Rv0396 Still unknown · low auto-curated
H37Rv Rv0396 · MTBC0 mtbc0_000415 ·
130 aa · 478714–479106 (+) ·
RefSeq NP_214910.1
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: 5qhm-assembly1_A PanDDA analysis group deposition of models with model (prob 0.66, TM 0.69). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95204
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 | 2BWWP |
|---|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 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 77.4 (confident). A confident model makes the fold comparison meaningful.
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 |
|---|---|---|---|---|
5qhm-assembly1_A |
0.66 | 0.69 | 6.7e-01 | 5qhm-assembly1_A PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of human FAM83B in complex with OX-145 |
4urj-assembly1_A |
0.63 | 0.52 | 3.1e-01 | 4urj-assembly1_A Crystal structure of human BJ-TSA-9 |
4urj-assembly2_C |
0.44 | 0.49 | 4.0e-01 | 4urj-assembly2_C Crystal structure of human BJ-TSA-9 |
5lzk-assembly1_A |
0.35 | 0.46 | 3.5e-01 | 5lzk-assembly1_A Structure of the domain of unknown function DUF1669 from human FAM83B |
3k6l-assembly3_C |
0.04 | 0.23 | 2.0e+00 | 3k6l-assembly3_C The structure of E.coli peptide deformylase (PDF) in complex with peptidomimetic ligand BB2827 |
3vqx-assembly1_A |
0.04 | 0.32 | 7.1e+00 | 3vqx-assembly1_A Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in triclinic crystal form |
2q7e-assembly1_A-2 |
0.04 | 0.31 | 5.5e+00 | 2q7e-assembly1_A-2 The structure of pyrrolysyl-tRNA synthetase bound to an ATP analogue |
8ifj-assembly4_H |
0.03 | 0.23 | 4.0e+00 | 8ifj-assembly4_H Crystal structure of pyrrolysyl-tRNA synthetase from methanogenic archaeon ISO4-G1 |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0395 hyp |
hypothetical protein | 889 | 889 ctx | neighborhood:882 |
Rv0397 hyp |
hypothetical protein | 619 | 619 ctx | neighborhood:615 |
Rv0394c hyp |
hypothetical protein | 598 | 598 ctx | neighborhood:596 |
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: 5qhm-assembly1_A PanDDA analysis group deposition of models with modelled events (prob 0.66, E=7e-01, TM=0.69)
- (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_214910.1)
- 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
2BWWP - Curated reference: UniProt P95204 (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 77.4, confident)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 3 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000415|Rv0396| MRALGWLREDRKPLLNAKLLVLGHLALNVYDPDNGYGEEVLDFEPRTVWWGSANWTVRAGSHLEVGFACDDPTLVEEATAFVADVIAFSEPIDTTCAGPEPNLVQVEFDDAAMAEAMEEMAEPDDDGEDW