Rv3898c Still unknown · low auto-curated
H37Rv Rv3898c · MTBC0 mtbc0_004131 ·
110 aa · 4407907–4408236 (-) ·
RefSeq NP_218415.1
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: 5sva-assembly1_T Mediator-RNA Polymerase II Pre-Initiation Complex (prob 0.38, TM 0.59). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05447
TrEMBL · unreviewed
· Predicted
|
|---|---|
| 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 | 2BK8T |
|---|
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 | 1.429 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.31% of strains (447) · 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)
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 49.4 (very 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 |
|---|---|---|---|---|
5sva-assembly1_T |
0.38 | 0.59 | 1.9e+00 | 5sva-assembly1_T Mediator-RNA Polymerase II Pre-Initiation Complex |
4jq5-assembly2_H |
0.16 | 0.43 | 1.9e+00 | 4jq5-assembly2_H Crystal structure of the human Nup49CCS2+3* coiled-coil segment |
4jq5-assembly1_B |
0.14 | 0.43 | 2.6e+00 | 4jq5-assembly1_B Crystal structure of the human Nup49CCS2+3* coiled-coil segment |
4jq5-assembly3_K |
0.14 | 0.42 | 2.4e+00 | 4jq5-assembly3_K Crystal structure of the human Nup49CCS2+3* coiled-coil segment |
4jq5-assembly3_L |
0.11 | 0.43 | 3.4e+00 | 4jq5-assembly3_L Crystal structure of the human Nup49CCS2+3* coiled-coil segment |
2osz-assembly2_D |
0.11 | 0.41 | 3.4e+00 | 2osz-assembly2_D Structure of Nup58/45 suggests flexible nuclear pore diameter by intermolecular sliding |
8bqs-assembly1_De |
0.08 | 0.41 | 4.2e+00 | 8bqs-assembly1_De Cryo-EM structure of the I-II-III2-IV2 respiratory supercomplex from Tetrahymena thermophila |
1vp7-assembly1_A |
0.07 | 0.42 | 5.4e+00 | 1vp7-assembly1_A Crystal structure of Exodeoxyribonuclease VII small subunit (NP_881400.1) from Bordetella pertussis at 2.40 A resolution |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccC2 (ESX-2 type VII secretion system protein EccC), medium confidence from genomic context alone (score 480 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) |
|---|---|---|---|---|
Rv3897c hyp |
hypothetical protein | 803 | 803 ctx | neighborhood:757 |
Rv1617 pykA |
pyruvate kinase | 508 | 509 | coexpression:509 |
Rv3900c hyp |
hypothetical protein | 503 | 503 ctx | neighborhood:498 |
Rv3899c hyp |
hypothetical protein | 486 | 486 ctx | neighborhood:484 |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 480 | 480 ctx | neighborhood:466 |
Rv3895c eccB2 |
ESX-2 secretion system protein EccB | 488 | 473 ctx | neighborhood:471 |
Rv3896c hyp |
hypothetical protein | 466 | 466 ctx | neighborhood:463 |
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: 5sva-assembly1_T Mediator-RNA Polymerase II Pre-Initiation Complex (prob 0.38, E=2e+00, TM=0.59)
- (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_218415.1)
- 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
2BK8T - Curated reference: UniProt O05447 (TrEMBL, unreviewed; Predicted)
- 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 49.4, very low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
7 functional partner(s); context anchor
eccC2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004131|Rv3898c| MTGDQNPAPGPAPGVPIKVTPEILLQVLTTPPASGPAPFPAVPVDLPAPADIANGALFAAGNSGVPGDVESSGLEDLDRRAHAADAVQKFSANEADAAQQFQGVGAQAEA