Rv2568c Family assigned · medium auto-curated
H37Rv Rv2568c · MTBC0 mtbc0_002735 ·
341 aa · 2915990–2917015 (-) ·
RefSeq NP_217084.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | putative zinc-binding metallopeptidase |
| Revised (this work) | Putative zinc-binding metallopeptidase. Pfam: Zn_ribbon_DZR_6 (PF10005.15), Peptidase_Mx (PF15887.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL95
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2568c |
UniProt still lists this protein as Uncharacterized protein Rv2568c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | protein conserved in bacteria |
| Orthologous group | COG4307 |
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 | 0.127 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Zn_ribbon_DZR_6 | PF10005.15 | 3.5e-17 | 4–81 | zinc-ribbon domain |
Peptidase_Mx | PF15887.12 | 1.5e-101 | 88–324 | Putative zinc-binding metallo-peptidase |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2569c hyp |
hypothetical protein | 952 | 952 ctx | neighborhood:882 cooccurence:569 |
Rv2566 hyp |
hypothetical protein | 846 | 846 ctx | neighborhood:544 cooccurence:675 |
Rv2567 hyp |
hypothetical protein | 815 | 816 ctx | neighborhood:544 cooccurence:613 |
Rv2570 hyp |
hypothetical protein | 655 | 655 ctx | neighborhood:655 |
Rv2411c hyp |
hypothetical protein | 430 | 430 | |
Rv2410c hyp |
hypothetical protein | 413 | 414 | |
Rv2409c hyp |
hypothetical protein | 411 | 411 |
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: putative zinc-binding metallopeptidase
- Pfam (hmmscan --cut_ga): Zn_ribbon_DZR_6 PF10005.15 (E=4e-17), Peptidase_Mx PF15887.12 (E=2e-101)
- (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_217084.1)
- Domains: Pfam-A via hmmscan --cut_ga — Zn_ribbon_DZR_6 (PF10005.15), Peptidase_Mx (PF15887.12)
- 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
COG4307 - Curated reference: UniProt P9WL95 (SwissProt, reviewed; 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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 7 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002735|Rv2568c| MRDFHCPNCGQRLAFENSACLSCGSALGFSLGRMALLVIADDADVQLCANLHLAQCNWLVPSDQLGGLCSSCVLTIERPSDTNTAGLAEFARAEGAKRRLIAELHELKLPIVGRDQDPDHGLAFRLLSSAHENVTTGHQNGVITLDLAEGDDVHREQLRVEMDEPYRTLLGHFRHEIGHYYFYRLIASSSDYLSRFNELFGDPDADYSQALDRHYRGGPPEGWQDSFVSSYATMHASEDWAETFAHYLHIRDALDTAAWCGLAPASATFDRPALGPSAFNTIIDKWLPLSWSLNMVNRSMGHDDLYPFVLPAAVLEKMRFIHTVVDEVAPDFEPAHSRRTV