mmpL1 Resolved · high auto-curated
H37Rv Rv0402c · MTBC0 mtbc0_000422 ·
958 aa · 483719–486595 (-) ·
RefSeq NP_214916.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transmembrane transport protein MmpL1 |
|---|---|
| MTBC0 PGAP re-annotation | RND transporter MmpL1 |
| Revised (this work) | RND transporter MmpL1. 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 |
P9WJV9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transport protein MmpL1 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| Preferred name | mmpL1 |
| eggNOG description | conserved transmembrane transport protein |
| Orthologous group | COG0642 |
| KEGG orthology |
K06994
|
| Gene Ontology (9) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | 1.157 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 16 missense, 1 nonsense, 3 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 15.05% of strains (21852) · 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 | 9.2e-121 | 53–381 | MMPL family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mmpS1 (membrane protein MmpS1), high confidence from genomic context alone (score 976 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0403c mmpS1 |
membrane protein MmpS1 | 975 | 976 ctx | neighborhood:881 coexpression:805 |
Rv1598c hyp |
hypothetical protein | 691 | 691 ctx | cooccurence:691 |
Rv1303 hyp |
hypothetical protein | 632 | 632 ctx | cooccurence:632 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 597 | 597 ctx | cooccurence:596 |
Rv0128 |
transmembrane protein | 551 | 551 ctx | cooccurence:550 |
Rv1145 mmpL13a |
transmembrane transport protein | 684 | 537 ctx | cooccurence:534 |
Rv0404 fadD30 |
long-chain-fatty-acid--AMP ligase FadD30 | 528 | 528 | |
Rv2945c lppX |
lipoprotein LppX | 559 | 507 ctx | cooccurence:504 |
Rv0466 hyp |
hypothetical protein | 504 | 505 ctx | cooccurence:503 |
Rv0523c hyp |
hypothetical protein | 489 | 490 ctx | cooccurence:489 |
Rv0283 eccB3 |
ESX-3 secretion system protein EccB3 | 472 | 472 ctx | cooccurence:453 |
Rv0405 pks6 |
membrane bound polyketide synthase | 539 | 470 | |
Rv1278 hyp |
hypothetical protein | 451 | 451 ctx | cooccurence:451 |
Rv0184 hyp |
hypothetical protein | 439 | 440 ctx | cooccurence:439 |
Rv0282 eccA3 |
ESX-3 secretion system protein EccA | 417 | 417 ctx | cooccurence:414 |
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 MmpL1
- MTBC0 PGAP product: RND transporter MmpL1
- Pfam (hmmscan --cut_ga): MMPL PF03176.22 (E=9e-121)
- (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_214916.1)
- 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
COG0642 - Curated reference: UniProt P9WJV9 (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 —
25 functional partner(s); context anchor
mmpS1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000422|Rv0402c|mmpL1 MRSQRLAGHLSAAARTIHALSLPIILFWVALTIVVNVVAPQLQSVARTHSVALGPHDAPSLIAMKRIGKDFQQFDSDTTAMVLLEGQEKLGDEAHRFYDVLVTKLSQDTTHVQHIENFWGDPLTAAGSQSADGKAAYVQLNLTGDQGGSQANESVAAVQRIVDSVPPPPGIKAYVTGPGPLGADRVVYGDRSLHTITGISIAVIAIMLFIAYRSLSAALIMLLTVGLELLAVRGIISTFAVNDLMGLSTFTVNVLVALTIAASTDYIIFLVGRYQEARATGQNREAAYYTMFGGTAHVVLASGLTVAGAMYCLGFTRLPYFNTLASPCAIGLVTVMLASLTLAPAIIAVASRFGLFDPKRATTKRRWRRIGTVVVRWPGPVLAATLLIALIGLLALPKYQTNYNERYYIPSAAPSNIGYLASDRHFPQARMEPEVLMVEADHDLRNPTDMLILDRIAKTVFHTPGIARVQSITRPLGAPIDHSSIPFQLGMQSTMTIENLQNLKDRVADLSTLTDQLQRMIDITQRTQELTRQLTDATHDMNAHTRQMRDNANELRDRIADFDDFWRPLRSFTYWERHCFDIPICWSMRSLLNSMDNVDKLTEDLANLTDDTERMDTTQRQLLAQLDPTIATMQTVKDLAQTLTSAFSGLVTQMEDMTRNATVMGRTFDAANNDDSFYLPPEAFQNPDFQRGLKLFLSPDGTCARFVITHRGDPASAEGISHIDPIMQAADEAVKGTPLQAASIYLAGTSSTYKDIHEGTLYDVMIAVVASLCLIFIIMLGITRSVVASAVIVGTVALSLGSAFGLSVLIWQHILHMPLHWLVLPMAIIVMLAVGSDYNLLLIARFQEEIGAGLKTGMIRAMAGTGRVVTIAGLVFAFTMGSMVASDLRVVGQIGTTIMIGLLFDTLVVRSYMTPALATLLGRWFWWPRRVDRLARQPQVLGPRRTTALSAERAALLQ