Rv0397A Still unknown · low auto-curated
H37Rv Rv0397A · MTBC0 - ·
82 aa · 476394–476642 (+) ·
RefSeq YP_004837048.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. Function unknown. Foldseek best (non-significant) hit: 7cjt-assembly1_D Crystal Structure of SETDB1 Tudor domain in complexed (prob 0.14, TM 0.67). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
I6Y3N9
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 | 2BB0I |
|---|
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 | 1.634 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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)
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 58.5 (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 |
|---|---|---|---|---|
7cjt-assembly1_D |
0.14 | 0.67 | 3.4e+00 | 7cjt-assembly1_D Crystal Structure of SETDB1 Tudor domain in complexed with (R,R)-59 |
3prb-assembly1_A |
0.08 | 0.56 | 6.3e+00 | 3prb-assembly1_A Structural analysis of protein folding by the Methanococcus jannaschii chaperone FKBP26 |
7n6g-assembly1_6N |
0.07 | 0.39 | 3.4e+00 | 7n6g-assembly1_6N C1 of central pair |
1u4p-assembly1_B |
0.06 | 0.31 | 1.8e+00 | 1u4p-assembly1_B Crystal Structure of human RANTES mutant K45E |
3pra-assembly1_B |
0.06 | 0.47 | 4.5e+00 | 3pra-assembly1_B Structural analysis of protein folding by the Methanococcus jannaschii chaperone FKBP26 |
6wzm-assembly1_E |
0.06 | 0.40 | 4.5e+00 | 6wzm-assembly1_E LY3041658 Fab bound to CXCL8 |
6vgj-assembly3_C |
0.06 | 0.39 | 3.9e+00 | 6vgj-assembly3_C N-terminal variant of CXCL13 |
5cba-assembly1_E |
0.05 | 0.40 | 5.1e+00 | 5cba-assembly1_E 3B4 in complex with CXCL13 - 3B4-CXCL13 |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0397 hyp |
hypothetical protein | 469 | 469 ctx | neighborhood:469 |
Rv0455c hyp |
hypothetical protein | 461 | 461 ctx | neighborhood:461 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Foldseek best: 7cjt-assembly1_D Crystal Structure of SETDB1 Tudor domain in complexed with (R,R (prob 0.14, E=3e+00, TM=0.67)
- (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 YP_004837048.2)
- 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
2BB0I - Curated reference: UniProt I6Y3N9 (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 58.5, low)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 2 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0397A| MHALRLVGLAILTAIAPIAVLIGSSPAHADTDIGQPCSPEGAKLWGNPGPIYCERTADGQLQWVSIPAWALCVAFCDRPGGP