Rv0584 Family assigned · medium auto-curated
H37Rv Rv0584 · MTBC0 mtbc0_000614 ·
877 aa · 682780–685413 (+) ·
RefSeq NP_215098.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycosidase |
|---|---|
| MTBC0 PGAP re-annotation | GH92 family glycosyl hydrolase |
| Revised (this work) | GH92 family glycosyl hydrolase. Pfam: Glyco_hydro_92N (PF17678.8), Glyco_hydro_92 (PF07971.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O86365
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized glycosidase Rv0584 |
| EC (curated) |
EC 3.2.1.-
|
UniProt still lists this protein as Uncharacterized glycosidase Rv0584; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Glycosyl hydrolase family 92 |
| Orthologous group | COG3537 |
| Gene Ontology (45) |
GO:0000224, GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006464, GO:0006508, GO:0006515, GO:0006516 +33 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 | 0.456 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 12 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.39% of strains (568) · 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 |
|---|---|---|---|---|
Glyco_hydro_92N | PF17678.8 | 6.1e-56 | 44–274 | Glycosyl hydrolase family 92 N-terminal domain |
Glyco_hydro_92 | PF07971.19 | 1.9e-139 | 280–749 | Glycosyl hydrolase family 92 catalytic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lpqN (lipoprotein LpqN), high confidence from genomic context alone (score 772 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0583c lpqN |
lipoprotein LpqN | 771 | 772 ctx | neighborhood:771 |
Rv1733c |
transmembrane protein | 451 | 451 ctx | cooccurence:446 |
Rv3912 rsmA |
anti-sigma-M factor RsmA | 407 | 408 ctx | cooccurence:404 |
Rv3903c cpnT hyp |
hypothetical protein | 873 | 64 | textmining:870 |
Rv3551 |
CoA-transferase subunit alpha | 575 | 52 | textmining:571 |
Rv1030 kdpB |
potassium-transporting ATPase subunit B | 662 | 47 | textmining:660 |
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: glycosidase
- MTBC0 PGAP product: GH92 family glycosyl hydrolase
- Pfam (hmmscan --cut_ga): Glyco_hydro_92N PF17678.8 (E=6e-56), Glyco_hydro_92 PF07971.19 (E=2e-139)
- (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_215098.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyco_hydro_92N (PF17678.8), Glyco_hydro_92 (PF07971.19)
- 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
COG3537 - Curated reference: UniProt O86365 (SwissProt, reviewed; Inferred from homology)
- 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 —
6 functional partner(s); context anchor
lpqN - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000614|Rv0584| MRARRLRRALAALLAVAGLFVPFIVGVPTAYDGEPVFVAIPVEHVNTLIGTGTGAAIVGEINNFPGASVPFGMVQYSPDTVDNYAGYDYDNPHSTGFSMTHASVGCPAFGDISMLPTTTPLGSQPWSAWEEIAHDDTEVGVPGYYTVRFPGTGVIAELTATTRTGVGRFRYPRNGWPALFHVRSGASLAGNYAATLQIEDNTTITGSATSGGFCGKKNLYTVYFAMKFSQPFSSYGTWDGYAVYPGSHSMNSSYSGGYVGFPAGSVLEVRTALSYVSVDGARANLDAEGGASFDDIRAATSSEWNAALSRIAVAGRGPGDVDTFYTCLYRSLLHPNTFNDVDGRYIGFDGVIHSVASGHTHYANFSDWDTYRSLAPLQGLLFPQRASDMIQSLVTDAEQSGAYPRWALANSATGMMSGDSVVPLIVNLYAFGARDFDLKSALHYMVNAATQGGVGLDGFLERPGIAAYLRLGYGPQTAEFRANGRIAGASVTLEWSVDDFAISRFADSLGDTATAAVFQNRSQYWQNLFNPTTGYISPRSAAGFFPDGPGFVAYPSGFGQDGYDEGNAEQYLWWVPHNVAGLVTALGGRTAVVKRLDRFTKKLNVGPNEPYLWAGNEPGFGVPWLYNYIGQPWKTQRTVDRVRGLFGPTPGGAPGNDDLGALSSWYVWAALGLYPSTPGTTILTVNTPLFDRAVIALPTGKSIQITAPGASGRNRLKYIDGLTIDRQPSNQTFLPESIVRTGGDLTFSLAGTPNKVWGTAASAAPPSFGAGSSAVTVNIARPIIGIVPGATGTVTVDAQRMIDGVDDYTVTPTSYVVGIAAEPLSGQFDDDGAVSASVAITVARSVPSGYYPIYVTTSAGDSARTLIVLVVVAEAVE