pimB Resolved · high auto-curated
H37Rv Rv2188c · MTBC0 mtbc0_002323 ·
385 aa · 2476000–2477157 (-) ·
RefSeq NP_216704.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase |
| Revised (this work) | GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase. Pfam: Glyco_transf_4 (PF13439.13), GT4-conflict (PF20706.4), Glycos_transf_1 (PF00534.27), Glyco_trans_1_4 (PF13692.13), Glyco_trans_1_2 (PF13524.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMZ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase |
| EC (curated) |
EC 2.4.1.346
|
| Curated function | Involved in the biosynthesis of phosphatidyl-myo-inositol mannosides (PIM) which are early precursors in the biosynthesis of lipomannans (LM) and lipoarabinomannans (LAM). Catalyzes the addition of a mannosyl residue from GDP-D-mannose (GDP-Man) to the position 6 of a phosphatidyl-myo-inositol bearing an alpha-1,2-linked mannose residue (PIM1) to generate phosphatidyl-myo-inositol bearing alpha-1,2- and alpha-1,6-linked mannose residues (Ac1PIM2). PimB also catalyzes the addition of a mannosyl residue from GDP-Man to the position 6 of phosphatidyl-myo-inositol bearing an acylated alpha-1,2-lin. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | pimB |
| eggNOG description | GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase |
| Orthologous group | COG0438 |
| EC number |
EC 2.4.1.346
|
| KEGG orthology |
K13668
|
| CAZy family |
GT4
|
| Gene Ontology (38) |
GO:0000009, GO:0000030, GO:0003674, GO:0003824, GO:0004376, GO:0005575, GO:0005623, GO:0005886, GO:0006629, GO:0006643, GO:0006664, GO:0008150 +26 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 | 0.949 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 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 |
|---|---|---|---|---|
Glyco_transf_4 | PF13439.13 | 9.4e-16 | 16–177 | Glycosyltransferase Family 4 |
GT4-conflict | PF20706.4 | 1.9e-09 | 134–374 | Family 4 Glycosyltransferase in conflict systems |
Glycos_transf_1 | PF00534.27 | 4.3e-44 | 186–360 | Glycosyl transferases group 1 |
Glyco_trans_1_4 | PF13692.13 | 2.2e-34 | 197–345 | Glycosyl transferases group 1 |
Glyco_trans_1_2 | PF13524.13 | 6.4e-06 | 255–375 | Glycosyl transferase-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2611c (phosphatidylinositol mannoside acyltransferase), high confidence from genomic context alone (score 960 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2611c |
phosphatidylinositol mannoside acyltransferase | 997 | 960 ctx | cooccurence:594 database:900 textmining:928 |
Rv2610c pimA |
alpha-(1-2)-phosphatidylinositol mannosyltransferase | 952 | 928 | database:900 |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 819 | 781 | coexpression:407 database:572 |
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 809 | 781 | coexpression:409 database:572 |
Rv2189c hyp |
hypothetical protein | 779 | 780 ctx | neighborhood:775 |
Rv2529 hyp |
hypothetical protein | 674 | 662 | database:516 |
Rv3231c hyp |
hypothetical protein | 618 | 618 ctx | cooccurence:618 |
Rv2190c ripC |
endopeptidase | 706 | 608 ctx | neighborhood:551 |
Rv0322 udgA |
UDP-glucose 6-dehydrogenase UdgA | 563 | 535 | coexpression:448 |
Rv3264c manB |
D-alpha-D-mannose-1-phosphate guanylyltransferase ManB | 554 | 527 | |
Rv2307c hyp |
hypothetical protein | 544 | 522 | experimental:443 |
Rv3909 hyp |
hypothetical protein | 507 | 496 ctx | cooccurence:494 |
Rv3809c glf |
UDP-galactopyranose mutase | 584 | 487 | coexpression:470 |
Rv1328 glgP |
glycogen phosphorylase | 523 | 480 | |
Rv3658c |
transmembrane protein | 479 | 479 ctx | cooccurence:476 |
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: alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase
- MTBC0 PGAP product: GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase
- Pfam (hmmscan --cut_ga): Glyco_transf_4 PF13439.13 (E=9e-16), GT4-conflict PF20706.4 (E=2e-09), Glycos_transf_1 PF00534.27 (E=4e-44), Glyco_trans_1_4 PF13692.13 (E=2e-34), Glyco_trans_1_2 PF13524.13 (E=6e-06)
- (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_216704.2)
- Domains: Pfam-A via hmmscan --cut_ga — Glyco_transf_4 (PF13439.13), GT4-conflict (PF20706.4), Glycos_transf_1 (PF00534.27), Glyco_trans_1_4 (PF13692.13), Glyco_trans_1_2 (PF13524.13)
- 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
COG0438 - Curated reference: UniProt P9WMZ3 (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 —
50 functional partner(s); context anchor
Rv2611c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002323|Rv2188c|pimB MSRVLLVTNDFPPRRGGIQSYLGEFVGRLVGSRAHAMTVYAPQWKGADAFDDAARAAGYRVVRHPSTVMLPGPTVDVRMRRLIAEHDIETVWFGAAAPLALLAPRARLAGASRVLASTHGHEVGWSMLPVARSVLRRIGDGTDVVTFVSSYTRSRFASAFGPAASLEYLPPGVDTDRFRPDPAARAELRKRYRLGERPTVVCLSRLVPRKGQDTLVTALPSIRRRVDGAALVIVGGGPYLETLRKLAHDCGVADHVTFTGGVATDELPAHHALADVFAMPCRTRGAGMDVEGLGIVFLEASAAGVPVIAGNSGGAPETVQHNKTGLVVDGRSVDRVADAVAELLIDRDRAVAMGAAGREWVTAQWRWDTLAAKLADFLRGDDAAR