mmpL6 Resolved · high auto-curated
H37Rv Rv1557 · MTBC0 - ·
397 aa · 1761744–1762937 (+) ·
RefSeq NP_216073.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane transport protein MmpL6 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transmembrane transport protein MmpL6. Pfam: MMPL (PF03176.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WJU9
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable transport protein MmpL6 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | mmpL6 |
| eggNOG description | MMPL family |
| Orthologous group | COG2409 |
| KEGG orthology |
K06994
|
| Gene Ontology (4) |
GO:0008150, GO:0010033, GO:0042221, GO:0050896
|
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 | 2.451 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 7 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 |
|---|---|---|---|---|
MMPL | PF03176.22 | 9.3e-105 | 29–364 | MMPL family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mmpL13a (transmembrane transport protein), medium confidence from genomic context alone (score 690 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1558 hyp |
hypothetical protein | 868 | 868 ctx | neighborhood:867 |
Rv1145 mmpL13a |
transmembrane transport protein | 706 | 690 ctx | cooccurence:687 |
Rv1559 ilvA |
threonine dehydratase IlvA | 680 | 681 ctx | neighborhood:676 |
Rv1556 |
HTH-type transcriptional regulator | 572 | 572 ctx | neighborhood:498 |
Rv1560 vapB11 |
antitoxin VapB11 | 561 | 561 ctx | neighborhood:556 |
Rv1561 vapC11 |
ribonuclease VapC11 | 561 | 561 ctx | neighborhood:556 |
Rv1598c hyp |
hypothetical protein | 460 | 461 ctx | cooccurence:459 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 428 | 429 ctx | cooccurence:427 |
Rv2147c sepF |
cell division protein SepF | 400 | 372 | |
Rv2945c lppX |
lipoprotein LppX | 489 | 323 | |
Rv0202c mmpL11 |
transmembrane transport protein MmpL11 | 446 | 310 | |
Rv1551 plsB1 |
acyltransferase PlsB | 405 | 233 | |
Rv1856c |
oxidoreductase | 430 | 196 | |
Rv0078 |
transcriptional regulator | 810 | 66 | textmining:805 |
Rv1472 echA12 |
enoyl-CoA hydratase EchA12 | 439 | 52 | textmining:433 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): transmembrane transport protein MmpL6
- Pfam (hmmscan --cut_ga): MMPL PF03176.22 (E=9e-105)
- (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_216073.1)
- 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 P9WJU9 (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 —
19 functional partner(s); context anchor
mmpL13a - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1557|mmpL6 MQGISVTGLVKRGWMVRSVFDTIDGIDQLGEQLASVTVTLDKLAAIQPQLVALLPDEIASQQINRELALANYATMSGIYAQTAALIENAAAMGQAFDAAKNDDSFYLPPEAFDNPDFQRGLKLFLSADGKAARMIISHEGDPATPEGISHIDAIKQAAHEAVKGTPMAGAGIYLAGTAATFKDIQDGATYDLLIAGIAALSLILLIMMIITRSLVAALVIVGTVALSLGASFGLSVLVWQHLLGIQLYWIVLALAVILLLAVGSDYNLLLISRFKEEIGAGLNTGIIRAMAGTGGVVTAAGLVFAATMSSFVFSDLRVLGQIGTTIGLGLLFDTLVVRAFMTPSIAVLLGRWFWWPQRVRPRPASRMLRPYGPRPVVRELLLREGNDDPRTQVATHR