plsC Family assigned · medium auto-curated
H37Rv Rv2483c · MTBC0 mtbc0_002643 ·
580 aa · 2812170–2813912 (-) ·
RefSeq NP_216999.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | bifunctional L-3-phosphoserine phosphatase/1-acyl-sn-glycerol-3-phosphate acyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | HAD-IB family hydrolase |
| Revised (this work) | HAD-IB family hydrolase. Pfam: HAD (PF12710.14), Hydrolase (PF00702.33), Acyltransferase (PF01553.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YDI9
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phospholipid/glycerol acyltransferase domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolismI Lipid transport and metabolism
|
|---|---|
| Preferred name | plsC |
| eggNOG description | HAD-superfamily subfamily IB hydrolase, TIGR01490 |
| Orthologous group | COG0204 |
| EC number |
EC 2.3.1.51, EC 3.1.3.3
|
| KEGG orthology |
K00655, K15781
|
| KEGG pathways |
map00561, map00564, map01100, map01110
|
| KEGG modules |
M00089
|
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 | 0.411 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (221) · clonal |
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 |
|---|---|---|---|---|
HAD | PF12710.14 | 4.5e-27 | 40–223 | haloacid dehalogenase-like hydrolase |
Hydrolase | PF00702.33 | 1.2e-06 | 40–220 | haloacid dehalogenase-like hydrolase |
Acyltransferase | PF01553.27 | 5.8e-33 | 313–438 | Acyltransferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2484c (diacyglycerol O-acyltransferase), high confidence from genomic context alone (score 995 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2484c |
diacyglycerol O-acyltransferase | 996 | 995 ctx | neighborhood:882 cooccurence:657 coexpression:833 |
Rv2482c plsB2 |
glycerol-3-phosphate acyltransferase | 996 | 991 ctx | neighborhood:881 cooccurence:753 coexpression:733 textmining:595 |
Rv2481c hyp |
hypothetical protein | 757 | 756 ctx | neighborhood:749 |
Rv1551 plsB1 |
acyltransferase PlsB | 821 | 711 ctx | cooccurence:664 textmining:407 |
Rv1605 hisF |
imidazole glycerol phosphate synthase subunit HisF | 630 | 595 | coexpression:572 |
Rv2477c ettA |
macrolide ABC transporter ATP-binding protein | 569 | 553 ctx | neighborhood:484 |
Rv2478c hyp |
hypothetical protein | 550 | 544 ctx | neighborhood:544 |
Rv0332 hyp |
hypothetical protein | 536 | 536 ctx | cooccurence:533 |
Rv1602 hisH |
imidazole glycerol phosphate synthase subunit HisH | 557 | 530 | coexpression:502 |
Rv1203c hyp |
hypothetical protein | 528 | 529 ctx | cooccurence:527 |
Rv1603 hisA |
1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase | 549 | 526 | coexpression:492 |
Rv1601 hisB |
imidazole glycerol-phosphate dehydratase | 579 | 513 | coexpression:468 |
Rv1606 hisI |
phosphoribosyl-AMP cyclohydrolase | 533 | 501 | coexpression:472 |
Rv2524c fas |
fatty acid synthase | 653 | 489 | |
Rv0425c ctpH |
metal cation transporting ATPase H | 510 | 488 | database:451 |
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: bifunctional L-3-phosphoserine phosphatase/1-acyl-sn-glycerol-3-phosphate acyltransferase
- MTBC0 PGAP product: HAD-IB family hydrolase
- Pfam (hmmscan --cut_ga): HAD PF12710.14 (E=5e-27), Hydrolase PF00702.33 (E=1e-06), Acyltransferase PF01553.27 (E=6e-33)
- (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_216999.1)
- Domains: Pfam-A via hmmscan --cut_ga — HAD (PF12710.14), Hydrolase (PF00702.33), Acyltransferase (PF01553.27)
- 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
COG0204 - Curated reference: UniProt I6YDI9 (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 —
67 functional partner(s); context anchor
Rv2484c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002643|Rv2483c|plsC MSAADEQGEERATRKSAPDLRLPGSVAEILASPAGPKVGAFFDLDGTLVAGFTAVILTQERLRRRDMGVGELLGMVQAGLNHTLGRIEFEDLIGKAAAALAGRLLTDLEEIGERLFAQRIESRIYPEMRELVRAHVARGHTVVLSSSALTIQVGPVARFLGINNMLTNKFETNEDGILTGGVLKPILWGPGKATAVQRFAAEHDIDLKDSYFYADGDEDVALMYLVGNPRPTNPEGKMAAVAKRRGWPILKFNSRGGVGIRRQLRTLAGLSTIVPVAAGAVGIGVLTGSRRRGVNFFTSTFSQLLLATSGVHLNVIGKENLTAQRPAVFIFNHRNQVDPVIAGALVRDNWVGVGKKELASDPIMGTLGKLLDGVFIDRDDPVAAVETLHTVEERARNGLSIVIAPEGTRLDTTEVGSFKKGPFRIAMAAKIPIVPIVIRNAEIVASRNSTTINPGTVDVAVFPPIPVDDWTLDALPDRIAEVRQLYLDTLADWPVDGLPAVDLYAEQKAARKARAQVAKATAKRVPAKKAPAKSAANKGAAATKAATKKASPKAKPSESKIAGKDGEASASPSSSAKGRS