lgt Resolved · high auto-curated
H37Rv Rv1614 · MTBC0 mtbc0_001720 ·
468 aa · 1825135–1826541 (+) ·
RefSeq NP_216130.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | prolipoprotein diacylglyceryl transferase |
|---|---|
| MTBC0 PGAP re-annotation | prolipoprotein diacylglyceryl transferase |
| Revised (this work) | Prolipoprotein diacylglyceryl transferase. Pfam: LGT (PF01790.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WK93
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphatidylglycerol--prolipoprotein diacylglyceryl transferase |
| EC (curated) |
EC 2.5.1.145
|
| Curated function | Catalyzes the transfer of the diacylglyceryl group from phosphatidylglycerol to the sulfhydryl group of the N-terminal cysteine of a prolipoprotein, the first step in the formation of mature lipoproteins. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | lgt |
| eggNOG description | Transfers the N-acyl diglyceride group on what will become the N-terminal cysteine of membrane lipoproteins |
| Orthologous group | COG0682 |
| Gene Ontology (14) |
GO:0005575, GO:0005623, GO:0005886, GO:0005887, GO:0008150, GO:0016020, GO:0016021, GO:0031224, GO:0031226, GO:0040007, GO:0044425, GO:0044459 +2 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 | 0.817 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 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 |
|---|---|---|---|---|
LGT | PF01790.24 | 7.3e-59 | 15–273 | Prolipoprotein diacylglyceryl transferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: trpA (tryptophan synthase subunit alpha), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1613 trpA |
tryptophan synthase subunit alpha | 995 | 996 ctx | neighborhood:882 coexpression:964 |
Rv1612 trpB |
tryptophan synthase subunit beta | 993 | 994 ctx | neighborhood:882 coexpression:948 |
Rv1611 trpC |
indole-3-glycerol phosphate synthase | 935 | 935 ctx | neighborhood:793 coexpression:700 |
Rv3806c ubiA |
decaprenyl-phosphate phosphoribosyltransferase | 808 | 808 | coexpression:797 |
Rv3921c yidC |
membrane protein insertase YidC | 850 | 804 | coexpression:788 |
Rv2257c hyp |
hypothetical protein | 793 | 794 | coexpression:788 |
Rv3920c hyp |
hypothetical protein | 784 | 784 | coexpression:767 |
Rv3156 nuoL |
NADH-quinone oxidoreductase subunit L | 783 | 784 | coexpression:777 |
Rv0014c pknB |
serine/threonine-protein kinase PknB | 770 | 762 | coexpression:732 |
Rv0721 rpsE |
30S ribosomal protein S5 | 734 | 734 | coexpression:734 |
Rv0178 |
Mce associated membrane protein | 753 | 731 | coexpression:731 |
Rv2128 |
transmembrane protein | 730 | 730 | coexpression:730 |
Rv1610 |
membrane protein | 727 | 727 ctx | neighborhood:721 |
Rv1609 trpE |
anthranilate synthase component I | 899 | 723 ctx | neighborhood:721 textmining:652 |
Rv3423c alr |
alanine racemase | 682 | 671 | coexpression:600 |
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: prolipoprotein diacylglyceryl transferase
- MTBC0 PGAP product: prolipoprotein diacylglyceryl transferase
- Pfam (hmmscan --cut_ga): LGT PF01790.24 (E=7e-59)
- (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_216130.1)
- Domains: Pfam-A via hmmscan --cut_ga — LGT (PF01790.24)
- 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
COG0682 - Curated reference: UniProt P9WK93 (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 —
48 functional partner(s); context anchor
trpA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001720|Rv1614|lgt MRMLPSYIPSPPRGVWYLGPLPVRAYAVCVITGIIVALLIGDRRLTARGGERGMTYDIALWAVPFGLIGGRLYHLATDWRTYFGDGGAGLAAALRIWDGGLGIWGAVTLGVMGAWIGCRRCGIPLPVLLDAVAPGVVLAQAIGRLGNYFNQELYGRETTMPWGLEIFYRRDPSGFDVPNSLDGVSTGQVAFVVQPTFLYELIWNVLVFVALIYIDRRFIIGHGRLFGFYVAFYCAGRFCVELLRDDPATLIAGIRINSFTSTFVFIGAVVYIILAPKGREAPGALRGSEYVVDEALEREPAELAAAAVASAASAVGPVGPGEPNQPDDVAEAVKAEVAEVTDEVAAESVVQVADRDGESTPAVEETSEADIEREQPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDETEPEVPEKAAPIPDPAKPDELAVAGPGDDPAEPDGIRRQDDFSSRRRRWWRLRRRRQ