lysE Resolved · high auto-curated
H37Rv Rv1986 · MTBC0 mtbc0_002110 ·
199 aa · 2253624–2254223 (+) ·
RefSeq NP_216502.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | amino acid transporter |
|---|---|
| MTBC0 PGAP re-annotation | L-lysine exporter |
| Revised (this work) | L-lysine exporter. Pfam: LysE (PF01810.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK31
SwissProt · reviewed
· Evidence at transcript level
|
|---|---|
| UniProt name | Lysine exporter LysE |
| Curated function | Catalyzes the efflux of L-lysine. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lysE |
| eggNOG description | Lysine exporter protein LysE YggA |
| Orthologous group | COG1279 |
| KEGG orthology |
K06895
|
| Gene Ontology (49) |
GO:0003333, GO:0003674, GO:0005215, GO:0005342, GO:0005575, GO:0005623, GO:0005886, GO:0006810, GO:0006811, GO:0006812, GO:0006820, GO:0006865 +37 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 | 0.389 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 5 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 |
|---|---|---|---|---|
LysE | PF01810.25 | 7.9e-40 | 14–197 | LysE type translocator |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lysG (HTH-type transcriptional regulator), high confidence from genomic context alone (score 905 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1985c lysG |
HTH-type transcriptional regulator | 973 | 905 ctx | neighborhood:595 cooccurence:774 textmining:727 |
Rv3291c lrpA |
transcriptional regulator LrpA | 604 | 193 | textmining:530 |
Rv2658c |
prophage protein | 444 | 55 | textmining:436 |
Rv1404 |
transcriptional regulator | 428 | 50 | textmining:423 |
Rv1979c |
permease | 513 | 48 | textmining:510 |
Rv0755A |
Rv0755A, len: 61 aa. Putative transposase (possibly gene fragment), similar to C-terminal part of Q9EZM2|ISMav2|AF286339_1 putative transpos | 433 | 43 | textmining:432 |
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: amino acid transporter
- MTBC0 PGAP product: L-lysine exporter
- Pfam (hmmscan --cut_ga): LysE PF01810.25 (E=8e-40)
- (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_216502.1)
- Domains: Pfam-A via hmmscan --cut_ga — LysE (PF01810.25)
- 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
COG1279 - Curated reference: UniProt P9WK31 (SwissProt, reviewed; Evidence at transcript 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 —
6 functional partner(s); context anchor
lysG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002110|Rv1986|lysE MNSPLVVGFLACFTLIAAIGAQNAFVLRQGIQREHVLPVVALCTVSDIVLIAAGIAGFGALIGAHPRALNVVKFGGAAFLIGYGLLAARRAWRPVALIPSGATPVRLAEVLVTCAAFTFLNPHVYLDTVVLLGALANEHSDQRWLFGLGAVTASAVWFATLGFGAGRLRGLFTNPGSWRILDGLIAVMMVALGISLTVT