lpqW Resolved · high auto-curated
H37Rv Rv1166 · MTBC0 mtbc0_001255 ·
635 aa · 1304593–1306500 (+) ·
RefSeq NP_215682.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | monoacyl phosphatidylinositol tetramannoside-binding protein LpqW |
|---|---|
| MTBC0 PGAP re-annotation | lipoarabinomannan biosynthesis protein LpqW |
| Revised (this work) | Lipoarabinomannan biosynthesis protein LpqW. Pfam: SBP_bac_5 (PF00496.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGU7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable monoacyl phosphatidylinositol tetramannoside-binding protein LpqW |
| Curated function | May directly or indirectly regulate the accessibility of the key branch point intermediate, monoacyl phosphatidylinositol tetramannoside (AcPIM4), to the elongating alpha-1,6 mannosyltransferases which could regulate the lipoarabinomannans (LAMs) biosynthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | lpqW |
| eggNOG description | Monoacyl phosphatidylinositol tetramannoside-binding protein |
| Orthologous group | COG0747 |
| Gene Ontology (28) |
GO:0005575, GO:0005576, GO:0005623, GO:0006629, GO:0006643, GO:0006664, GO:0008150, GO:0008152, GO:0008610, GO:0009058, GO:0009247, GO:0009987 +16 more
|
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 | 0.362 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 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 |
|---|---|---|---|---|
SBP_bac_5 | PF00496.28 | 2.6e-31 | 119–485 | Bacterial extracellular solute-binding proteins, family 5 Middle |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: typA (GTP-binding translation elongation factor), high confidence from genomic context alone (score 901 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1165 typA |
GTP-binding translation elongation factor | 900 | 901 ctx | neighborhood:773 coexpression:580 |
Rv1632c hyp |
hypothetical protein | 778 | 778 ctx | cooccurence:721 |
Rv3850 hyp |
hypothetical protein | 769 | 769 ctx | cooccurence:767 |
Rv0556 |
transmembrane protein | 768 | 768 ctx | cooccurence:767 |
Rv3438 hyp |
hypothetical protein | 767 | 768 ctx | cooccurence:767 |
Rv3212 hyp |
hypothetical protein | 775 | 767 ctx | cooccurence:764 |
Rv2732c |
transmembrane protein | 767 | 767 ctx | cooccurence:765 |
Rv1164 narI |
nitrate reductase subunit gamma | 767 | 767 ctx | neighborhood:755 |
Rv1163 narJ |
nitrate reductase subunit delta | 766 | 766 ctx | neighborhood:755 |
Rv1109c hyp |
hypothetical protein | 765 | 766 ctx | cooccurence:765 |
Rv0383c ttfA hyp |
hypothetical protein | 763 | 763 ctx | cooccurence:759 |
Rv2446c |
integral membrane protein | 756 | 757 ctx | cooccurence:755 |
Rv0817c lmeA hyp |
hypothetical protein | 751 | 751 ctx | cooccurence:751 |
Rv0358 hyp |
hypothetical protein | 748 | 748 ctx | cooccurence:744 |
Rv0996 |
transmembrane protein | 748 | 748 ctx | cooccurence:747 |
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: monoacyl phosphatidylinositol tetramannoside-binding protein LpqW
- MTBC0 PGAP product: lipoarabinomannan biosynthesis protein LpqW
- Pfam (hmmscan --cut_ga): SBP_bac_5 PF00496.28 (E=3e-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_215682.1)
- Domains: Pfam-A via hmmscan --cut_ga — SBP_bac_5 (PF00496.28)
- 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
COG0747 - Curated reference: UniProt P9WGU7 (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 —
136 functional partner(s); context anchor
typA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001255|Rv1166|lpqW MGVPSPVRRVCVTVGALVALACMVLAGCTVSPPPAPQSTDTPRSTPPPPRRPTQIIMGIDWIGPGFNPHLLSDLSPVNAAISALVLPSAFRPIPDPNTPTGSRWEMDPTLLVSADVTNNHPFTVTYKIRPEAQWTDNAPIAADDFWYLWQQMVTQPGVVDPAGYHLITSVQSLEGGKQAVVTFAQPYPAWRELFTDILPAHIVKDIPGGFASGLARALPVTGGQFRVENIDPQRDEILIARNDRYWGPPSKPGIILFRRAGAPAALADSVRNGDTQVAQVHGGSAAFAQLSAIPDVRTARIVTPRVMQFTLRANVPKLADTQVRKAILGLLDVDLLAAVGAGTDNTVTLDQAQIRSPSDPGYVPTAPPAMSSAAALGLLEASGFQVDTNTSVSPAPSVPDSTTTSVSTGPPEVIRGRISKDGEQLTLVIGVAANDPTSVAVANTAADQLRDVGIAATVLALDPVTLYHDALNDNRVDAIVGWRQAGGNLATLLASRYGCPALQATTVPAANAPTTAPSAPIGPTPSAAPDTATPPPTAPRRPSDPGALVKAPSNLTGICDRSIQSNIDAALNGTKNINDVITAVEPRLWNMSTVLPILQDTTIVAAGPSVQNVSLSGAVPVGIVGDAGQWVKTGQ