Rv2575 Resolved · high auto-curated
H37Rv Rv2575 · MTBC0 mtbc0_002742 ·
293 aa · 2922883–2923764 (+) ·
RefSeq NP_217091.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | neutral zinc metallopeptidase |
| Revised (this work) | Neutral zinc metallopeptidase. Pfam: Zn_peptidase (PF04228.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WL85
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized protein Rv2575 |
UniProt still lists this protein as Uncharacterized protein Rv2575; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | ypfJ |
| eggNOG description | Putative neutral zinc metallopeptidase |
| Orthologous group | COG2321 |
| KEGG orthology |
K07054
|
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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 | 2.298 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 6 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.47% of strains (679) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Zn_peptidase | PF04228.20 | 9.0e-74 | 14–287 | Putative neutral zinc metallopeptidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2573 (2-dehydropantoate 2-reductase), high confidence from genomic context alone (score 812 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2573 |
2-dehydropantoate 2-reductase | 811 | 812 ctx | neighborhood:811 |
Rv2574 hyp |
hypothetical protein | 697 | 697 ctx | neighborhood:682 |
Rv2510c hyp |
hypothetical protein | 658 | 659 ctx | cooccurence:653 |
Rv2572c aspS |
aspartate--tRNA ligase | 518 | 518 ctx | neighborhood:515 |
Rv3092c |
integral membrane protein | 408 | 409 | |
Rv2571c |
transmembrane protein | 407 | 407 ctx | neighborhood:404 |
Rv2367c ybeY |
endoribonuclease | 671 | 44 | textmining:670 |
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: membrane protein
- MTBC0 PGAP product: neutral zinc metallopeptidase
- Pfam (hmmscan --cut_ga): Zn_peptidase PF04228.20 (E=9e-74)
- (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_217091.1)
- Domains: Pfam-A via hmmscan --cut_ga — Zn_peptidase (PF04228.20)
- 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
COG2321 - Curated reference: UniProt P9WL85 (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); context anchor
Rv2573 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002742|Rv2575| MTFNEGVQIDTSTTSTSGSGGGRRLAIGGGLGGLLVVVVAMLLGVDPGGVLSQQPLDTRDHVAPGFDLSQCRTGADANRFVQCRVVATGNSVDAVWKPLLPGYTRPHMRLFSGQVGTGCGPASSEVGPFYCPVDKTAYFDTDFFQVLVTQFGSSGGPFAEEYVVAHEYGHHVQNLLGVLGRAQQGAQGAAGSGVRTELQADCYAGVWAYYASTVKQESTGVPYLEPLSDKDIQDALAAAAAVGDDRIQQQTTGRTNPETWTHGSAAQRQKWFTVGYQTGDPNICDTFSAADLG