treY Resolved · high auto-curated
H37Rv Rv1563c · MTBC0 - ·
765 aa · 1767135–1769432 (-) ·
RefSeq YP_177820.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | maltooligosyl trehalose synthase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Maltooligosyl trehalose synthase. Pfam: Alpha-amylase (PF00128.32). |
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 |
P9WQ21
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative maltooligosyl trehalose synthase |
| EC (curated) |
EC 5.4.99.15
|
| Curated function | Catalyzes the conversion of maltooligosaccharide into the non-reducing saccharide, maltooligosyl trehalose (alpha-maltooligosyl alpha-D-glucoside) by intramolecular transglycosylation. |
UniProt still lists this protein as Putative maltooligosyl trehalose synthase; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | treY |
| eggNOG description | synthase |
| Orthologous group | COG3280 |
| EC number |
EC 5.4.99.15
|
| KEGG orthology |
K06044
|
| KEGG pathways |
map00500, map01100, map01110
|
| KEGG modules |
M00565
|
| CAZy family |
GH13
|
| Gene Ontology (49) |
GO:0000272, GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005975, GO:0005976, GO:0005984, GO:0005991 +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 | 1.254 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
Alpha-amylase | PF00128.32 | 1.4e-15 | 31–243 | Alpha amylase, catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: treZ (malto-oligosyltrehalose trehalohydrolase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 999 | 1000 ctx | neighborhood:882 fusion:635 coexpression:889 database:900 textmining:747 |
Rv1564c treX |
maltooligosyl trehalose synthase | 999 | 999 ctx | neighborhood:882 cooccurence:726 coexpression:832 database:900 textmining:593 |
Rv0126 treS |
trehalose synthase/amylase TreS | 998 | 977 ctx | cooccurence:722 database:900 textmining:948 |
Rv1781c malQ |
4-alpha-glucanotransferase | 982 | 969 ctx | fusion:899 cooccurence:438 coexpression:423 textmining:458 |
Rv1565c |
acyltransferase | 830 | 830 ctx | neighborhood:827 |
Rv1327c glgE |
alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase | 983 | 802 ctx | cooccurence:745 textmining:921 |
Rv0127 mak |
maltokinase | 961 | 795 ctx | cooccurence:741 textmining:822 |
Rv1566c ripD hyp |
hypothetical protein | 740 | 740 ctx | neighborhood:740 |
Rv1571 hyp |
hypothetical protein | 686 | 686 ctx | neighborhood:623 |
Rv1570 bioD |
ATP-dependent dethiobiotin synthetase BioD | 626 | 626 ctx | neighborhood:623 |
Rv1568 bioA |
adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA | 635 | 625 ctx | neighborhood:623 |
Rv1569 bioF1 |
8-amino-7-oxononanoate synthase | 625 | 625 ctx | neighborhood:623 |
Rv1567c |
membrane protein | 612 | 612 ctx | neighborhood:612 |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 909 | 556 | coexpression:426 textmining:804 |
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 959 | 454 | textmining:928 |
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): maltooligosyl trehalose synthase
- Pfam (hmmscan --cut_ga): Alpha-amylase PF00128.32 (E=1e-15)
- (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 YP_177820.1)
- Domains: Pfam-A via hmmscan --cut_ga — Alpha-amylase (PF00128.32)
- 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
COG3280 - Curated reference: UniProt P9WQ21 (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 —
26 functional partner(s); context anchor
treZ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1563c|treY MAFPVISTYRVQMRGRSNGFGFTFADAENLLDYLDDLGVSHLYLSPILTAVGGSTHGYDVTDPTTVSPELGGSDGLARLSAAARSRGMGLIVDIVPSHVGVGKPEQNAWWWDVLKFGRSSAYAEFFDIDWELGDGRIILPLLGSDSDVANLRVDGDLLRLGDLALPVAPGSGDGTGPAVHDRQHYRLVGWRHGLCGYRRFFSITSLAGLRQEDRAVFDASHAEVARWFTEGLVDGVRVDHLDGLSDPSGYLAQLRELLGPNAWIVVEKILAVDEALEPTLPVDGSTGYDVLREIGGVLVDPQGESPLTALVESAGVDYQEMPAMLADLKVHAAVHTLASELRRLRRCIAAAAGADHPLLPAAVAALLRHIGRYRCDYPGQAAVLPCALAETHSTTPQLAPGLQLIAAAVARGGEPAVRLQQLCGAVSAKAVEDCMFYRDARLVSLNEVGGEPRRFGVGAAEFHHRAATRARLWPRSMTTLSTHDTKRGEDVRARIGVLSQVPWLWAKFIGHAQAIAPAPDAVTGQFLWQNVFGVWPVSGEVSAALRGRLHTYAEKAIREAAWHTSWHNPNRAFEDDVHGWLDLVLDGPLASELTGLVAHLNSHAESDALAAKLLALTVPGVPDVYQGSELWDDSLVDPDNRRPVDYGTRRVALKALQHPKIRVLAAALRLRRTHPESFLGGAYHPVFAAGPAADHVVAFRRGDDILVAVTRWTVRLQQTGWDHTVLPLPDGSWTDALTGFTASGHTPAVELFADLPVVLLVRDNA