Rv1401 Family assigned · medium auto-curated
H37Rv Rv1401 · MTBC0 - ·
200 aa · 1576930–1577532 (+) ·
RefSeq NP_215917.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Membrane protein. Pfam: YhhN (PF07947.20). |
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 |
P9WG51
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Lysoplasmalogenase |
| EC (curated) |
EC 3.3.2.2
|
| Curated function | Specifically hydrolyzes the vinyl ether bond of lysoplasmenylcholine (pLPC) and lysoplasmenylethanolamine (pLPE) to release a fatty aldehyde and glycerophospho-choline or glycerophospho-ethanolamine. The cleavage activity is specific for lysoplasmalogen substrates, and there is no activity on 1-alkenyl-sn-2-acyl-glycerophospho-ethanolamine or 1-alkenyl-sn-2-acyl-glycerophospho-choline (plasmalogen) substrates. Confers a growth advantage for mycobacteria in host macrophages, possibly by cleaving toxic host pLPC into potentially energy-producing products. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | membrane |
| Orthologous group | COG3714 |
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 | 0.482 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 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 |
|---|---|---|---|---|
YhhN | PF07947.20 | 1.2e-49 | 3–183 | YhhN family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: priA (primosomal protein N'), high confidence from genomic context alone (score 795 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1402 priA |
primosomal protein N' | 795 | 795 ctx | neighborhood:784 |
Rv1400c lipI |
lipase | 718 | 718 ctx | neighborhood:711 |
Rv2721c hyp |
hypothetical protein | 660 | 660 ctx | cooccurence:655 |
Rv1399c nlhH |
carboxylesterase NlhH | 630 | 630 ctx | neighborhood:626 |
Rv2015c hyp |
hypothetical protein | 617 | 617 ctx | cooccurence:615 |
Rv1765c hyp |
hypothetical protein | 570 | 571 ctx | cooccurence:568 |
Rv1393c |
monoxygenase | 534 | 534 ctx | neighborhood:462 |
Rv3810 pirG |
cell surface protein | 497 | 497 ctx | cooccurence:493 |
Rv3577 hyp |
hypothetical protein | 457 | 457 ctx | cooccurence:454 |
Rv0176 |
Mce associated transmembrane protein | 449 | 449 ctx | cooccurence:446 |
Rv2434c |
transmembrane protein | 439 | 440 ctx | cooccurence:435 |
Rv1874 hyp |
hypothetical protein | 433 | 434 ctx | cooccurence:432 |
Rv0139 |
oxidoreductase | 405 | 406 ctx | cooccurence:400 |
Rv0632c echA3 |
enoyl-CoA hydratase EchA3 | 403 | 403 ctx | cooccurence:402 |
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): membrane protein
- Pfam (hmmscan --cut_ga): YhhN PF07947.20 (E=1e-49)
- (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_215917.1)
- Domains: Pfam-A via hmmscan --cut_ga — YhhN (PF07947.20)
- 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
COG3714 - Curated reference: UniProt P9WG51 (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 —
14 functional partner(s); context anchor
priA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1401| MLQPAFKASMAVLLAAAAVAHPIGRERRWLVPALLLSATGDWLLAIPWWTWAFVFGLGAFLLAHLCFIGALLPLARQAAPSRGRVAAVVAMCVASAGLLVWFWPHLGKDNLTIPVTVYIVALSAMVCTALLARLPTIWTAVGAVCFAASDSMIGIGRFILGNEALAVPIWWSYAAAEILITAGFFFGREVPDNAAAPTDS