mshA Resolved · high auto-curated
H37Rv Rv0486 · MTBC0 mtbc0_000511 ·
480 aa · 578713–580155 (+) ·
RefSeq NP_215000.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | D-inositol 3-phosphate glycosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | D-inositol-3-phosphate glycosyltransferase |
| Revised (this work) | D-inositol-3-phosphate glycosyltransferase. Pfam: Glyco_trans_4_4 (PF13579.13), Glyco_transf_4 (PF13439.13), GT4-conflict (PF20706.4), Glycos_transf_1 (PF00534.27), Glyco_trans_1_4 (PF13692.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMY7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | D-inositol 3-phosphate glycosyltransferase |
| EC (curated) |
EC 2.4.1.250
|
| Curated function | Catalyzes the transfer of an N-acetyl-glucosamine moiety to 1D-myo-inositol 3-phosphate to produce 1D-myo-inositol 2-acetamido-2-deoxy-glucopyranoside 3-phosphate in the mycothiol (MSH) biosynthesis pathway. MSH and WhiB3 are probably part of a regulatory circuit that mediates gene expression upon acid stress (like that found in host macrophage phagosomes). MSH is one of the major redox buffers which protects bacteria against redox stressors and antibiotics; loss of MSH or ergothioneine (ERG, the other major redox buffer in this bacteria) leads to respiratory alterations and bioenergetic defic. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | mshA |
| eggNOG description | Catalyzes the transfer of a N-acetyl-glucosamine moiety to 1D-myo-inositol 3-phosphate to produce 1D-myo-inositol 2- acetamido-2-deoxy-glucopyranoside 3-phosphate in the mycothiol biosynthesis pathway |
| Orthologous group | COG0438 |
| EC number |
EC 2.4.1.250
|
| KEGG orthology |
K15521
|
| Gene Ontology (35) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006790, GO:0008150, GO:0008152, GO:0008194, GO:0008375 +23 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 | 0.449 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 6 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 |
|---|---|---|---|---|
Glyco_trans_4_4 | PF13579.13 | 2.7e-32 | 66–241 | Glycosyl transferase 4-like domain |
Glyco_transf_4 | PF13439.13 | 1.3e-26 | 66–245 | Glycosyltransferase Family 4 |
GT4-conflict | PF20706.4 | 1.7e-16 | 136–437 | Family 4 Glycosyltransferase in conflict systems |
Glycos_transf_1 | PF00534.27 | 1.3e-36 | 252–407 | Glycosyl transferases group 1 |
Glyco_trans_1_4 | PF13692.13 | 4.3e-27 | 266–406 | Glycosyl transferases group 1 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mshB (1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase), high confidence from genomic context alone (score 797 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0487 hyp |
hypothetical protein | 898 | 898 ctx | neighborhood:882 |
Rv1170 mshB |
1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase | 986 | 797 ctx | fusion:471 cooccurence:602 textmining:935 |
Rv0113 gmhA |
phosphoheptose isomerase | 800 | 788 ctx | fusion:776 |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 815 | 781 | coexpression:407 database:572 |
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 800 | 781 | coexpression:407 database:572 |
Rv0485 |
transcriptional regulator | 728 | 718 ctx | neighborhood:718 |
Rv0490 senX3 |
two component sensor histidine kinase SenX3 | 706 | 696 ctx | neighborhood:622 |
Rv1082 mca |
mycothiol S-conjugate amidase | 919 | 692 ctx | cooccurence:668 textmining:748 |
Rv0491 regX3 |
two component sensory transduction protein RegX | 689 | 678 ctx | neighborhood:604 |
Rv0046c ino1 |
inositol-3-phosphate synthase | 690 | 672 | database:500 |
Rv2529 hyp |
hypothetical protein | 673 | 661 | database:516 |
Rv0489 gpm1 |
2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | 671 | 658 ctx | neighborhood:654 |
Rv0819 mshD |
mycothiol acetyltransferase | 972 | 610 ctx | cooccurence:610 textmining:932 |
Rv2466c hyp |
hypothetical protein | 628 | 552 ctx | cooccurence:552 |
Rv3264c manB |
D-alpha-D-mannose-1-phosphate guanylyltransferase ManB | 536 | 507 |
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: D-inositol 3-phosphate glycosyltransferase
- MTBC0 PGAP product: D-inositol-3-phosphate glycosyltransferase
- Pfam (hmmscan --cut_ga): Glyco_trans_4_4 PF13579.13 (E=3e-32), Glyco_transf_4 PF13439.13 (E=1e-26), GT4-conflict PF20706.4 (E=2e-16), Glycos_transf_1 PF00534.27 (E=1e-36), Glyco_trans_1_4 PF13692.13 (E=4e-27)
- (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_215000.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyco_trans_4_4 (PF13579.13), Glyco_transf_4 (PF13439.13), GT4-conflict (PF20706.4), Glycos_transf_1 (PF00534.27), Glyco_trans_1_4 (PF13692.13)
- 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 P9WMY7 (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 —
62 functional partner(s); context anchor
mshB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000511|Rv0486|mshA MAGVRHDDGSGLIAQRRPVRGEGATRSRGPSGPSNRNVSAADDPRRVALLAVHTSPLAQPGTGDAGGMNVYMLQSALHLARRGIEVEIFTRATASADPPVVRVAPGVLVRNVVAGPFEGLDKYDLPTQLCAFAAGVLRAEAVHEPGYYDIVHSHYWLSGQVGWLARDRWAVPLVHTAHTLAAVKNAALADGDGPEPPLRTVGEQQVVDEADRLIVNTDDEARQVISLHGADPARIDVVHPGVDLDVFRPGDRRAARAALGLPVDERVVAFVGRIQPLKAPDIVLRAAAKLPGVRIIVAGGPSGSGLASPDGLVRLADELGISARVTFLPPQSHTDLATLFRAADLVAVPSYSESFGLVAVEAQACGTPVVAAAVGGLPVAVRDGITGTLVSGHEVGQWADAIDHLLRLCAGPRGRVMSRAAARHAATFSWENTTDALLASYRRAIGEYNAERQRRGGEVISDLVAVGKPRHWTPRRGVGA