lpqO Still unknown · low auto-curated
H37Rv Rv0604 · MTBC0 mtbc0_000634 ·
316 aa · 703791–704741 (+) ·
RefSeq NP_215118.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqO |
|---|---|
| MTBC0 PGAP re-annotation | DUF1259 domain-containing protein |
| Revised (this work) | Conserved hypothetical protein; DUF domain(s) DUF1529. 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 |
I6X9E2
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved lipoprotein LpqO |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | lpqO |
| eggNOG description | Domain of Unknown Function (DUF1259) |
| Orthologous group | COG1388 |
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 | 0.711 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
DUF1529 | PF07485.17 | 4.8e-46 | 194–311 | Domain of Unknown Function (DUF1259) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: tcrA (two component DNA binding transcriptional regulator TcrA), medium confidence from genomic context alone (score 562 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0603 hyp |
hypothetical protein | 879 | 879 ctx | neighborhood:568 coexpression:731 |
Rv1167c |
transcriptional regulator | 793 | 793 | coexpression:793 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 778 | 778 | coexpression:746 |
Rv1190 hyp |
hypothetical protein | 770 | 770 | coexpression:770 |
Rv1267c embR |
transcriptional regulator EmbR | 767 | 767 | coexpression:767 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 767 | 767 | coexpression:716 |
Rv1931c |
transcriptional regulator | 745 | 745 | coexpression:740 |
Rv1151c cobB |
NAD-dependent protein deacylase | 734 | 734 | coexpression:734 |
Rv0452 |
transcriptional regulator | 733 | 733 | coexpression:733 |
Rv3167c |
TetR family transcriptional regulator | 732 | 732 | coexpression:732 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 731 | 731 | coexpression:730 |
Rv0494 |
HTH-type transcriptional regulator | 730 | 730 | coexpression:730 |
Rv1556 |
HTH-type transcriptional regulator | 651 | 651 | coexpression:651 |
Rv0602c tcrA |
two component DNA binding transcriptional regulator TcrA | 562 | 562 ctx | neighborhood:423 |
Rv0601c |
two component sensor kinase HK2 | 478 | 478 |
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 LpqO
- MTBC0 PGAP product: DUF1259 domain-containing protein
- Pfam (hmmscan --cut_ga): DUF1529 PF07485.17 (E=5e-46)
- (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_215118.1)
- Domains: Pfam-A via hmmscan --cut_ga — DUF1529 (PF07485.17)
- 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
COG1388 - Curated reference: UniProt I6X9E2 (TrEMBL, unreviewed; 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 —
27 functional partner(s); context anchor
tcrA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000634|Rv0604|lpqO MIRRRGARMAALLAAAALALTACAGSDDKGEPDDGGDRGASLATTSDADWKPVADILGRTGKLNDGSVYKIGFARSDLSVQTKGVTVAPALSLGSWVAFARTPDGQTMLMGDLVVTEDELASVTDAVQAGGLQQTALHKHLLEQSPPIWWTHIAGHGDAADLARAVRSALDATDTPPPAPATSGQTSLDLDTAAIDEALGRSGTIAGGVYKFFIARRDPVTMSGMLIPPSMGLATALNFQPTGNGRAAINGDFVMTAAEVQDVVQALRGGGIDIVAIHNHGFDEQPRLFYMHFWAENDAVALARTLRAAVDATAAR