mgtA Resolved · high auto-curated
H37Rv Rv0557 · MTBC0 - ·
378 aa · 648536–649672 (+) ·
RefSeq NP_215071.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | GDP-mannose-dependent alpha-mannosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | GDP-mannose-dependent alpha-mannosyltransferase. Pfam: Glyco_transf_4 (PF13439.13), Glyco_trans_4_4 (PF13579.13), 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.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WMY5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | GDP-mannose-dependent alpha-mannosyltransferase |
| EC (curated) |
EC 2.4.1.-
|
| Curated function | Catalyzes the addition of a mannose residue from GDP-D-mannose to GlcAGroAc2 to generate 1,2-di-O-C16/C18:1-(alpha-D-mannopyranosyl)-(1-4)-(alpha-D-glucopyranosyluronic acid)-(1-3)-glycerol(ManGlcAGroAc2). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | mgtA |
| eggNOG description | PFAM Glycosyl transferase, group 1 |
| Orthologous group | COG0438 |
| KEGG orthology |
K12583
|
| CAZy family |
GT4
|
| Gene Ontology (28) |
GO:0000030, GO:0003674, GO:0003824, GO:0006629, GO:0006643, GO:0006664, GO:0008150, GO:0008152, GO:0008610, GO:0009058, GO:0009247, GO:0009987 +16 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 | 0.756 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 8 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 | 1.3e-30 | 17–187 | Glycosyltransferase Family 4 |
Glyco_trans_4_4 | PF13579.13 | 6.1e-23 | 18–176 | Glycosyl transferase 4-like domain |
Glycos_transf_1 | PF00534.27 | 4.3e-22 | 202–340 | Glycosyl transferases group 1 |
Glyco_trans_1_4 | PF13692.13 | 3.2e-21 | 207–336 | Glycosyl transferases group 1 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: menH (demethylmenaquinone methyltransferase), high confidence from genomic context alone (score 861 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0558 menH |
demethylmenaquinone methyltransferase | 866 | 861 ctx | neighborhood:861 |
Rv0555 menD |
bifunctional 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase/2-oxoglutarate decarboxylase | 888 | 800 ctx | neighborhood:800 textmining:468 |
Rv0556 |
transmembrane protein | 799 | 800 ctx | neighborhood:800 |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 818 | 781 | coexpression:407 database:572 |
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 805 | 781 | coexpression:407 database:572 |
Rv0553 menC |
muconate cycloisomerase | 756 | 756 ctx | neighborhood:756 |
Rv0552 hyp |
hypothetical protein | 761 | 749 ctx | neighborhood:749 |
Rv0554 bpoC |
non-heme bromoperoxidase BpoC | 711 | 712 ctx | neighborhood:705 |
Rv2529 hyp |
hypothetical protein | 673 | 661 | database:516 |
Rv0322 udgA |
UDP-glucose 6-dehydrogenase UdgA | 824 | 583 | coexpression:442 textmining:596 |
Rv1510 hyp |
hypothetical protein | 575 | 548 | coexpression:420 |
Rv2307c hyp |
hypothetical protein | 568 | 548 | experimental:443 |
Rv3630 |
integral membrane protein | 556 | 534 | coexpression:414 |
Rv3809c glf |
UDP-galactopyranose mutase | 575 | 487 | coexpression:470 |
Rv1328 glgP |
glycogen phosphorylase | 521 | 478 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): GDP-mannose-dependent alpha-mannosyltransferase
- Pfam (hmmscan --cut_ga): Glyco_transf_4 PF13439.13 (E=1e-30), Glyco_trans_4_4 PF13579.13 (E=6e-23), Glycos_transf_1 PF00534.27 (E=4e-22), Glyco_trans_1_4 PF13692.13 (E=3e-21)
- (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_215071.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyco_transf_4 (PF13439.13), Glyco_trans_4_4 (PF13579.13), 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 P9WMY5 (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 —
48 functional partner(s); context anchor
menH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0557|mgtA MCGVRVAIVAESFLPQVNGVSNSVVKVLEHLRRTGHEALVIAPDTPPGEDRAERLHDGVRVHRVPSRMFPKVTTLPLGVPTFRMLRALRGFDPDVVHLASPALLGYGGLHAARRLGVPTVAVYQTDVPGFASSYGIPMTARAAWAWFRHLHRLADRTLAPSTATMESLIAQGIPRVHRWARGVDVQRFAPSARNEVLRRRWSPDGKPIVGFVGRLAPEKHVDRLTGLAASGAVRLVIVGDGIDRARLQSAMPTAVFTGARYGKELAEAYASMDVFVHSGEHETFCQVVQEALASGLPVIAPDAGGPRDLITPHRTGLLLPVGEFEHRLPDAVAHLVHERQRYALAARRSVLGRSWPVVCDELLGHYEAVRGRRTTQAA