lpqE Family assigned · medium auto-curated
H37Rv Rv3584 · MTBC0 mtbc0_003803 ·
182 aa · 4049507–4050055 (+) ·
RefSeq NP_218101.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqE |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains LpqE-like (PF04314.19) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK63
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative lipoprotein LpqE |
UniProt still lists this protein as Putative lipoprotein LpqE; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lpqE |
| eggNOG description | Copper chaperone PCu(A)C |
| Orthologous group | COG2847 |
| Gene Ontology (9) |
GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886, GO:0016020, 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 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 |
|---|---|---|---|---|
LpqE-like | PF04314.19 | 6.2e-26 | 56–173 | Putative lipoprotein LpqE-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2876 (transmembrane protein), high confidence from genomic context alone (score 955 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2876 |
transmembrane protein | 954 | 955 ctx | cooccurence:541 experimental:902 |
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 924 | 924 | experimental:902 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 960 | 921 | experimental:902 textmining:518 |
Rv2200c ctaC |
cytochrome C oxidase subunit II | 919 | 919 | experimental:902 |
Rv2194 qcrC |
ubiquinol-cytochrome C reductase cytochrome subunit C | 962 | 913 | experimental:902 textmining:592 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 944 | 907 | experimental:902 textmining:428 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 898 | 895 | experimental:889 |
Rv2193 ctaE |
cytochrome C oxidase subunit III | 872 | 872 | experimental:855 |
Rv0432 sodC |
superoxide dismutase | 823 | 824 | experimental:790 |
Rv3586 disA |
DNA integrity scanning protein DisA | 809 | 797 ctx | neighborhood:796 |
Rv3850 hyp |
hypothetical protein | 732 | 733 ctx | cooccurence:729 |
Rv1546 hyp |
hypothetical protein | 731 | 731 ctx | cooccurence:730 |
Rv0513 |
transmembrane protein | 719 | 719 ctx | cooccurence:715 |
Rv0996 |
transmembrane protein | 718 | 718 ctx | cooccurence:717 |
Rv0910 |
toxin | 709 | 710 ctx | cooccurence:707 |
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 LpqE
- MTBC0 PGAP product: hypothetical protein
- Pfam (hmmscan --cut_ga): LpqE-like PF04314.19 (E=6e-26)
- (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_218101.1)
- Domains: Pfam-A via hmmscan --cut_ga — LpqE-like (PF04314.19)
- 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
COG2847 - Curated reference: UniProt P9WK63 (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 —
110 functional partner(s); context anchor
Rv2876 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003803|Rv3584|lpqE MNRCNIRLRLAGMTTWVASIALLAAALSGCGAGQISQTANQKPAVNGNRLTINNVLLRDIRIQAVQTSDFIQPGKAVDLVLVAVNQSPDVSDRLVGITSDIGSVTVAGDARLPASGMLFVGTPDGQIVAPGPLPSNQAAKATVNLTKPIANGLTYNFTFKFEKAGQGSVMVPISAGLATPHE