mycP1 Resolved · high auto-curated
H37Rv Rv3883c · MTBC0 mtbc0_004117 ·
446 aa · 4387663–4389003 (-) ·
RefSeq NP_218400.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane-anchored mycosin |
|---|---|
| MTBC0 PGAP re-annotation | type VII secretion system ESX-1 serine protease mycosin MycP1 |
| Revised (this work) | Type VII secretion system ESX-1 serine protease mycosin MycP1. 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 |
O05461
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Mycosin-1 |
| EC (curated) |
EC 3.4.21.-
|
| Curated function | May play a dual role in regulation of ESX-1 secretion and virulence. Acts as a protease that cleaves EspB. Essential for ESX-1 function, required for early replication in macrophages and full virulence in mice. |
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 (34) |
GO:0003674, GO:0003824, GO:0004175, GO:0004252, GO:0005575, GO:0005623, GO:0005886, GO:0006508, GO:0006807, GO:0008150, GO:0008152, GO:0008233 +22 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 | 0.832 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 13 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 | 7.1e-35 | 81–379 | Subtilase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccE1 (ESX-1 secretion system protein EccE1), high confidence from genomic context alone (score 987 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 996 | 987 ctx | neighborhood:882 cooccurence:503 coexpression:802 textmining:697 |
Rv3881c espB |
ESX-1 secretion-associated protein EspB | 950 | 745 ctx | neighborhood:731 textmining:812 |
Rv3884c eccA2 |
ESX-2 secretion system protein EccA | 912 | 742 ctx | neighborhood:728 textmining:673 |
Rv3869 eccB1 |
ESX-1 secretion system protein EccB | 842 | 717 ctx | cooccurence:654 textmining:466 |
Rv3880c espL |
ESX-1 secretion-associated protein EspL | 824 | 653 ctx | neighborhood:648 textmining:514 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 695 | 609 ctx | cooccurence:583 |
Rv3870 eccCa1 |
ESX-1 secretion system protein EccCa | 681 | 556 ctx | cooccurence:538 |
Rv3871 eccCb1 |
ESX-1 secretion system protein EccCb | 663 | 506 ctx | cooccurence:485 |
Rv2189c hyp |
hypothetical protein | 530 | 502 | |
Rv2235 |
transmembrane protein | 498 | 499 | experimental:412 |
Rv3876 espI |
ESX-1 secretion-associated protein EspI | 596 | 474 ctx | cooccurence:461 |
Rv3886c mycP2 |
membrane-anchored mycosin | 517 | 473 ctx | neighborhood:419 |
Rv0425c ctpH |
metal cation transporting ATPase H | 491 | 469 | |
Rv0107c ctpI |
cation-transporter ATPase I | 491 | 469 | |
Rv1997 ctpF |
cation transporter ATPase F | 491 | 469 |
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-1 serine protease mycosin MycP1
- Pfam (hmmscan --cut_ga): Peptidase_S8 PF00082.28 (E=7e-35)
- (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_218400.1)
- 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 O05461 (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 —
67 functional partner(s); context anchor
eccE1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004117|Rv3883c|mycP1 MHRIFLITVALALLTASPASAITPPPIDPGALPPDVTGPDQPTEQRVLCASPTTLPGSGFHDPPWSNTYLGVADAHKFATGAGVTVAVIDTGVDASPRVPAEPGGDFVDQAGNGLSDCDAHGTLTASIIAGRPAPTDGFVGVAPDARLLSLRQTSEAFEPVGSQANPNDPNATPAAGSIRSLARAVVHAANLGVGVINISEAACYKVSRPIDETSLGASIDYAVNVKGVVVVVAAGNTGGDCVQNPAPDPSTPGDPRGWNNVQTVVTPAWYAPLVLSVGGIGQTGMPSSFSMHGPWVDVAAPAENIVALGDTGEPVNALQGREGPVPIAGTSFAAAYVSGLAALLRQRFPDLTPAQIIHRITATARHPGGGVDDLVGAGVIDAVAALTWDIPPGPASAPYNVRRLPPPVVEPGPDRRPITAVALVAVGLTLALGLGALARRALSRR