mycP3 Resolved · high auto-curated
H37Rv Rv0291 · MTBC0 mtbc0_000310 ·
461 aa · 357792–359177 (+) ·
RefSeq NP_214805.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane-anchored mycosin MycP |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-3 serine protease mycosin MycP3 |
| Revised (this work) | Type VII secretion system ESX-3 serine protease mycosin MycP3. 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 |
O53695
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Mycosin-3 |
| EC (curated) |
EC 3.4.21.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | mycP3 |
| eggNOG description | Peptidase S8 |
| Orthologous group | COG1404 |
| KEGG orthology |
K14743
|
| Gene Ontology (17) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886, GO:0005887, GO:0008150, GO:0016020, GO:0016021, GO:0030312, GO:0031224, GO:0031226 +5 more
|
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 | 0.952 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 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 |
|---|---|---|---|---|
Peptidase_S8 | PF00082.28 | 4.0e-34 | 86–389 | Subtilase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccD3 (ESX-3 secretion system protein EccD), high confidence from genomic context alone (score 987 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 995 | 987 ctx | neighborhood:882 coexpression:860 textmining:645 |
Rv0292 eccE3 |
ESX-3 secretion system protein EccE | 991 | 983 ctx | neighborhood:882 coexpression:860 textmining:541 |
Rv0289 espG3 |
ESX-3 secretion-associated protein EspG3 | 989 | 970 ctx | neighborhood:815 coexpression:845 textmining:667 |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 985 | 955 ctx | neighborhood:535 cooccurence:474 coexpression:803 textmining:684 |
Rv0284 eccC3 |
ESX-3 secretion system protein EccC3 | 974 | 933 ctx | neighborhood:581 coexpression:769 textmining:633 |
Rv0286 PPE4 |
PPE family protein PPE4 | 904 | 904 ctx | neighborhood:469 coexpression:827 |
Rv0282 eccA3 |
ESX-3 secretion system protein EccA | 926 | 832 ctx | neighborhood:581 coexpression:515 textmining:578 |
Rv0288 esxH |
ESAT-6-like protein EsxH | 737 | 721 ctx | neighborhood:658 |
Rv0287 esxG |
ESAT-6 like protein EsxG | 726 | 687 ctx | neighborhood:592 |
Rv1997 ctpF |
cation transporter ATPase F | 553 | 534 | |
Rv0285 PE5 |
PE family protein PE5 | 547 | 526 ctx | neighborhood:526 |
Rv2301 cut2 |
cutinase | 534 | 516 | |
Rv3724B cut5b |
Rv3724B, (MTV025.072), len: 187 aa. Probable cut5b,truncated cutinase, similar to C-terminal end of others e.g. Q9XB09|RVD2-RV1758 protein ( | 533 | 515 | |
Rv2189c hyp |
hypothetical protein | 538 | 511 | |
Rv3451 cut3 |
cutinase | 518 | 499 |
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 MycP
- MTBC0 PGAP product: type VII secretion system ESX-3 serine protease mycosin MycP3
- Pfam (hmmscan --cut_ga): Peptidase_S8 PF00082.28 (E=4e-34)
- (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_214805.1)
- 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 O53695 (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 —
58 functional partner(s); context anchor
eccD3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000310|Rv0291|mycP3 MIRAAFACLAATVVVAGWWTPPAWAIGPPVVDAAAQPPSGDPGPVAPMEQRGACSVSGVIPGTDPGVPTPSQTMLNLPAAWQFSRGEGQLVAIIDTGVQPGPRLPNVDAGGDFVESTDGLTDCDGHGTLVAGIVAGQPGNDGFSGVAPAARLLSIRAMSTKFSPRTSGGDPQLAQATLDVAVLAGAIVHAADLGAKVINVSTITCLPADRMVDQAALGAAIRYAAVDKDAVIVAAAGNTGASGSVSASCDSNPLTDLSRPDDPRNWAGVTSVSIPSWWQPYVLSVASLTSAGQPSKFSMPGPWVGIAAPGENIASVSNSGDGALANGLPDAHQKLVALSGTSYAAGYVSGVAALVRSRYPGLNATEVVRRLTATAHRGARESSNIVGAGNLDAVAALTWQLPAEPGGGAAPAKPVADPPVPAPKDTTPRNVAFAGAAALSVLVGLTAATVAIARRRREPTE