mmpS1 Family assigned · medium auto-curated
H37Rv Rv0403c · MTBC0 mtbc0_000423 ·
142 aa · 486592–487020 (-) ·
RefSeq NP_214917.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein MmpS1 |
|---|---|
| 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 |
P9WJT5
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable transport accessory protein MmpS1 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | mmpS1 |
| 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 | 0.67 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 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 | 2.7e-66 | 6–142 | Mycobacterium membrane protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mmpL1 (transmembrane transport protein MmpL1), high confidence from genomic context alone (score 976 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0402c mmpL1 |
transmembrane transport protein MmpL1 | 975 | 976 ctx | neighborhood:881 coexpression:805 |
Rv0404 fadD30 |
long-chain-fatty-acid--AMP ligase FadD30 | 530 | 530 | |
Rv0405 pks6 |
membrane bound polyketide synthase | 405 | 405 | |
Rv1754c hyp |
hypothetical protein | 871 | 53 | textmining:870 |
Rv2336 hyp |
hypothetical protein | 655 | 53 | textmining:651 |
Rv3096 hyp |
hypothetical protein | 548 | 50 | textmining:544 |
Rv3383c idsB |
polyprenyl synthetase IdsB | 525 | 50 | textmining:521 |
Rv0556 |
transmembrane protein | 752 | 47 | textmining:751 |
Rv1682 hyp |
hypothetical protein | 656 | 47 | textmining:654 |
Rv1469 ctpD |
cobalt/nickel-exporting P-type ATPase | 520 | 47 | textmining:517 |
Rv0176 |
Mce associated transmembrane protein | 433 | 47 | textmining:430 |
Rv0835 lpqQ |
lipoprotein LpqQ | 660 | 46 | textmining:659 |
Rv2735c hyp |
hypothetical protein | 660 | 46 | textmining:659 |
Rv3630 |
integral membrane protein | 625 | 46 | textmining:624 |
Rv0264c hyp |
hypothetical protein | 750 | 44 | textmining:750 |
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 MmpS1
- MTBC0 PGAP product: MmpS family protein
- Pfam (hmmscan --cut_ga): Mycobact_memb PF05423.19 (E=3e-66)
- (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_214917.1)
- 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 P9WJT5 (SwissProt, reviewed; Inferred from homology)
- 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 —
31 functional partner(s); context anchor
mmpL1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000423|Rv0403c|mmpS1 MFGVAKRFWIPMVIVIVVAVAAVTVSRLHSVFGSHQHAPDTGNLDPIIAFYPKHVLYEVFGPPGTVASINYLDADAQPHEVVNAAVPWSFTIVTTLTAVVANVVARGDGASLGCRITVNEVIREERIVNAYHAHTSCLVKSA