pimA Resolved · high auto-curated
H37Rv Rv2610c · MTBC0 mtbc0_002778 ·
378 aa · 2961418–2962554 (-) ·
RefSeq NP_217126.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | alpha-(1-2)-phosphatidylinositol mannosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | phosphatidyl-myo-inositol alpha-mannosyltransferase |
| Revised (this work) | Phosphatidyl-myo-inositol alpha-mannosyltransferase. Pfam: Glyco_transf_4 (PF13439.13), Glyco_trans_4_4 (PF13579.13), 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 |
P9WMZ5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Phosphatidyl-myo-inositol mannosyltransferase |
| EC (curated) |
EC 2.4.1.345
|
| 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 2 of the carrier lipid phosphatidyl-myo-inositol (PI) to generate a phosphatidyl-myo-inositol bearing an alpha-1,2-linked mannose residue (PIM1). PimA plays an essential role for growth in macrophages and during both the acute and chronic phases of infection. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | pimA |
| eggNOG description | GDP-mannose-dependent alpha-(1-2)-phosphatidylinositol mannosyltransferase |
| Orthologous group | COG0438 |
| EC number |
EC 2.4.1.345
|
| KEGG orthology |
K08256
|
| CAZy family |
GT4
|
| Gene Ontology (49) |
GO:0000026, GO:0000030, GO:0000287, GO:0003674, GO:0003824, GO:0004376, GO:0004377, GO:0005488, GO:0005575, GO:0005623, GO:0005886, GO:0006629 +37 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 | 0.118 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 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 | 7.4e-26 | 14–173 | Glycosyltransferase Family 4 |
Glyco_trans_4_4 | PF13579.13 | 2.6e-11 | 15–153 | Glycosyl transferase 4-like domain |
GT4-conflict | PF20706.4 | 6.4e-07 | 163–305 | Family 4 Glycosyltransferase in conflict systems |
Glycos_transf_1 | PF00534.27 | 3.2e-29 | 187–344 | Glycosyl transferases group 1 |
Glyco_trans_1_4 | PF13692.13 | 2.6e-33 | 189–332 | Glycosyl transferases group 1 |
Glyco_trans_1_2 | PF13524.13 | 9.5e-06 | 216–361 | 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 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2611c |
phosphatidylinositol mannoside acyltransferase | 999 | 996 ctx | neighborhood:879 cooccurence:725 database:900 textmining:897 |
Rv2609c |
membrane protein | 982 | 968 ctx | neighborhood:781 cooccurence:506 coexpression:732 textmining:479 |
Rv2612c pgsA1 |
CDP-diacylglycerol--inositol 3-phosphatidyltransferase | 963 | 952 ctx | neighborhood:879 cooccurence:510 |
Rv2188c pimB |
alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase | 952 | 928 | database:900 |
Rv2613c |
AP-4-A phosphorylase | 945 | 905 ctx | neighborhood:879 textmining:456 |
Rv2614c thrS |
threonine--tRNA ligase | 887 | 881 ctx | neighborhood:879 |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 817 | 783 | coexpression:414 database:572 |
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 801 | 782 | coexpression:411 database:572 |
Rv2529 hyp |
hypothetical protein | 673 | 662 | database:516 |
Rv3670 ephE |
epoxide hydrolase EphE | 579 | 579 ctx | cooccurence:566 |
Rv2614A hyp |
hypothetical protein | 549 | 549 ctx | neighborhood:546 |
Rv1698 mctB |
copper transporter MctB | 526 | 527 ctx | cooccurence:518 |
Rv0322 udgA |
UDP-glucose 6-dehydrogenase UdgA | 551 | 523 | coexpression:444 |
Rv2606c snzP |
pyridoxine biosynthesis protein | 527 | 515 ctx | neighborhood:510 |
Rv3784 |
dTDP-glucose 4,6-dehydratase | 526 | 502 | coexpression:415 |
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-(1-2)-phosphatidylinositol mannosyltransferase
- MTBC0 PGAP product: phosphatidyl-myo-inositol alpha-mannosyltransferase
- Pfam (hmmscan --cut_ga): Glyco_transf_4 PF13439.13 (E=7e-26), Glyco_trans_4_4 PF13579.13 (E=3e-11), GT4-conflict PF20706.4 (E=6e-07), Glycos_transf_1 PF00534.27 (E=3e-29), Glyco_trans_1_4 PF13692.13 (E=3e-33), Glyco_trans_1_2 PF13524.13 (E=1e-05)
- (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_217126.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyco_transf_4 (PF13439.13), Glyco_trans_4_4 (PF13579.13), 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 P9WMZ5 (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 —
45 functional partner(s); context anchor
Rv2611c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002778|Rv2610c|pimA MRIGMICPYSFDVPGGVQSHVLQLAEVMRTRGHLVSVLAPASPHAALPDYFVSGGRAVPIPYNGSVARLRFGPATHRKVKKWLAHGDFDVLHLHEPNAPSLSMLALNIAEGPIVATFHTSTTKSLTLTVFQGILRPMHEKIVGRIAVSDLARRWQMEALGSDAVEIPNGVDVDSFASAARLDGYPRQGKTVLFLGRYDEPRKGMAVLLDALPKVVQRFPDVQLLIVGHGDADQLRGQAGRLAAHLRFLGQVDDAGKASAMRSADVYCAPNTGGESFGIVLVEAMAAGTAVVASDLDAFRRVLRDGEVGHLVPVDPPDLQAAALADGLIAVLENDVLRERYVAAGNAAVRRYDWSVVASQIMRVYETVAGSGAKVQVAS