treX Resolved · high auto-curated
H37Rv Rv1564c · MTBC0 - ·
721 aa · 1769436–1771601 (-) ·
RefSeq YP_177821.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | maltooligosyl trehalose synthase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Maltooligosyl trehalose synthase. Pfam: CBM_48 (PF02922.25), Alpha-amylase (PF00128.32), Isoamylase_C (PF21331.5). |
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 |
P9WQ25
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glycogen operon protein GlgX homolog |
| EC (curated) |
EC 3.2.1.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| Preferred name | glgX |
| eggNOG description | Belongs to the glycosyl hydrolase 13 family |
| Orthologous group | COG1523 |
| EC number |
EC 3.2.1.68
|
| KEGG orthology |
K01214
|
| KEGG pathways |
map00500, map01100, map01110
|
| KEGG modules |
M00565
|
| CAZy family |
CBM48, GH13
|
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 | 0.305 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 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 |
|---|---|---|---|---|
CBM_48 | PF02922.25 | 5.0e-21 | 26–112 | Carbohydrate-binding module 48 (Isoamylase N-terminal domain) |
Alpha-amylase | PF00128.32 | 1.2e-06 | 324–551 | Alpha amylase, catalytic domain |
Isoamylase_C | PF21331.5 | 6.3e-08 | 612–692 | Isoamylase, C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: treY (maltooligosyl trehalose synthase), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1563c treY |
maltooligosyl trehalose synthase | 999 | 999 ctx | neighborhood:882 cooccurence:726 coexpression:832 database:900 textmining:593 |
Rv1781c malQ |
4-alpha-glucanotransferase | 998 | 997 ctx | fusion:900 cooccurence:557 coexpression:412 database:900 textmining:622 |
Rv1562c treZ |
malto-oligosyltrehalose trehalohydrolase | 991 | 990 ctx | neighborhood:882 coexpression:741 database:500 |
Rv1326c glgB |
1,4-alpha-glucan branching protein | 993 | 981 | coexpression:704 database:900 textmining:666 |
Rv0126 treS |
trehalose synthase/amylase TreS | 989 | 975 ctx | cooccurence:537 coexpression:428 database:900 textmining:593 |
Rv1328 glgP |
glycogen phosphorylase | 997 | 969 | coexpression:631 database:900 textmining:936 |
Rv3031 |
1,4-alpha-glucan-branching protein | 949 | 901 | database:900 textmining:511 |
Rv1213 glgC |
glucose-1-phosphate adenylyltransferase | 978 | 843 ctx | cooccurence:489 coexpression:668 textmining:866 |
Rv1565c |
acyltransferase | 843 | 837 ctx | neighborhood:827 |
Rv1327c glgE |
alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase | 965 | 820 ctx | cooccurence:650 coexpression:425 textmining:815 |
Rv0127 mak |
maltokinase | 900 | 754 ctx | cooccurence:538 coexpression:422 textmining:611 |
Rv1566c ripD hyp |
hypothetical protein | 748 | 748 ctx | neighborhood:740 |
Rv2471 aglA |
alpha-glucosidase AglA | 744 | 595 | coexpression:428 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 543 | 544 | coexpression:479 |
Rv1568 bioA |
adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA | 440 | 428 ctx | neighborhood:426 |
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): CBM_48 PF02922.25 (E=5e-21), Alpha-amylase PF00128.32 (E=1e-06), Isoamylase_C PF21331.5 (E=6e-08)
- (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_177821.1)
- Domains: Pfam-A via hmmscan --cut_ga — CBM_48 (PF02922.25), Alpha-amylase (PF00128.32), Isoamylase_C (PF21331.5)
- 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
COG1523 - Curated reference: UniProt P9WQ25 (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 —
23 functional partner(s); context anchor
treY - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1564c|treX MSSNNAGESDGTGPALPTVWPGNAYPLGATYDGAGTNFSLFSEIAEKVELCLIDEDGVESRIPLDEVDGYVWHAYLPNITPGQRYGFRVHGPFDPAAGHRCDPSKLLLDPYGKSFHGDFTFGQALYSYDVNAVDPDSTPPMVDSLGHTMTSVVINPFFDWAYDRSPRTPYHETVIYEAHVKGMTQTHPSIPPELRGTYAGLAHPVIIDHLNELNVTAVELMPVHQFLHDSRLLDLGLRNYWGYNTFGFFAPHHQYASTRQAGSAVAEFKTMVRSLHEAGIEVILDVVYNHTAEGNHLGPTINFRGIDNTAYYRLMDHDLRFYKDFTGTGNSLNARHPHTLQLIMDSLRYWVIEMHVDGFRFDLASTLARELHDVDRLSAFFDLVQQDPVVSQVKLIAEPWDVGEGGYQVGNFPGLWTEWNGKYRDTVRDYWRGEPATLGEFASRLTGSSDLYEATGRRPSASINFVTAHDGFTLNDLVSYNDKHNEANGENNRDGESYNRSWNCGVEGPTDDPDILALRARQMRNMWATLMVSQGTPMIAHGDEIGRTQYGNNNVYCQDSELSWMDWSLVDKNADLLAFARKATTLRKNHKVFRRRRFFEGEPIRSGDEVRDIAWLTPSGREMTHEDWGRGFDRCVAVFLNGEAITAPDARGERVVDDSFLLCFNAHDHDVEFVMPHDGYAQQWTGELDTNDPVGDIDLTVTATDTFSVPARSLLVLRKTL