lprB Still unknown · low auto-curated
H37Rv Rv1274 · MTBC0 mtbc0_001364 ·
185 aa · 1433180–1433737 (+) ·
RefSeq NP_215790.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LprB |
|---|---|
| MTBC0 PGAP re-annotation | DUF3558 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF3558. 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 |
P9WK53
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative lipoprotein LprB |
UniProt still lists this protein as Putative lipoprotein LprB; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | lprB |
| eggNOG description | Protein of unknown function (DUF3558) |
| Orthologous group | COG1188 |
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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 |
|---|---|---|---|---|
DUF3558 | PF12079.14 | 7.7e-34 | 21–183 | Protein of unknown function (DUF3558) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lprC (lipoprotein LprC), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1275 lprC |
lipoprotein LprC | 999 | 994 ctx | neighborhood:882 cooccurence:774 coexpression:802 textmining:852 |
Rv2904c rplS |
50S ribosomal protein L19 | 925 | 925 | coexpression:416 experimental:867 |
Rv1643 rplT |
50S ribosomal protein L20 | 871 | 872 | experimental:865 |
Rv3456c rplQ |
50S ribosomal protein L17 | 883 | 870 | experimental:865 |
Rv3443c rplM |
50S ribosomal protein L13 | 869 | 870 | experimental:868 |
Rv0714 rplN |
50S ribosomal protein L14 | 869 | 869 | experimental:868 |
Rv2441c rpmA |
50S ribosomal protein L27 | 869 | 869 | experimental:865 |
Rv2442c rplU |
50S ribosomal protein L21 | 868 | 869 | experimental:865 |
Rv0706 rplV |
50S ribosomal protein L22 | 867 | 868 | experimental:867 |
Rv0719 rplF |
50S ribosomal protein L6 | 866 | 867 | experimental:865 |
Rv0704 rplB |
50S ribosomal protein L2 | 870 | 866 | experimental:865 |
Rv0703 rplW |
50S ribosomal protein L23 | 866 | 866 | experimental:865 |
Rv0701 rplC |
50S ribosomal protein L3 | 866 | 866 | experimental:865 |
Rv1642 rpmI |
50S ribosomal protein L35 | 866 | 866 | experimental:865 |
Rv0715 rplX |
50S ribosomal protein L24 | 866 | 866 | experimental:865 |
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 LprB
- MTBC0 PGAP product: DUF3558 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF3558 PF12079.14 (E=8e-34)
- (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_215790.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF3558 (PF12079.14)
- 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
COG1188 - Curated reference: UniProt P9WK53 (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 —
174 functional partner(s); context anchor
lprC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001364|Rv1274|lprB MRRKVRRLTLAVSALVALFPAVAGCSDSGDNKPGATIPSTPANAEGRHGPFFPQCGGVSDQTVTELTRVTGLVNTAKNSVGCQWLAGGGILGPHFSFSWYRGSPIGRERKTEELSRASVEDINIDGHSGFIAIGNEPSLGDSLCEVGIQFSDDFIEWSVSFSQKPFPPPCDIAKELTRQSIANSK