mmpL12 Resolved · high auto-curated
H37Rv Rv1522c · MTBC0 mtbc0_001629 ·
1146 aa · 1723981–1727421 (-) ·
RefSeq NP_216038.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane transport protein MmpL12 |
|---|---|
| MTBC0 PGAP re-annotation | RND transporter MmpL12 |
| Revised (this work) | RND transporter MmpL12. 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 |
P9WJT7
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Probable transport protein MmpL12 |
| Curated function | May be involved in glycolipid transport. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | mmpL8 |
| eggNOG description | transport protein |
| Orthologous group | COG1033 |
| KEGG orthology |
K06994
|
| Gene Ontology (26) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0008150, GO:0009605, GO:0009607, GO:0030312, GO:0043207, GO:0044403 +14 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 | 0.821 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 18 missense, 1 nonsense, 3 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 11.95% of strains (17354) · 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 | 9.4e-106 | 57–383 | MMPL family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1523 (methyltransferase), medium confidence from genomic context alone (score 575 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1523 |
methyltransferase | 833 | 575 ctx | neighborhood:567 textmining:624 |
Rv1598c hyp |
hypothetical protein | 514 | 515 ctx | cooccurence:512 |
Rv1524 |
glycosyltransferase | 526 | 509 ctx | neighborhood:497 |
Rv1145 mmpL13a |
transmembrane transport protein | 503 | 485 ctx | cooccurence:483 |
Rv1303 hyp |
hypothetical protein | 441 | 442 ctx | cooccurence:440 |
Rv1525 wbbL2 |
rhamnosyl transferase WbbL | 661 | 422 ctx | neighborhood:411 textmining:438 |
Rv3824c papA1 |
acyltransferase | 483 | 312 | |
Rv3820c papA2 |
trehalose-2-sulfate acyltransferase | 465 | 298 | |
Rv1182 papA3 |
acyltransferase papA3 | 490 | 294 | |
Rv1527c pks5 |
polyketide synthase | 448 | 196 | |
Rv1518 hyp |
hypothetical protein | 650 | 108 | textmining:624 |
Rv1505c hyp |
hypothetical protein | 550 | 67 | textmining:538 |
Rv3322c |
methyltransferase | 804 | 47 | textmining:803 |
Rv2813 hyp |
hypothetical protein | 441 | 42 | textmining:441 |
Rv1895 |
zinc-binding alcohol dehydrogenase | 803 | 41 | textmining:803 |
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 MmpL12
- MTBC0 PGAP product: RND transporter MmpL12
- Pfam (hmmscan --cut_ga): MMPL PF03176.22 (E=9e-106)
- (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_216038.1)
- 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
COG1033 - Curated reference: UniProt P9WJT7 (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 —
18 functional partner(s); context anchor
Rv1523 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001629|Rv1522c|mmpL12 MARHDEAKAGGLFDRIGNFVVRWPLIVIGCWIAVAAALTLLLPTLQAQAAKREQAPLPPGAPSMVLQKEMSAAFQEKIETSALLLVLLTNENGLGPADEAVYRKLIENLRADTQDKISVQDFLAVPEMKELLASKDNKAWNLPITFAGDAASPETQAAFKRVAAIVKQTVAGTSLTVHLSGPIATVADLTELGEKDVRIIEIGTAVSVLIILILVYRNLVTMLVPLATIGASVVTAQGTLSGLAEFGLAVNMQAIVFMSAVMIGAGTDYAVFLISRYHDYVRHGEKSDMAVKKALMSIGKVITASAATVAVTFLAMVFTKLEVFSAVGPAIAVAITVSLLGAVTLLPAILTLTGRRGWIKPRRDLTSRMWRRSGVRIVRRPTIHLVGSLIVLVALAGCTLLIRFNYDDLKTVPQHVESVKGYEAMNRHFPMNAMTPMVLFIKSPRDLRTPGALADIEMMSREIAELPNIVMVRGLTRPNGEPLKETKVSFQAGEVGGKLDEATTLLEEHGGELDQLTGGAHQLADALAQIRNEINGAVASSSGIVNTLQAMMDLMGGDKTIRQLENASQYVGRMRALGDNLSGTVTDAEQIATWASPMVNALNSSPVCNSDPACRTSRAQLAAIVQAQDDGLLRSIRALAVTLQQTQEYQTLARTVSTLDGQLKQVVSTLKAVDGLPTKLAQMQQGANALADGSAALAAGVQELVDQVKKMGSGLNEAADFLLGIKRDADKPSMAGFNIPPQIFSRDEFKKGAQIFLSADGHAARYFVQSALNPATTEAMDQVNDILRVADSARPNTELEDATIGLAGVPTALRDIRDYYNSDMKFIVIATIVIVFLILVILLRALVAPIYLIGSVLISYLSALGIGTLVFQLILGQEMHWSLPGLSFILLVAIGADYNMLLISRIRDESPHGIRIGVIRTVGSTGGVITSAGLIFAASMFGLVGASINTMAQAGFTIGIGIVLDTFLVRTVTVPALTTMIGRANWWPSELGRDPSTPPTKADRWLRRVKGHRRKAPIPAPKPPHTKVVRNTNGHASKAATKSVPNGKPADLAEGNGEYLIDHLRRHSLPLFGYAAMPAYDVVDGVSKPNGDGAHIGKEPVDHLLGHSLPLFGLAGLPSYDRWDDTSIGEPAVGHAGSKPDAKLST