Rv2402 Resolved · high auto-curated
H37Rv Rv2402 · MTBC0 - ·
642 aa · 2698529–2700457 (+) ·
RefSeq NP_216918.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | trehalase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Trehalase. Pfam: TREH_N (PF19291.5), Glyco_hydro_15 (PF00723.28). |
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 |
P71741
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Trehalase |
| EC (curated) |
EC 3.2.1.28
|
| Curated function | Catalyzes the hydrolysis of alpha,alpha-trehalose into two molecules of D-glucose. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | hydrolase |
| Orthologous group | COG3387 |
| Gene Ontology (36) |
GO:0003674, GO:0003824, GO:0004553, GO:0004555, GO:0005488, GO:0005575, GO:0005623, GO:0005886, GO:0005975, GO:0005984, GO:0005991, GO:0005993 +24 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 | 0.294 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 10 synonymous, 8 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.21% of strains (303) · 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 |
|---|---|---|---|---|
TREH_N | PF19291.5 | 6.5e-15 | 14–90 | Trehalase-like, N-terminal |
Glyco_hydro_15 | PF00723.28 | 2.4e-68 | 254–619 | Glycosyl hydrolases family 15 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: otsB2 (trehalose 6-phosphate phosphatase), high confidence from genomic context alone (score 966 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 988 | 966 ctx | cooccurence:633 database:900 textmining:664 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 973 | 935 | database:900 textmining:618 |
Rv0126 treS |
trehalose synthase/amylase TreS | 986 | 933 | database:900 textmining:810 |
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 980 | 923 | database:900 textmining:755 |
Rv3401 |
glycosyl hydrolase | 906 | 901 | database:900 |
Rv3490 otsA |
trehalose-phosphate synthase | 941 | 739 ctx | cooccurence:695 textmining:786 |
Rv2401A |
membrane protein | 713 | 713 ctx | neighborhood:711 |
Rv1751 |
oxidoreductase | 544 | 544 ctx | neighborhood:544 |
Rv0727c fucA |
L-fuculose phosphate aldolase FucA | 441 | 409 | coexpression:409 |
Rv1327c glgE |
alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase | 644 | 307 | textmining:508 |
Rv1563c treY |
maltooligosyl trehalose synthase | 796 | 259 | textmining:737 |
Rv0127 mak |
maltokinase | 568 | 252 | textmining:446 |
Rv1328 glgP |
glycogen phosphorylase | 417 | 173 | |
Rv1213 glgC |
glucose-1-phosphate adenylyltransferase | 400 | 122 | |
Rv0794c |
oxidoreductase | 568 | 86 | textmining:547 |
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): trehalase
- Pfam (hmmscan --cut_ga): TREH_N PF19291.5 (E=6e-15), Glyco_hydro_15 PF00723.28 (E=2e-68)
- (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_216918.3)
- Domains: Pfam-A via hmmscan --cut_ga — TREH_N (PF19291.5), Glyco_hydro_15 (PF00723.28)
- 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
COG3387 - Curated reference: UniProt P71741 (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 —
20 functional partner(s); context anchor
otsB2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2402| MALSSSSPLRNPFPPIADYAFLSDWETTCLISPAGSVEWLCVPRPDSPSVFGAILDRSAGHFRLGPYGVSVPSARRYLPGSLIMETTWQTHTGWLIVRDALVMGKWHDIERRSRTHRRTPMDWDAEHILLRTVRCVSGTVELMMSCEPAFDYHRLGATWEYSAEAYGEAIARANTEPDAHPTLRLTTNLRIGLEGREARARTRMKEGDDVFVALSWTKHPPPQTYDEAADKMWQTTECWRQWINIGNFPDHPWRAYLQRSALTLKGLTYSPTGALLAASTTSLPETPRGERNWDYRYAWIRDSTFALWGLYTLGLDREADDFFAFIADVSGANNNERHPLQVMYGVGGERSLVEAELHHLSGYDHARPVRIGNGAYNQRQHDIWGSILDSFYLHAKSREQVPENLWPVLKRQVEEAIKHWREPDRGIWEVRGEPQHFTSSKVMCWVALDRGAKLAERQGEKSYAQQWRAIADEIKADILEHGVDSRGVFTQRYGDEALDASLLLVVLTRFLPPDDPRVRNTVLAIADELTEDGLVLRYRVHETDDGLSGEEGTFTICSFWLVSALVEIGEVGRAKRLCERLLSFASPLLLYAEEIEPRSGRHLGNFPQAFTHLALINAVVHVIRAEEEADSSGMFQPANAPM