lpqG Family assigned · medium auto-curated
H37Rv Rv3623 · MTBC0 mtbc0_003840 ·
240 aa · 4086231–4086953 (+) ·
RefSeq NP_218140.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqG |
|---|---|
| MTBC0 PGAP re-annotation | SIMPL domain-containing protein |
| Revised (this work) | SIMPL domain-containing protein. Pfam: SIMPL (PF04402.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X7X3
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved lipoprotein LpqG |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | lpqG |
| eggNOG description | Protein of unknown function (DUF541) |
| Orthologous group | COG2968 |
| KEGG orthology |
K09807
|
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 | 0.489 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
SIMPL | PF04402.20 | 7.4e-49 | 38–237 | Protein of unknown function (DUF541) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pheT (phenylalanine--tRNA ligase subunit beta), medium confidence from genomic context alone (score 505 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 504 | 505 ctx | neighborhood:500 |
Rv0995 rimJ |
ribosomal-protein-alanine acetyltransferase RimJ | 411 | 411 | |
Rv3422c tsaE |
tRNA threonylcarbamoyladenosine biosynthesis protein | 410 | 411 ctx | cooccurence:409 |
Rv3619c esxV |
ESAT-6 like protein EsxV | 504 | 291 | |
Rv3629c |
integral membrane protein | 512 | 167 | textmining:439 |
Rv1539 lspA |
lipoprotein signal peptidase | 521 | 112 | textmining:483 |
Rv3759c proX |
glycine betaine/carnitine/choline/L-proline ABC transporter substrate-binding lipoprotein ProX | 481 | 112 | textmining:440 |
Rv1252c lprE |
lipoprotein LprE | 419 | 87 | |
Rv2585c |
lipoprotein | 716 | 76 | textmining:705 |
Rv1899c lppD |
lipoprotein LppD | 529 | 75 | textmining:512 |
Rv3859c gltB |
glutamate synthase large subunit | 443 | 70 | textmining:426 |
Rv0411c glnH |
glutamine-binding lipoprotein GlnH | 422 | 64 | textmining:408 |
Rv2563 |
glutamine ABC transporter permease | 520 | 59 | textmining:511 |
Rv3390 lpqD |
lipoprotein LpqD | 581 | 54 | textmining:575 |
Rv0483 lprQ |
lipoprotein LprQ | 456 | 52 | textmining:450 |
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 LpqG
- MTBC0 PGAP product: SIMPL domain-containing protein
- Pfam (hmmscan --cut_ga): SIMPL PF04402.20 (E=7e-49)
- (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_218140.1)
- Domains: Pfam-A via hmmscan --cut_ga — SIMPL (PF04402.20)
- 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
COG2968 - Curated reference: UniProt I6X7X3 (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 —
29 functional partner(s); context anchor
pheT - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003840|Rv3623|lpqG MIRLVRHSIALVAAGLAAALSGCDSHNSGSLGADPRQVTVFGSGQVQGVPDTLIADVGIQVTAADVTSAMNQTNDRQQAVIDALVGAGLDRKDIRTTRVTVAPQYSNPEPAGTATITGYRADNDIEVKIHPTDAASRLLALVVSTGGDATRISSVSYSIGDDSQLVKDARARAFQDAKNRADQYAQLSGLRLGKVISISEASGAAPTHEAPAPPRGLSAVPLEPGQQTVGFSVTVVWELT