mmpS2 Family assigned · medium auto-curated
H37Rv Rv0506 · MTBC0 mtbc0_000534 ·
147 aa · 600216–600659 (+) ·
RefSeq NP_215020.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein MmpS2 |
|---|---|
| MTBC0 PGAP re-annotation | MmpS family protein |
| Revised (this work) | MmpS family protein. Pfam: Mycobact_memb (PF05423.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJT3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transport accessory protein MmpS2 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | mmpS2 |
| eggNOG description | Mycobacterium membrane protein |
| Orthologous group | 2BG05 |
| 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (198) · 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 |
|---|---|---|---|---|
Mycobact_memb | PF05423.19 | 6.6e-64 | 10–146 | Mycobacterium membrane protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mmpL2 (transmembrane transport protein MmpL2), high confidence from genomic context alone (score 883 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0507 mmpL2 |
transmembrane transport protein MmpL2 | 900 | 883 ctx | neighborhood:881 |
Rv0508 hyp |
hypothetical protein | 879 | 879 ctx | neighborhood:878 |
Rv0509 hemA |
glutamyl-tRNA reductase | 638 | 637 ctx | neighborhood:637 |
Rv0510 hemC |
porphobilinogen deaminase | 618 | 619 ctx | neighborhood:619 |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 540 | 540 ctx | neighborhood:540 |
Rv0505c serB1 |
phosphoserine phosphatase SerB | 513 | 514 ctx | neighborhood:511 |
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 MmpS2
- MTBC0 PGAP product: MmpS family protein
- Pfam (hmmscan --cut_ga): Mycobact_memb PF05423.19 (E=7e-64)
- (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_215020.1)
- Domains: Pfam-A via hmmscan --cut_ga — Mycobact_memb (PF05423.19)
- 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
2BG05 - Curated reference: UniProt P9WJT3 (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 —
6 functional partner(s); context anchor
mmpL2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000534|Rv0506|mmpS2 MRMISVSGAVKRMWLLLAIVVVAVVGGLGIYRLHSIFGVHEQPTVMVKPDFDVPLFNPKRVTYEVFGPAKTAKIAYLDPDARVHRLDSVSLPWSVTVETTLPAVSVNLMAQSNADVISCRIIVNGAVKDERSETSPRALTSCQVSSG