treZ Resolved · high auto-curated
H37Rv Rv1562c · MTBC0 - ·
580 aa · 1765400–1767142 (-) ·
RefSeq YP_177819.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | malto-oligosyltrehalose trehalohydrolase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Malto-oligosyltrehalose trehalohydrolase. Pfam: Alpha-amylase (PF00128.32), DUF3459 (PF11941.15). |
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 |
P9WQ23
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Malto-oligosyltrehalose trehalohydrolase |
| EC (curated) |
EC 3.2.1.141
|
| Curated function | Is involved in the biosynthesis of trehalose but not in that of capsular glucan and glycogen. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | treZ |
| eggNOG description | 4-alpha-D-((1- 4)-alpha-D-glucano)trehalose trehalohydrolase |
| Orthologous group | COG0296 |
| EC number |
EC 3.2.1.141
|
| KEGG orthology |
K01236
|
| KEGG pathways |
map00500, map01100, map01110
|
| KEGG modules |
M00565
|
| CAZy family |
CBM48, GH13
|
| Gene Ontology (50) |
GO:0000272, GO:0003674, GO:0003824, GO:0004553, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005975, GO:0005976, GO:0005984 +38 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) pseudogene candidate
| pN/pS | 0.33 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 8 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 16.16% of strains (23468) · clonal |
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 | 4.2e-12 | 109–193 | Alpha amylase, catalytic domain |
DUF3459 | PF11941.15 | 9.4e-09 | 508–572 | Domain of unknown function (DUF3459) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: treY (maltooligosyl trehalose synthase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1563c treY |
maltooligosyl trehalose synthase | 999 | 1000 ctx | neighborhood:882 fusion:635 coexpression:889 database:900 textmining:747 |
Rv1564c treX |
maltooligosyl trehalose synthase | 991 | 990 ctx | neighborhood:882 coexpression:741 database:500 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 992 | 968 | coexpression:496 database:900 textmining:773 |
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 994 | 964 | coexpression:407 database:900 textmining:865 |
Rv0126 treS |
trehalose synthase/amylase TreS | 988 | 948 | database:900 textmining:796 |
Rv2402 |
trehalase | 980 | 923 | database:900 textmining:755 |
Rv3401 |
glycosyl hydrolase | 925 | 923 | database:900 |
Rv1212c glgA |
capsular glucan synthase | 987 | 834 | coexpression:407 database:572 textmining:925 |
Rv1565c |
acyltransferase | 829 | 829 ctx | neighborhood:827 |
Rv1327c glgE |
alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase | 990 | 814 ctx | cooccurence:728 textmining:949 |
Rv0127 mak |
maltokinase | 976 | 811 ctx | cooccurence:706 textmining:879 |
Rv1328 glgP |
glycogen phosphorylase | 930 | 802 | coexpression:729 textmining:663 |
Rv1213 glgC |
glucose-1-phosphate adenylyltransferase | 980 | 798 | coexpression:732 textmining:909 |
Rv3032 |
glycogen synthase | 929 | 782 | coexpression:411 database:572 textmining:688 |
Rv2610c pimA |
alpha-(1-2)-phosphatidylinositol mannosyltransferase | 801 | 782 | coexpression:411 database:572 |
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): malto-oligosyltrehalose trehalohydrolase
- Pfam (hmmscan --cut_ga): Alpha-amylase PF00128.32 (E=4e-12), DUF3459 PF11941.15 (E=9e-09)
- (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_177819.1)
- Domains: Pfam-A via hmmscan --cut_ga — Alpha-amylase (PF00128.32), DUF3459 (PF11941.15)
- 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
COG0296 - Curated reference: UniProt P9WQ23 (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
treY - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1562c|treZ MPEFRVWAPKPALVRLDVNGAVHAMTRSADGWWHTTVAAPADARYGYLLDDDPTVLPDPRSARQPDGVHARSQRWEPPGQFGAARTDTGWPGRSVEGAVIYELHIGTFTTAGTFDAAIEKLDYLVDLGIDFVELMPVNSFAGTRGWGYDGVLWYSVHEPYGGPDGLVRFIDACHARRLGVLIDAVFNHLGPSGNYLPRFGPYLSSASNPWGDGINIAGADSDEVRHYIIDCALRWMRDFHADGLRLDAVHALVDTTAVHVLEELANATRWLSGQLGRPLSLIAETDRNDPRLITRPSHGGYGITAQWNDDIHHAIHTAVSGERQGYYADFGSLATLAYTLRNGYFHAGTYSSFRRRRHGRALDTSAIPATRLLAYTCTHDQVGNRALGDRPSQYLTGGQLAIKAALTLGSPYTAMLFMGEEWGASSPFQFFCSHPEPELAHSTVAGRKEEFAEHGWAADDIPDPQDPQTFQRCKLNWAEAGSGEHARLHRFYRDLIALRHNEADLADPWLDHLMVDYDEQQRWVVMRRGQLMIACNLGAEPTCVPVSGELVLAWESPIIGDNSTELAAYSLAILRAAEPA