Rv3259 Family assigned · medium auto-curated
H37Rv Rv3259 · MTBC0 mtbc0_003467 ·
139 aa · 3661568–3661987 (+) ·
RefSeq NP_217776.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | metallopeptidase family protein |
| Revised (this work) | Metallopeptidase family protein. Pfam: Zincin_1 (PF06262.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53352
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Exonuclease |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Zincin-like metallopeptidase |
| Orthologous group | COG3824 |
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 | 0.689 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Zincin_1 | PF06262.18 | 1.6e-07 | 41–134 | Zincin-like metallopeptidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pmmA (phosphomannomutase PmmA), high confidence from genomic context alone (score 704 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) |
|---|---|---|---|---|
Rv3258c hyp |
hypothetical protein | 806 | 806 ctx | neighborhood:777 |
Rv3257c pmmA |
phosphomannomutase PmmA | 704 | 704 ctx | neighborhood:658 |
Rv3256c hyp |
hypothetical protein | 698 | 698 ctx | neighborhood:554 |
Rv1417 |
membrane protein | 675 | 675 ctx | cooccurence:674 |
Rv3231c hyp |
hypothetical protein | 651 | 651 ctx | cooccurence:650 |
Rv0011c crgA |
cell division protein CrgA | 613 | 613 ctx | cooccurence:611 |
Rv2413c hyp |
hypothetical protein | 598 | 598 ctx | cooccurence:598 |
Rv3605c hyp |
hypothetical protein | 595 | 595 ctx | cooccurence:595 |
Rv2170 |
GCN5-like N-acetyltransferase | 591 | 591 ctx | cooccurence:591 |
Rv2119 hyp |
hypothetical protein | 582 | 582 ctx | cooccurence:582 |
Rv3669 |
transmembrane protein | 567 | 568 ctx | cooccurence:546 |
Rv3255c manA |
mannose-6-phosphate isomerase | 554 | 554 ctx | neighborhood:552 |
Rv3311 hyp |
hypothetical protein | 544 | 545 ctx | cooccurence:542 |
Rv0948c |
chorismate mutase | 535 | 535 ctx | cooccurence:534 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 521 | 521 ctx | cooccurence:516 |
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: metallopeptidase family protein
- Pfam (hmmscan --cut_ga): Zincin_1 PF06262.18 (E=2e-07)
- (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_217776.1)
- Domains: Pfam-A via hmmscan --cut_ga — Zincin_1 (PF06262.18)
- 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
COG3824 - Curated reference: UniProt O53352 (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)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
34 functional partner(s); context anchor
pmmA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003467|Rv3259| MRGPLLPPTVPGWRSRAERFDMAVLEAYEPIERRWQERVSQLDIAVDEIPRIAAKDPESVQWPPEVIADGPIALARLIPAGVDVRGNATRARIVLFRKPIERRAKDTEELGELLHEILVAQVAIYLDVDPSVIDPTIDD