Rv2668 Family assigned · low auto-curated · to review
H37Rv Rv2668 · MTBC0 mtbc0_002842 ·
173 aa · 3006936–3007457 (+) ·
RefSeq NP_217184.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | No Pfam domain above threshold; Foldseek indicates a fold similar to 3cfu-assembly1_A Crystal structure of the yjhA protein from Bacillus subtilis. N (prob 1.00, TM 0.61). Structure-based, putative. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed (flagged for human review).
Curated reference (UniProt)
| UniProt |
P71965
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible exported alanine and valine rich protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| Orthologous group | 2ARUH |
|---|
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 | 0.875 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 84.5 (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 |
|---|---|---|---|---|
3cfu-assembly1_A |
1.00 | 0.61 | 2.7e-04 sig | 3cfu-assembly1_A Crystal structure of the yjhA protein from Bacillus subtilis. Northeast Structural Genomics Consortium target SR562 |
3cfu-assembly2_B |
1.00 | 0.66 | 8.0e-04 sig | 3cfu-assembly2_B Crystal structure of the yjhA protein from Bacillus subtilis. Northeast Structural Genomics Consortium target SR562 |
5bxg-assembly1_A |
1.00 | 0.52 | 8.9e-04 sig | 5bxg-assembly1_A Crystal structure of an uncharacterized beta-sandwich protein (CD630_09570) from Clostridium difficile 630 at 1.90 A resolution |
4les-assembly1_A |
0.99 | 0.49 | 1.4e-02 | 4les-assembly1_A 2.2 Angstrom Crystal Structure of Conserved Hypothetical Protein from Bacillus anthracis. |
3nrf-assembly1_B |
0.98 | 0.48 | 1.2e-02 | 3nrf-assembly1_B Crystal structure of an apag protein (PA1934) from pseudomonas aeruginosa pao1 at 1.50 A resolution |
4eae-assembly1_B |
0.96 | 0.43 | 9.9e-03 sig | 4eae-assembly1_B The crystal structure of a functionally unknown protein from Listeria monocytogenes EGD-e |
4eae-assembly1_A |
0.95 | 0.41 | 8.9e-03 sig | 4eae-assembly1_A The crystal structure of a functionally unknown protein from Listeria monocytogenes EGD-e |
1tza-assembly1_B |
0.72 | 0.36 | 2.1e-02 | 1tza-assembly1_B X-ray structure of Northeast Structural Genomics Consortium target SoR45 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2669 (GCN5-like N-acetyltransferase), high confidence from genomic context alone (score 841 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) |
|---|---|---|---|---|
Rv2669 |
GCN5-like N-acetyltransferase | 841 | 841 ctx | neighborhood:839 |
Rv2667 clpC2 |
ATP-dependent protease ATP-binding subunit ClpC | 787 | 787 ctx | neighborhood:786 |
Rv2666 |
Probable transposase for insertion sequence element IS1081 (fragment); Required for the transposition of the insertion element. | 518 | 518 ctx | neighborhood:518 |
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: 3cfu-assembly1_A Crystal structure of the yjhA protein from Bacillus subtilis. N (prob 1.00, E=3e-04, TM=0.61)
- (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_217184.1)
- 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
2ARUH - Curated reference: UniProt P71965 (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 84.5, 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); context anchor
Rv2669 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002842|Rv2668| MRRWLIVLATLLVAAAGVAAANDVPRAWAGDAPIGHIGDTLRVDTGTYVADVTVSSVVPVDPPPGFGYTRSGVPVKSFPDSSVTRADVTVRAVRVPNSFILATNFSFTGVTPFADAYKPRPCDASDWLDAALGNAPQGSIVRGGVYWDAYRDPVSVVVLLDKKTGQHLAQWNL