lprD Still unknown · low auto-curated
H37Rv Rv1343c · MTBC0 mtbc0_001440 ·
126 aa · 1519245–1519625 (-) ·
RefSeq NP_215859.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | lipoprotein LprD |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Conserved hypothetical protein; no recognised domain. 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 |
P9WK51
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Putative lipoprotein LprD |
UniProt still lists this protein as Putative lipoprotein LprD; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
V Defense mechanisms
|
|---|---|
| Preferred name | lprD |
| eggNOG description | Glucitol operon activator |
| Orthologous group | COG1566 |
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 | 1.993 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2446c (integral membrane protein), high confidence from genomic context alone (score 746 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1342c hyp |
hypothetical protein | 888 | 888 ctx | neighborhood:882 |
Rv3850 hyp |
hypothetical protein | 753 | 753 ctx | cooccurence:696 |
Rv2446c |
integral membrane protein | 746 | 746 ctx | cooccurence:746 |
Rv0049 hyp |
hypothetical protein | 734 | 735 ctx | cooccurence:731 |
Rv0358 hyp |
hypothetical protein | 733 | 734 ctx | cooccurence:733 |
Rv1209 hyp |
hypothetical protein | 721 | 721 ctx | cooccurence:710 |
Rv0556 |
transmembrane protein | 719 | 719 ctx | cooccurence:719 |
Rv3205c hyp |
hypothetical protein | 712 | 712 ctx | cooccurence:711 |
Rv3438 hyp |
hypothetical protein | 704 | 704 ctx | cooccurence:701 |
Rv2732c |
transmembrane protein | 693 | 694 ctx | cooccurence:693 |
Rv3605c hyp |
hypothetical protein | 689 | 689 ctx | cooccurence:689 |
Rv1632c hyp |
hypothetical protein | 684 | 684 ctx | cooccurence:683 |
Rv1332 |
transcriptional regulator | 678 | 678 ctx | cooccurence:678 |
Rv0863 hyp |
hypothetical protein | 673 | 673 ctx | cooccurence:672 |
Rv3256c hyp |
hypothetical protein | 671 | 671 ctx | cooccurence:671 |
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 LprD
- MTBC0 PGAP product: hypothetical protein
- (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_215859.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG1566 - Curated reference: UniProt P9WK51 (SwissProt, reviewed; Inferred from homology)
- 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 —
108 functional partner(s); context anchor
Rv2446c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001440|Rv1343c|lprD MSTTRRRRPALIALVIIATCGCLALGWWQWTRFQSTSGTFQNLGYALQWPLFAWFCVYAYRNFVRYEETPPQPPTGGAAAEIPAGLLPERPKPAQQPPDDPVLREYNAYLAELAKDDARKQNRTTA