Rv0612 Still unknown · low auto-curated
H37Rv Rv0612 · MTBC0 mtbc0_000644 ·
201 aa · 709876–710481 (+) ·
RefSeq NP_215126.1
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: 6lja-assembly1_A Crystal Structure of exoHep from Bacteroides intestin (prob 0.23, TM 0.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X9E8
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 | 29FX3 |
|---|
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, 3 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 83.1 (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 |
|---|---|---|---|---|
6lja-assembly1_A |
0.23 | 0.31 | 7.8e-01 | 6lja-assembly1_A Crystal Structure of exoHep from Bacteroides intestinalis DSM 17393 complexed with disaccharide product |
6ljl-assembly1_A |
0.14 | 0.31 | 1.9e+00 | 6ljl-assembly1_A Crystal Structure of exoHep-Y390A/H555A complexed with a tetrasaccharide substrate |
6qnx-assembly1_A |
0.09 | 0.37 | 6.5e+00 | 6qnx-assembly1_A Structure of the SA2/SCC1/CTCF complex |
5yvi-assembly1_A |
0.08 | 0.19 | 1.8e+00 | 5yvi-assembly1_A Crystal structure of Karyopherin beta2 in complex with FUS(456-526) |
6e10-assembly1_A |
0.07 | 0.23 | 3.3e+00 | 6e10-assembly1_A PTEX Core Complex in the Engaged (Extended) State |
8j2y-assembly1_A |
0.06 | 0.28 | 5.6e+00 | 8j2y-assembly1_A Acidimicrobiaceae bacterium photocobilins protein, dark state |
7ml2-assembly1_1 |
0.06 | 0.35 | 8.0e+00 | 7ml2-assembly1_1 RNA polymerase II pre-initiation complex (PIC3) |
5imu-assembly1_A |
0.05 | 0.35 | 8.0e+00 | 5imu-assembly1_A A fragment of conserved hypothetical protein Rv3899c (residues 184-410) from Mycobacterium tuberculosis |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0611c hyp |
hypothetical protein | 582 | 582 ctx | neighborhood:579 |
Rv0610c hyp |
hypothetical protein | 470 | 470 ctx | neighborhood:467 |
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: 6lja-assembly1_A Crystal Structure of exoHep from Bacteroides intestinalis DSM 1 (prob 0.23, E=8e-01, TM=0.31)
- (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_215126.1)
- 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
29FX3 - Curated reference: UniProt I6X9E8 (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 83.1, confident)
- 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
>mtbc0_000644|Rv0612| MLGPIRQPRLTVRPGRLPGMIAGVAAKRMNREQFFRAASGLDEDRLRKALWNLYWRGTANMRERIEAELASAGRARPARKIKPPADPDIVGWEVDEFVSLARSGAYLGGDRRVSPRERSRWRFTFKRLAAEAQDALRAEDAEPAASALEQLIDLAREADGYDYFRSDDPVAAAGFVVSDVAAAGHPHFREFAAEIGAAIPP