zmp1 Resolved · high auto-curated
H37Rv Rv0198c · MTBC0 mtbc0_000212 ·
663 aa · 234868–236859 (-) ·
RefSeq NP_214712.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | zinc metalloprotease |
|---|---|
| MTBC0 PGAP re-annotation | zinc metalloprotease Zmp1 |
| Revised (this work) | Zinc metalloprotease Zmp1. Pfam: Peptidase_M13_N (PF05649.19), Peptidase_M13 (PF01431.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X8R2
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable zinc metalloprotease Zmp1 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | pepO |
| eggNOG description | peptidase |
| Orthologous group | COG3590 |
| EC number |
EC 3.4.24.11, EC 3.4.24.71
|
| KEGG orthology |
K01389, K01415, K07386
|
| KEGG pathways |
map04614, map04640, map04974, map05010
|
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 | 0.179 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 30 synonymous, 17 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_M13_N | PF05649.19 | 5.7e-121 | 20–400 | Peptidase family M13 |
Peptidase_M13 | PF01431.28 | 2.3e-80 | 452–659 | Peptidase family M13 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0199 (membrane protein), high confidence from genomic context alone (score 784 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0199 |
membrane protein | 795 | 784 ctx | neighborhood:759 |
Rv0200 |
transmembrane protein | 795 | 784 ctx | neighborhood:758 |
Rv1629 polA |
DNA polymerase I | 595 | 529 | coexpression:424 |
Rv2592c ruvB |
Holliday junction ATP-dependent DNA helicase RuvB | 527 | 527 | coexpression:527 |
Rv3633 hyp |
hypothetical protein | 525 | 526 | database:521 |
Rv1501 hyp |
hypothetical protein | 523 | 524 | database:521 |
Rv1436 gap |
glyceraldehyde 3-phosphate dehydrogenase | 623 | 498 | coexpression:498 |
Rv0457c |
peptidase | 669 | 486 ctx | cooccurence:444 |
Rv3794 embA |
arabinosyltransferase A | 451 | 452 | coexpression:405 |
Rv3795 embB |
arabinosyltransferase B | 449 | 449 | coexpression:402 |
Rv3793 embC |
arabinosyltransferase C | 447 | 448 | coexpression:400 |
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 | 441 | 441 | coexpression:441 |
Rv3864 espE |
ESX-1 secretion-associated protein EspE | 425 | 425 | coexpression:414 |
Rv1887 hyp |
hypothetical protein | 425 | 425 | coexpression:414 |
Rv1782 eccB5 |
ESX-5 type VII secretion system protein EccB5 | 415 | 416 | coexpression:405 |
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: zinc metalloprotease Zmp1
- Pfam (hmmscan --cut_ga): Peptidase_M13_N PF05649.19 (E=6e-121), Peptidase_M13 PF01431.28 (E=2e-80)
- (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_214712.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_M13_N (PF05649.19), Peptidase_M13 (PF01431.28)
- 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
COG3590 - Curated reference: UniProt I6X8R2 (TrEMBL, unreviewed; 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 —
74 functional partner(s); context anchor
Rv0199 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000212|Rv0198c|zmp1 MTLAIPSGIDLSHIDADARPQDDLFGHVNGRWLAEHEIPADRATDGAFRSLFDRAETQVRDLIIQASQAGAAVGTDAQRIGDLYASFLDEEAVERAGVQPLHDELATIDSAADATELAAALGTLQRAGVGGGIGVYVDTDSKDSTRYLVHFTQSGIGLPDESYYRDEQHAAVLAAYPGHIARMFGLVYGGESRDHAKTADRIVALETKLADAHWDVVKRRDADLGYNLRTFAQLQTEGAGFDWVSWVTALGSAPDAMTELVVRQPDYLVTFASLWASVNVEDWKCWARWRLIRARAPWLTRALVAEDFEFYGRTLTGAQQLRDRWKRGVSLVENLMGDAVGKLYVQRHFPPDAKSRIDTLVDNLQEAYRISISELDWMTPQTRQRALAKLNKFTAKVGYPIKWRDYSKLAIDRDDLYGNVQRGYAVNHDRELAKLFGPVDRDEWFMTPQTVNAYYNPGMNEIVFPAAILQPPFFDPQADEAANYGGIGAVIGHEIGHGFDDQGAKYDGDGNLVDWWTDDDRTEFAARTKALIEQYHAYTPRDLVDHPGPPHVQGAFTIGENIGDLGGLSIALLAYQLSLNGNPAPVIDGLTGMQRVFFGWAQIWRTKSRAAEAIRRLAVDPHSPPEFRCNGVVRNVDAFYQAFDVTEDDALFLDPQRRVRIWN