mycP2 Resolved · high auto-curated
H37Rv Rv3886c · MTBC0 mtbc0_004120 ·
550 aa · 4392764–4394416 (-) ·
RefSeq NP_218403.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane-anchored mycosin |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-2 serine protease mycosin MycP2 |
| Revised (this work) | Type VII secretion system ESX-2 serine protease mycosin MycP2. Pfam: Peptidase_S8 (PF00082.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05458
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Mycosin-2 |
| EC (curated) |
EC 3.4.21.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | mycP |
| eggNOG description | Peptidase S8 |
| Orthologous group | COG1404 |
| KEGG orthology |
K14743
|
| Gene Ontology (12) |
GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0016020, GO:0016021, GO:0031224, GO:0031226, GO:0044425, GO:0044459, GO:0044464, GO:0071944
|
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 | 1.487 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 8 missense, 0 nonsense, 4 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 4.26% of strains (6180) · convergent |
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 |
|---|---|---|---|---|
Peptidase_S8 | PF00082.28 | 1.2e-25 | 235–482 | Subtilase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccD2 (ESX-2 secretion system protein EccD), high confidence from genomic context alone (score 952 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 952 | 952 ctx | neighborhood:881 cooccurence:531 |
Rv3888c |
membrane protein | 930 | 930 ctx | neighborhood:881 cooccurence:410 |
Rv3885c eccE2 |
ESX-2 secretion system protein EccE | 928 | 928 ctx | neighborhood:881 coexpression:423 |
Rv3884c eccA2 |
ESX-2 secretion system protein EccA | 845 | 835 ctx | neighborhood:794 |
Rv3895c eccB2 |
ESX-2 secretion system protein EccB | 784 | 783 ctx | cooccurence:685 |
Rv3450c eccB4 |
ESX-4 secretion system protein EccB4 | 788 | 771 ctx | cooccurence:717 |
Rv1782 eccB5 |
ESX-5 type VII secretion system protein EccB5 | 804 | 724 ctx | cooccurence:670 |
Rv3899c hyp |
hypothetical protein | 731 | 721 ctx | cooccurence:592 |
Rv3448 eccD4 |
ESX-4 secretion system protein EccD4 | 703 | 700 ctx | cooccurence:678 |
Rv1006 hyp |
hypothetical protein | 697 | 697 ctx | cooccurence:693 |
Rv1868 hyp |
hypothetical protein | 691 | 691 ctx | cooccurence:685 |
Rv3894c eccC2 |
ESX-2 type VII secretion system protein EccC | 686 | 646 ctx | cooccurence:548 |
Rv1435c hyp |
hypothetical protein | 646 | 641 ctx | cooccurence:639 |
Rv2047c hyp |
hypothetical protein | 615 | 616 ctx | cooccurence:595 |
Rv1795 eccD5 |
ESX-5 type VII secretion system protein EccD | 711 | 606 ctx | cooccurence:555 |
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-anchored mycosin
- MTBC0 PGAP product: type VII secretion system ESX-2 serine protease mycosin MycP2
- Pfam (hmmscan --cut_ga): Peptidase_S8 PF00082.28 (E=1e-25)
- (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_218403.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_S8 (PF00082.28)
- 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
COG1404 - Curated reference: UniProt O05458 (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 —
71 functional partner(s); context anchor
eccD2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004120|Rv3886c|mycP2 MASPLNRPGLRAAAASAALTLVALSANVPAAQAIPPPSVDPAMVPADARPGPDQPMRRSNSCSTPITVRNPDVAQLAPGFNLVNISKAWQYSTGNGVPVAVIDTGVSPNPRLPVVPGGDYIMGEDGLSDCDAHGTVVSSIIAAAPLGILPMPRAMPATAAFPPPAGPPPVTAAPAPPVEVPPPMPPPPPVTITQTVAPPPPPPEDAGAMAPSNGPPDPQTEDEPAVPPPPPGAPDGVVGVAPHATIISIRQSSRAFEPVNPSSAGPNSDEKVKAGTLDSVARAVVHAANMGAKVINISVTACLPAAAPGDQRVLGAALWYAATVKDAVIVAAAGNDGEAGCGNNPMYDPLDPSDPRDWHQVTVVSSPSWFSDYVLSVGAVDAYGAALDKSMSGPWVGVAAPGTHIMGLSPQGGGPVNAYPPSRPGEKNMPFWGTSFSAAYVSGVAALVRAKFPELTAYQVINRIVQSAHNPPAGVDNKLGYGLVDPVAALTFNIPSGDRMAPGAQSRVITPAAPPPPPDHRARNIAIGFVGAVATGVLAMAIGARLRRAR