTBC0 mtbc0_004048 ·
111 aa · 4308106–4308441 (+) ·
RefSeq NP_218336.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 3dcx-assembly1_A Crystal structure of a duf1696 family protein with a (prob 0.99, TM 0.50). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07804
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein |
UniProt still lists this protein as Uncharacterized protein; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | arCOG09609 |
|---|
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 | 0.171 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 1 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 65.1 (low). Low-confidence model: the fold may be unreliable, so treat these structural hits with caution.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
3dcx-assembly1_A |
0.99 | 0.50 | 2.7e-03 sig | 3dcx-assembly1_A Crystal structure of a duf1696 family protein with a pleckstrin-homology domain (shew_0819) from shewanella loihica pv-4 at 2.00 A resolution |
3hsa-assembly1_B |
0.96 | 0.50 | 2.3e-02 | 3hsa-assembly1_B Crystal structure of pleckstrin homology domain (YP_926556.1) from SHEWANELLA AMAZONENSIS SB2B at 1.99 A resolution |
5yqr-assembly1_A |
0.82 | 0.56 | 2.0e-01 | 5yqr-assembly1_A Crystal structure of the PH-like domain of Lam6 |
2cay-assembly1_A |
0.63 | 0.51 | 2.3e-01 | 2cay-assembly1_A Vps36 N-terminal PH domain |
2d4q-assembly1_B |
0.51 | 0.48 | 3.0e-01 | 2d4q-assembly1_B Crystal structure of the Sec-PH domain of the human neurofibromatosis type 1 protein |
8e20-assembly1_A |
0.51 | 0.46 | 2.0e-01 | 8e20-assembly1_A Cryo-EM structure of the full-length human NF1 dimer |
7pgu-assembly1_N |
0.51 | 0.47 | 2.6e-01 | 7pgu-assembly1_N Autoinhibited structure of human neurofibromin isoform 2 stabilized by Zinc. |
3p7z-assembly1_B |
0.47 | 0.49 | 3.8e-01 | 3p7z-assembly1_B Crystal structure of the Neurofibromin Sec14-PH module containing the patient derived mutation I1584V |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3817 (phosphotransferase), medium confidence from genomic context alone (score 671 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) |
|---|---|---|---|---|
Rv3818 hyp |
hypothetical protein | 970 | 970 ctx | neighborhood:881 coexpression:761 |
Rv3817 |
phosphotransferase | 671 | 671 ctx | neighborhood:671 |
Rv3815c |
acyltransferase | 513 | 513 ctx | neighborhood:513 |
Rv3816c |
acyltransferase | 501 | 501 ctx | neighborhood:501 |
Rv3814c |
acyltransferase | 495 | 495 ctx | neighborhood:495 |
Rv3813c hyp |
hypothetical protein | 428 | 429 ctx | neighborhood:425 |
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: hypothetical protein
- Foldseek best: 3dcx-assembly1_A Crystal structure of a duf1696 family protein with a pleckstrin (prob 0.99, E=3e-03, TM=0.50)
- (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_218336.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
arCOG09609 - Curated reference: UniProt O07804 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 65.1, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
6 functional partner(s); context anchor
Rv3817 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004048|Rv3819| MMQFYDDGVVQLDRAALTLRRYHFPSGTAKVIPLDQIRGYQAESLGFLMARFNIWGRPDLRRWLPLDVYRPLKSTLVTLDVPGMRPKPACTPTRPKEFIALLDELLALHRT