mmpL9 Resolved · high auto-curated
H37Rv Rv2339 · MTBC0 mtbc0_002489 ·
962 aa · 2639443–2642331 (+) ·
RefSeq NP_216855.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane transport protein MmpL9 |
|---|---|
| MTBC0 PGAP re-annotation | RND transporter MmpL9 |
| Revised (this work) | RND transporter MmpL9. Pfam: MMPL (PF03176.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJU3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transport protein MmpL9 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | mmpL9 |
| eggNOG description | transport protein |
| Orthologous group | COG2409 |
| KEGG orthology |
K06994
|
| Gene Ontology (32) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0008150, GO:0009605, GO:0009607, GO:0020012, GO:0030312, GO:0030682, GO:0042783, GO:0043207 +20 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 | 2.431 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 19 missense, 3 nonsense, 3 frameshift |
| Disruption | 6 distinct premature-stop/frameshift site(s); most common in 25.74% of strains (37374) · convergent |
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 |
|---|---|---|---|---|
MMPL | PF03176.22 | 1.1e-122 | 59–387 | MMPL family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccD3 (ESX-3 secretion system protein EccD), medium confidence from genomic context alone (score 618 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1598c hyp |
hypothetical protein | 702 | 703 ctx | cooccurence:702 |
Rv1303 hyp |
hypothetical protein | 640 | 640 ctx | cooccurence:638 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 618 | 618 ctx | cooccurence:618 |
Rv2945c lppX |
lipoprotein LppX | 683 | 580 ctx | cooccurence:580 |
Rv0128 |
transmembrane protein | 538 | 538 ctx | cooccurence:537 |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 506 | 507 ctx | cooccurence:489 |
Rv0466 hyp |
hypothetical protein | 490 | 491 ctx | cooccurence:490 |
Rv1278 hyp |
hypothetical protein | 477 | 477 ctx | cooccurence:477 |
Rv0523c hyp |
hypothetical protein | 474 | 474 ctx | cooccurence:471 |
Rv1270c lprA |
lipoprotein LprA | 449 | 449 ctx | cooccurence:447 |
Rv0309 hyp |
hypothetical protein | 442 | 443 ctx | cooccurence:441 |
Rv0184 hyp |
hypothetical protein | 434 | 434 ctx | cooccurence:434 |
Rv1411c lprG |
lipoprotein LprG | 431 | 432 ctx | cooccurence:430 |
Rv0477 hyp |
hypothetical protein | 429 | 429 ctx | cooccurence:429 |
Rv1277 hyp |
hypothetical protein | 429 | 429 ctx | cooccurence:429 |
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: transmembrane transport protein MmpL9
- MTBC0 PGAP product: RND transporter MmpL9
- Pfam (hmmscan --cut_ga): MMPL PF03176.22 (E=1e-122)
- (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_216855.1)
- Domains: Pfam-A via hmmscan --cut_ga — MMPL (PF03176.22)
- 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
COG2409 - Curated reference: UniProt P9WJU3 (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 —
42 functional partner(s); context anchor
eccD3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002489|Rv2339|mmpL9 MVPGEVHMSDTPSGPHPIIPRTIRLAAIPILLCWLGFTVFVSVAVPPLEAIGETRAVAVAPDDAQSMRAMRRAGKVFNEFDSNSIAMVVLESDQPLGEKAHRYYDHLVDTLVLDQSHIQHIQDFWRDPLTAAGAVSADGKAAYVQLYLAGNMGEALANESVEAVRKIVANSTPPEGIRTYVTGPAALFADQIAAGDRSMKLITGLTFAVITVLLLLVYRSIATTLLILPMVFIGLGATRGTIAFLGYHGMVGLSTFVVNILTALAIAAGTDYAIFLVGRYQEARHIGQNREASFYTMYRGTANVILGSGLTIAGATYCLSFARLTLFHTMGPPLAIGMLVSVAAALTLAPAIIAIAGRFGLLDPKRRLKTRGWRRVGTAVVRWPGPILATSVALALVGLLALPGYRPGYNDRYYLRAGTPVNRGYAAADRHFGPARMNPEMLLVESDQDMRNPAGMLVIDKIAKEVLHVSGVERVQAITRPQGVPLEHASIPFQISMMGATQTMSLPYMRERMADMLTMSDEMLVAINSMEQMLDLVQQLNDVTHEMAATTREIKATTSELRDHLADIDDFVRPLRSYFYWEHHCFDIPLCSATRSLFDTLDGVDTLTDQLRALTDDMNKMEALTPQFLALLPPMITTMKTMRTMMLTMRSTISGVQDQMADMQDHATAMGQAFDTAKSGDSFYLPPEAFDNAEFQQGMKLFLSPNGKAVRFVISHESDPASTEGIDRIEAIRAATKDAIKATPLQGAKIYIGGTAATYQDIRDGTKYDILIVGIAAVCLVFIVMLMITQSLIASLVIVGTVLLSLGTAFGLSVLIWQHFVGLQVHWTIVAMSVIVLLAVGSDYNLLLVSRFKEEVGAGLKTGIIRAMAGTGAVVTSAGLVFAFTMASMAVSELRVIGQVGTTIGLGLLFDTLVVRSFMTPSIAALLGRWFWWPNMIHSRPTVPEAHTRQGARRIQPHLHRG