lppO Resolved · high auto-curated
H37Rv Rv2290 · MTBC0 mtbc0_002431 ·
171 aa · 2587346–2587861 (+) ·
RefSeq NP_216806.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LppO |
|---|---|
| MTBC0 PGAP re-annotation | lipoprotein LpqH |
| Revised (this work) | Lipoprotein LpqH. Pfam: Myco_19_kDa (PF05481.18). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK71
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative lipoprotein LppO |
UniProt still lists this protein as Putative lipoprotein LppO; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lppO |
| eggNOG description | Mycobacterium 19 kDa lipoprotein antigen |
| Orthologous group | 29KF0 |
| Gene Ontology (2) |
GO:0005575, GO:0005576
|
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) pseudogene candidate
| pN/pS | 0.627 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 9.92% of strains (14405) · 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 |
|---|---|---|---|---|
Myco_19_kDa | PF05481.18 | 7.3e-13 | 44–170 | Mycobacterium 19 kDa lipoprotein antigen |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: sseB (thiosulfate sulfurtransferase SseB), medium confidence from genomic context alone (score 649 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2291 sseB |
thiosulfate sulfurtransferase SseB | 945 | 649 ctx | neighborhood:644 textmining:852 |
Rv2288 hyp |
hypothetical protein | 512 | 512 ctx | neighborhood:487 |
Rv2289 cdh |
CDP-diacylglycerol pyrophosphatase | 510 | 511 ctx | neighborhood:487 |
Rv2287 yjcE |
Na(+)/H(+) transporter | 502 | 502 ctx | neighborhood:499 |
Rv3669 |
transmembrane protein | 807 | 65 | textmining:803 |
Rv1352 hyp |
hypothetical protein | 634 | 55 | textmining:629 |
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL | 522 | 54 | textmining:516 |
Rv2339 mmpL9 |
transmembrane transport protein MmpL9 | 579 | 53 | textmining:574 |
Rv3469c mhpE |
4-hydroxy-2-oxovalerate aldolase MhpE | 907 | 52 | textmining:907 |
Rv1810 hyp |
hypothetical protein | 805 | 51 | textmining:803 |
Rv1573 |
phage protein | 523 | 51 | textmining:518 |
Rv3634c galE1 |
UDP-glucose 4-epimerase | 655 | 50 | textmining:652 |
Rv3467 hyp |
hypothetical protein | 811 | 47 | textmining:810 |
Rv3470c ilvB2 |
acetolactate synthase large subunit | 653 | 47 | textmining:651 |
Rv1275 lprC |
lipoprotein LprC | 581 | 47 | textmining:579 |
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 LppO
- MTBC0 PGAP product: lipoprotein LpqH
- Pfam (hmmscan --cut_ga): Myco_19_kDa PF05481.18 (E=7e-13)
- (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_216806.1)
- Domains: Pfam-A via hmmscan --cut_ga — Myco_19_kDa (PF05481.18)
- 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
29KF0 - Curated reference: UniProt P9WK71 (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 —
29 functional partner(s); context anchor
sseB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002431|Rv2290|lppO MTDPRHTVRIAVGATALGVSALGATLPACSAHSGPGSPPSAPSAPAAATVMVEGHTHTISGAVECRTSPAVRTATPSESGTQTTRVNAHDDSASVTLSLSDSTPPDVNGFGISLKIGSVDYQMPYQPVQSPTQVEATRQGKSYTLTGTGHAVIPGQTGMRELPFGVHVTCP