otsA Resolved · high auto-curated
H37Rv Rv3490 · MTBC0 mtbc0_003705 ·
500 aa · 3932818–3934320 (+) ·
RefSeq NP_218007.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | trehalose-phosphate synthase |
|---|---|
| MTBC0 PGAP re-annotation | trehalose-6-phosphate synthase |
| Revised (this work) | Trehalose-6-phosphate synthase. Pfam: Glyco_transf_20 (PF00982.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN11
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Trehalose-6-phosphate synthase |
| EC (curated) |
EC 2.4.1.15, EC 2.4.1.347
|
| Curated function | Involved in the production of glycogen and alpha-glucan via the TreS-Pep2 branch involved in the biosynthesis of maltose-1-phosphate (M1P), and probably in the osmoprotection via the biosynthesis of trehalose. Catalyzes the transfer of glucose from UDP-glucose (UDP-Glc) to D-glucose 6-phosphate (Glc-6-P) to form trehalose-6-phosphate. Is specific for the glucosyl acceptor (Glc-6-P cannot be replaced by either mannose-6-P, fructose-6-P or glucosamine-6-P), but any of the glucose sugar nucleotides can be used as glucosyl donors. It is more active with the purine sugar nucleotides than with the p. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | otsA |
| eggNOG description | Probably involved in the osmoprotection via the biosynthesis of trehalose and in the production of glycogen and alpha-glucan via the TreS-Pep2 branch involved in the biosynthesis of maltose-1-phosphate (M1P). Catalyzes the transfer of glucose from UDP-glucose (UDP-Glc) to D-glucose 6-phosphate (Glc-6-P) to form trehalose-6-phosphate. Probably also able to use ADP-Glc, CDP-Glc, GDP-Glc and TDP-Glc as glucosyl donors |
| Orthologous group | COG0380 |
| EC number |
EC 2.4.1.15, EC 2.4.1.347, EC 3.1.3.12
|
| KEGG orthology |
K00697, K16055
|
| KEGG pathways |
map00500, map01100
|
| CAZy family |
GT20
|
| Gene Ontology (61) |
GO:0003674, GO:0003824, GO:0003825, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0005975 +49 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 | 0.578 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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_20 | PF00982.28 | 9.9e-164 | 21–491 | Glycosyltransferase family 20 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: otsB2 (trehalose 6-phosphate phosphatase), high confidence from genomic context alone (score 996 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3372 otsB2 |
trehalose 6-phosphate phosphatase | 999 | 996 ctx | fusion:545 cooccurence:769 coexpression:651 database:900 textmining:963 |
Rv0993 galU |
UTP--glucose-1-phosphate uridylyltransferase | 981 | 904 | database:900 textmining:815 |
Rv3032 |
glycogen synthase | 947 | 903 | database:900 textmining:479 |
Rv3489 hyp |
hypothetical protein | 887 | 887 ctx | neighborhood:882 |
Rv2006 otsB1 |
trehalose-6-phosphate phosphatase OtsB | 973 | 816 | coexpression:650 textmining:861 |
Rv1213 glgC |
glucose-1-phosphate adenylyltransferase | 978 | 802 | database:800 textmining:898 |
Rv2402 |
trehalase | 941 | 739 ctx | cooccurence:695 textmining:786 |
Rv3488 hyp |
hypothetical protein | 610 | 610 ctx | neighborhood:608 |
Rv3491 hyp |
hypothetical protein | 559 | 559 ctx | neighborhood:539 |
Rv1954A |
Rv1954A, len: 100 aa. Hypothetical unknown protein. | 432 | 432 | coexpression:432 |
Rv0007 |
membrane protein | 431 | 432 | coexpression:432 |
Rv1884c rpfC |
resuscitation-promoting factor RpfC | 431 | 410 | coexpression:410 |
Rv1449c tkt |
transketolase | 407 | 408 | coexpression:408 |
Rv0888 spmT hyp |
hypothetical protein | 407 | 408 | coexpression:408 |
Rv2771c hyp |
hypothetical protein | 404 | 405 | coexpression:404 |
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: trehalose-phosphate synthase
- MTBC0 PGAP product: trehalose-6-phosphate synthase
- Pfam (hmmscan --cut_ga): Glyco_transf_20 PF00982.28 (E=1e-163)
- (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_218007.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyco_transf_20 (PF00982.28)
- 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
COG0380 - Curated reference: UniProt P9WN11 (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 —
36 functional partner(s); context anchor
otsB2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003705|Rv3490|otsA MAPSGGQEAQICDSETFGDSDFVVVANRLPVDLERLPDGSTTWKRSPGGLVTALEPVLRRRRGAWVGWPGVNDDGAEPDLHVLDGPIIQDELELHPVRLSTTDIAQYYEGFSNATLWPLYHDVIVKPLYHREWWDRYVDVNQRFAEAASRAAAHGATVWVQDYQLQLVPKMLRMLRPDLTIGFFLHIPFPPVELFMQMPWRTEIIQGLLGADLVGFHLPGGAQNFLILSRRLVGTDTSRGTVGVRSRFGAAVLGSRTIRVGAFPISVDSGALDHAARDRNIRRRAREIRTELGNPRKILLGVDRLDYTKGIDVRLKAFSELLAEGRVKRDDTVLVQLATPSRERVESYQTLRNDIERQVGHINGEYGEVGHPVVHYLHRPAPRDELIAFFVASDVMLVTPLRDGMNLVAKEYVACRSDLGGALVLSEFTGAAAELRHAYLVNPHDLEGVKDGIEEALNQTEEAGRRRMRSLRRQVLAHDVDRWAQSFLDALAGAHPRGQG