Rv0359 Family assigned · low auto-curated
H37Rv Rv0359 · MTBC0 mtbc0_000379 ·
259 aa · 440880–441659 (+) ·
RefSeq NP_214873.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | zinc metalloprotease |
|---|---|
| MTBC0 PGAP re-annotation | site-2 protease family protein |
| Revised (this work) | Site-2 protease family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
L0T550
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative zinc metalloprotease Rip2 |
UniProt still lists this protein as Putative zinc metalloprotease Rip2; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | rip2 |
| eggNOG description | Peptidase M50 |
| Orthologous group | COG1994 |
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 | 2.624 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (176) · clonal |
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).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: purA (adenylosuccinate synthetase), medium confidence from genomic context alone (score 637 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0358 hyp |
hypothetical protein | 850 | 850 ctx | neighborhood:845 |
Rv0357c purA |
adenylosuccinate synthetase | 638 | 637 ctx | neighborhood:626 |
Rv0356c hyp |
hypothetical protein | 561 | 560 ctx | neighborhood:551 |
Rv2795c hyp |
hypothetical protein | 422 | 422 ctx | cooccurence:403 |
Rv1010 ksgA |
rRNA small subunit methyltransferase A | 488 | 60 | textmining:478 |
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: zinc metalloprotease
- MTBC0 PGAP product: site-2 protease family protein
- (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_214873.1)
- 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
COG1994 - Curated reference: UniProt L0T550 (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 —
5 functional partner(s); context anchor
purA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000379|Rv0359| MSETGQRESVRPSPIFLGLLGLTAVGGALAWLAGETVQPLAYAGVFVMVIAGWLVSLCLHEFGHAFTAWRFGDHDVAVRGYLTLDPRRYSHPMLSLGLPMLFIALGGIGLPGAAVYVHTWFMTTARRTLVSLAGPTVNLALAMLLLAATRLLFDPIHAVLWAGVAFLAFLQLTALVLNLLPIPGLDGYAALEPHLRPETQRALAPAKQFALVFLLVLFLAPTLNGWFFGVVYWLFDLSGVSHRLAAAGSVLTRFWSIWF