pimE Resolved · high auto-curated
H37Rv Rv1159 · MTBC0 mtbc0_001247 ·
431 aa · 1293433–1294728 (+) ·
RefSeq NP_215675.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | polyprenol-phosphate-mannose-dependent alpha-(1-2)-phosphatidylinositol pentamannoside mannosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | mannosyltransferase |
| Revised (this work) | Mannosyltransferase. Pfam: GT87 (PF09594.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN01
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Polyprenol-phosphate-mannose-dependent alpha-(1-2)-phosphatidylinositol pentamannoside mannosyltransferase |
| EC (curated) |
EC 2.4.1.-
|
| Curated function | Catalyzes the alpha-1,2 addition of a mannose residue from polyprenol-phosphate-mannose (PPM) to a monoacyl phosphatidylinositol tetramannoside (AcPIM4) to generate a monoacyl phosphatidylinositol pentamannoside (AcPIM5). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | pimE |
| eggNOG description | GDP-Man:Man3GlcNAc2-PP-Dol alpha-1,2-mannosyltransferase activity |
| Orthologous group | COG1051 |
| KEGG orthology |
K13669
|
| CAZy family |
GT87
|
| Gene Ontology (31) |
GO:0000026, GO:0000030, GO:0003674, GO:0003824, GO:0004376, GO:0004377, GO:0006629, GO:0006643, GO:0006664, GO:0008150, GO:0008152, GO:0008610 +19 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 | 0.862 · 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 |
|---|---|---|---|---|
GT87 | PF09594.17 | 7.1e-56 | 103–334 | Glycosyltransferase family 87 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3604c (transmembrane protein), high confidence from genomic context alone (score 769 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1158c hyp |
hypothetical protein | 831 | 832 ctx | neighborhood:776 |
Rv3604c |
transmembrane protein | 769 | 769 ctx | cooccurence:754 |
Rv0955 |
integral membrane protein | 762 | 762 ctx | cooccurence:760 |
Rv0051 |
transmembrane protein | 865 | 736 ctx | cooccurence:734 textmining:510 |
Rv1157c hyp |
hypothetical protein | 735 | 735 ctx | neighborhood:561 cooccurence:418 |
Rv0236c aftD |
alpha-(1->3)-arabinofuranosyltransferase | 806 | 729 ctx | cooccurence:711 |
Rv2378c mbtG |
L-lysine N6-monooxygenase | 698 | 698 ctx | cooccurence:698 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 690 | 679 ctx | cooccurence:670 |
Rv1863c |
integral membrane protein | 647 | 648 ctx | cooccurence:637 |
Rv0804 hyp |
hypothetical protein | 631 | 631 ctx | cooccurence:628 |
Rv0365c hyp |
hypothetical protein | 585 | 585 ctx | cooccurence:583 |
Rv1057 hyp |
hypothetical protein | 522 | 522 ctx | cooccurence:519 |
Rv3304 hyp |
hypothetical protein | 493 | 494 ctx | cooccurence:492 |
Rv2551c hyp |
hypothetical protein | 484 | 484 ctx | cooccurence:462 |
Rv2609c |
membrane protein | 550 | 469 ctx | cooccurence:431 |
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: polyprenol-phosphate-mannose-dependent alpha-(1-2)-phosphatidylinositol pentamannoside mannosyltransferase
- MTBC0 PGAP product: mannosyltransferase
- Pfam (hmmscan --cut_ga): GT87 PF09594.17 (E=7e-56)
- (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_215675.1)
- Domains: Pfam-A via hmmscan --cut_ga — GT87 (PF09594.17)
- 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
COG1051 - Curated reference: UniProt P9WN01 (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 —
52 functional partner(s); context anchor
Rv3604c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001247|Rv1159|pimE MCRTLIDGPVRSAIAKVRQIDTTSSTPAAARRVTSPPARETRAAVLLLVLSVGARLAWTYLAPNGANFVDLHVYVSGAASLDHPGTLYGYVYADQTPDFPLPFTYPPFAAVVFYPLHLVPFGLIALLWQVVTMAALYGAVRISQRLMGGTAETGHFAAMLWTAIAIWIEPLRSTFDYGQINVLLMLAALWAVYTPRWWLSGLLVGVASGVKLTPAITAVYLVGVRRLHAAAFSVVVFLATVGVSLLVVGDEARYYFTDLLGDAGRVGPIATSFNQSWRGAISRILGHDAGFGPLVLAAIASTAVLAILAWRALDRSDRLGKLLVVELFGLLLSPISWTHHWVWLVPLMIWLIDGPARERPGARILGWGWLVLTIVGVPWLLSFAQPSIWQIGRPWYLAWAGLVYVVATLATLGWIAASERYVRIRPRRMAN