lpqD Family assigned · medium auto-curated
H37Rv Rv3390 · MTBC0 mtbc0_003602 ·
236 aa · 3830304–3831014 (+) ·
RefSeq NP_217907.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LpqD |
|---|---|
| MTBC0 PGAP re-annotation | histidine phosphatase family protein |
| Revised (this work) | Histidine phosphatase family protein. Pfam: His_Phos_1 (PF00300.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O50416
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable conserved lipoprotein LpqD |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | lpqD |
| eggNOG description | phosphoglycerate mutase |
| Orthologous group | COG0406 |
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 | 0.487 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
His_Phos_1 | PF00300.28 | 1.7e-20 | 37–219 | Histidine phosphatase superfamily (branch 1) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: acrA1 (acyl-CoA-reductase AcrA), medium confidence from genomic context alone (score 681 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3391 acrA1 |
acyl-CoA-reductase AcrA | 681 | 681 ctx | neighborhood:672 |
Rv3389c htdY |
3-hydroxyacyl-thioester dehydratase HtdY | 634 | 635 ctx | neighborhood:632 |
Rv2066 cobIJ |
bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase | 541 | 520 | coexpression:459 |
Rv1244 lpqZ |
lipoprotein LpqZ | 516 | 517 ctx | cooccurence:516 |
Rv0365c hyp |
hypothetical protein | 469 | 469 ctx | cooccurence:469 |
Rv0255c cobQ1 |
cobyric acid synthase | 457 | 432 | coexpression:413 |
Rv3256c hyp |
hypothetical protein | 401 | 402 | |
Rv0358 hyp |
hypothetical protein | 720 | 232 | textmining:651 |
Rv0357c purA |
adenylosuccinate synthetase | 685 | 153 | textmining:644 |
Rv3061c fadE22 |
acyl-CoA dehydrogenase FadE22 | 684 | 145 | textmining:646 |
Rv0215c fadE3 |
Rv0215c, (MTCY08D5.10c), len: 357 aa. Probable fadE3, acyl- dehydrogenase, similar to many e.g. ACDB_BACSU|P45857 acyl-CoA dehydrogenase fro | 569 | 141 | textmining:519 |
Rv3564 fadE33 |
acyl-CoA dehydrogenase FadE33 | 442 | 141 | |
Rv1274 lprB |
lipoprotein LprB | 704 | 84 | textmining:691 |
Rv0418 lpqL |
lipoprotein aminopeptidase LpqL | 603 | 83 | textmining:585 |
Rv1275 lprC |
lipoprotein LprC | 596 | 78 | textmining:581 |
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 LpqD
- MTBC0 PGAP product: histidine phosphatase family protein
- Pfam (hmmscan --cut_ga): His_Phos_1 PF00300.28 (E=2e-20)
- (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_217907.1)
- Domains: Pfam-A via hmmscan --cut_ga — His_Phos_1 (PF00300.28)
- 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
COG0406 - Curated reference: UniProt O50416 (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 —
26 functional partner(s); context anchor
acrA1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003602|Rv3390|lpqD MAKRTPVRKACTVLAVLAATLLLGACGGPTQPRSITLTFIRNAQSQANADGIIDTDMPGSGLSADGKAEAQQVAHQVSRRDVDSIYSSPMAADQQTAGPLAGELGKQVEILPGLQAINAGWFNGKPESMANSTYMLAPADWLAGDVHNTIPGSISGTEFNSQFSAAVRKIYDSGHNTPVVFSQGVAIMIWTLMNARNSRDSLLTTHPLPNIGRVVITGNPVTGWRLVEWDGIRNFT