lppC Family assigned · medium auto-curated
H37Rv Rv1911c · MTBC0 mtbc0_002026 ·
201 aa · 2175492–2176097 (-) ·
RefSeq NP_216427.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LppC |
|---|---|
| MTBC0 PGAP re-annotation | YbhB/YbcL family Raf kinase inhibitor-like protein |
| Revised (this work) | YbhB/YbcL family Raf kinase inhibitor-like protein. Pfam: PBP (PF01161.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFN3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative lipoprotein LppC |
| Curated function | Probably involved in bacterial recognition and uptake by its host (human). |
UniProt still lists this protein as Putative lipoprotein LppC; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lppC |
| eggNOG description | Phosphatidylethanolamine-binding protein |
| Orthologous group | COG1881 |
| KEGG orthology |
K06910
|
| Gene Ontology (7) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, 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 | 0.566 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 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 |
|---|---|---|---|---|
PBP | PF01161.26 | 1.9e-31 | 69–199 | Phosphatidylethanolamine-binding protein |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0708 rplP |
50S ribosomal protein L16 | 866 | 861 | experimental:784 |
Rv0704 rplB |
50S ribosomal protein L2 | 840 | 834 | experimental:779 |
Rv2890c rpsB |
30S ribosomal protein S2 | 832 | 832 | experimental:783 |
Rv3443c rplM |
50S ribosomal protein L13 | 828 | 822 | experimental:783 |
Rv0721 rpsE |
30S ribosomal protein S5 | 818 | 819 | experimental:783 |
Rv2785c rpsO |
30S ribosomal protein S15 | 818 | 818 | experimental:783 |
Rv3461c rpmJ |
50S ribosomal protein L36 | 823 | 817 | experimental:785 |
Rv0979A rpmF |
50S ribosomal protein L32 | 815 | 816 | experimental:786 |
Rv2441c rpmA |
50S ribosomal protein L27 | 823 | 815 | experimental:787 |
Rv2904c rplS |
50S ribosomal protein L19 | 820 | 809 | experimental:787 |
Rv2909c rpsP |
30S ribosomal protein S16 | 808 | 806 | experimental:785 |
Rv3442c rpsI |
30S ribosomal protein S9 | 805 | 806 | experimental:785 |
Rv3456c rplQ |
50S ribosomal protein L17 | 811 | 805 | experimental:785 |
Rv0723 rplO |
50S ribosomal protein L15 | 804 | 804 | experimental:787 |
Rv0701 rplC |
50S ribosomal protein L3 | 802 | 803 | experimental:785 |
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 LppC
- MTBC0 PGAP product: YbhB/YbcL family Raf kinase inhibitor-like protein
- Pfam (hmmscan --cut_ga): PBP PF01161.26 (E=2e-31)
- (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_216427.1)
- Domains: Pfam-A via hmmscan --cut_ga — PBP (PF01161.26)
- 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
COG1881 - Curated reference: UniProt P9WFN3 (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 — 105 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002026|Rv1911c|lppC MTSTLHRTPLATAGLALVVALGGCGGGGGDSRETPPYVPKATTVDATTPAPAAEPLTIASPMFADGAPIPVQFSCKGANVAPPLTWSSPAGAAELALVVDDPDAVGGLYVHWIVTGIAPGSGSTADGQTPAGGHSVPNSGGRQGYFGPCPPAGTGTHHYRFTLYHLPVALQLPPGATGVQAAQAIAQAASGQARLVGTFEG