lppY Still unknown · low auto-curated
H37Rv Rv2999 · MTBC0 mtbc0_003188 ·
321 aa · 3378911–3379876 (+) ·
RefSeq NP_217515.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LppY |
|---|---|
| MTBC0 PGAP re-annotation | DUF1259 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF1529. Function unknown. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53246
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved lipoprotein LppY |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | lpqO |
| eggNOG description | Domain of Unknown Function (DUF1259) |
| Orthologous group | COG1388 |
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 | 0.688 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (159) · clonal |
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 |
|---|---|---|---|---|
DUF1529 | PF07485.17 | 1.0e-41 | 53–174 | Domain of Unknown Function (DUF1259) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3000 (transmembrane protein), medium confidence from genomic context alone (score 681 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3000 |
transmembrane protein | 681 | 681 ctx | neighborhood:634 |
Rv2998A |
Rv2998A, len: 67 aa. Probable conserved hypothetical protein, (possibly gene fragment), highly similar to central part of two-component sens | 518 | 518 ctx | neighborhood:518 |
Rv2954c hyp |
hypothetical protein | 466 | 466 ctx | cooccurence:466 |
Rv2275 |
cyclo(L-tyrosyl-L-tyrosyl) synthase | 426 | 427 ctx | cooccurence:423 |
Rv3727 |
oxidoreductase | 402 | 402 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
- Legacy H37Rv annotation: lipoprotein LppY
- MTBC0 PGAP product: DUF1259 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF1529 PF07485.17 (E=1e-41)
- (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_217515.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF1529 (PF07485.17)
- 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
COG1388 - Curated reference: UniProt O53246 (TrEMBL, unreviewed; 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 —
5 functional partner(s); context anchor
Rv3000 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003188|Rv2999|lppY MAGAKHAGRIVAITTAAAVILAACSSGSKGGAGSGHAGKARSAVTTTDADWKPVADALGRSGKLGDNNTAYRINLPRNDLHITSYGVDIKPGLSLGGYAAFARYDNNETLLMGDLVITEEELPKVTDALQAHGIAQTALHKHLLQQDPPVWWTHIHGMGDAARLAQGLKAALDATTIGPPTPPPARQPPVDIDVAGVDQALGRKGTQDGGLLKYSIPRKDTIIEDGHVLPAVSLNLTTVINFQPVGRGRAAINGDFILIAPEVQEVIRAMRAGNITIVELHNHGLTEEPRLFYMHYWAVDDAVTLARALRPAMDATNLQSS