Rv0315 Resolved · high auto-curated
H37Rv Rv0315 · MTBC0 mtbc0_000335 ·
294 aa · 386925–387809 (+) ·
RefSeq NP_214829.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | beta-1,3-glucanase |
|---|---|
| MTBC0 PGAP re-annotation | family 16 glycosylhydrolase |
| Revised (this work) | Family 16 glycosylhydrolase. Pfam: Glyco_hydro_16 (PF00722.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07242
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible beta-1,3-glucanase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | family 16 |
| Orthologous group | COG2273 |
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 | 0.314 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.22% of strains (314) · 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_16 | PF00722.29 | 5.6e-10 | 141–226 | Glycosyl hydrolases family 16 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0316 (muconolactone isomerase), high confidence from genomic context alone (score 843 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0316 |
muconolactone isomerase | 843 | 843 ctx | neighborhood:714 coexpression:474 |
Rv0314c |
membrane protein | 757 | 757 ctx | neighborhood:755 |
Rv3810 pirG |
cell surface protein | 698 | 699 ctx | cooccurence:692 |
Rv3707c hyp |
hypothetical protein | 673 | 673 ctx | cooccurence:672 |
Rv1987 |
chitinase | 662 | 617 ctx | cooccurence:602 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 580 | 580 ctx | cooccurence:576 |
Rv2743c hyp |
hypothetical protein | 558 | 558 ctx | cooccurence:557 |
Rv2120c |
integral membrane protein | 520 | 521 ctx | cooccurence:514 |
Rv3593 lpqF |
lipoprotein LpqF | 506 | 504 ctx | cooccurence:501 |
Rv0262c aac |
aminoglycoside 2'-N-acetyltransferase | 500 | 501 ctx | cooccurence:499 |
Rv1288 hyp |
hypothetical protein | 474 | 474 ctx | cooccurence:470 |
Rv1836c hyp |
hypothetical protein | 444 | 444 ctx | cooccurence:432 |
Rv0817c lmeA hyp |
hypothetical protein | 442 | 443 ctx | cooccurence:441 |
Rv0273c |
transcriptional regulator | 434 | 435 ctx | cooccurence:434 |
Rv3630 |
integral membrane protein | 462 | 429 |
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: beta-1,3-glucanase
- MTBC0 PGAP product: family 16 glycosylhydrolase
- Pfam (hmmscan --cut_ga): Glyco_hydro_16 PF00722.29 (E=6e-10)
- (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_214829.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyco_hydro_16 (PF00722.29)
- 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
COG2273 - Curated reference: UniProt O07242 (TrEMBL, unreviewed; 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 —
39 functional partner(s); context anchor
Rv0316 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000335|Rv0315| MLMPEMDRRRMMMMAGFGALAAALPAPTAWADPSRPAAPAGPTPAPAAPAAATGGLLFHDEFDGPAGSVPDPSKWQVSNHRTPIKNPVGFDRPQFFGQYRDSRQNVFLDGNSNLVLRATREGNRYFGGLVHGLWRGGIGTTWEARIKFNCLAPGMWPAWWLSNDDPGRSGEIDLIEWYGNGTWPSGTTVHANPDGTAFETCPIGVDGGWHNWRVTWNPSGMYFWLDYADGIEPYFSVPATGIEDLNEPIREWPFNDPGYTVFPVLNLAVGGSGGGDPATGSYPQEMLVDWVRVF