mmpS3 Family assigned · medium auto-curated
H37Rv Rv2198c · MTBC0 mtbc0_002334 ·
299 aa · 2488305–2489204 (-) ·
RefSeq NP_216714.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein MmpS3 |
|---|---|
| MTBC0 PGAP re-annotation | MmpS family transport accessory protein |
| Revised (this work) | MmpS family transport accessory 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 |
P9WJT1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transport accessory protein MmpS3 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | mmpS3 |
| eggNOG description | Mycobacterium membrane protein |
| Orthologous group | 2A3D5 |
| Gene Ontology (14) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0005887, GO:0016020, GO:0016021, GO:0030312, GO:0031224, GO:0031226, GO:0044425, GO:0044459 +2 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 0 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 |
|---|---|---|---|---|
Mycobact_memb | PF05423.19 | 1.1e-06 | 205–286 | Mycobacterium membrane protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2197c (transmembrane protein), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2197c |
transmembrane protein | 884 | 884 ctx | neighborhood:881 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 699 | 699 ctx | neighborhood:696 |
Rv2200c ctaC |
cytochrome C oxidase subunit II | 526 | 527 ctx | neighborhood:515 |
Rv2145c wag31 |
cell wall synthesis protein Wag31 | 534 | 86 | textmining:512 |
Rv0020c fhaA |
FHA domain-containing protein FhaA | 560 | 70 | textmining:547 |
Rv2151c ftsQ |
cell division protein FtsQ | 459 | 55 | textmining:451 |
Rv0014c pknB |
serine/threonine-protein kinase PknB | 440 | 54 | textmining:433 |
Rv3628 ppa |
inorganic pyrophosphatase | 521 | 52 | textmining:516 |
Rv3360 hyp |
hypothetical protein | 531 | 44 | textmining:530 |
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 MmpS3
- MTBC0 PGAP product: MmpS family transport accessory protein
- Pfam (hmmscan --cut_ga): Mycobact_memb PF05423.19 (E=1e-06)
- (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_216714.1)
- 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
2A3D5 - Curated reference: UniProt P9WJT1 (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 —
9 functional partner(s); context anchor
Rv2197c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002334|Rv2198c|mmpS3 MSGPNPPGREPDEPESEPVSDTGDERASGNHLPPVAGGGDKLPSDQTGETDAYSRAYSAPESEHVTGGPYVPADLRLYDYDDYEESSDLDDELAAPRWPWVVGVAAIIAAVALVVSVSLLVTRPHTSKLATGDTTSSAPPVQDEITTTKPAPPPPPPAPPPTTEIPTATETQTVTVTPPPPPPPATTTAPPPATTTTAAAPPPTTTTPTGPRQVTYSVTGTKAPGDIISVTYVDAAGRRRTQHNVYIPWSMTVTPISQSDVGSVEASSLFRVSKLNCSITTSDGTVLSSNSNDGPQTSC