Rv0320 Family assigned · medium auto-curated
H37Rv Rv0320 · MTBC0 mtbc0_000341 ·
220 aa · 391211–391873 (+) ·
RefSeq NP_214834.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | hypothetical protein |
| Revised (this work) | Contains VldE (PF26571.1) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07246
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible conserved exported protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| eggNOG description | sh3 domain protein |
| Orthologous group | COG3103 |
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 | 0.359 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 2 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 |
|---|---|---|---|---|
VldE | PF26571.1 | 3.2e-20 | 103–192 | VldE, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pcp (pyrrolidone-carboxylate peptidase), high confidence from genomic context alone (score 756 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0319 pcp |
pyrrolidone-carboxylate peptidase | 757 | 756 ctx | neighborhood:754 |
Rv0321 dcd |
deoxycytidine triphosphate deaminase | 702 | 703 ctx | neighborhood:700 |
Rv2862c hyp |
hypothetical protein | 686 | 687 ctx | cooccurence:673 |
Rv2721c hyp |
hypothetical protein | 681 | 681 ctx | cooccurence:677 |
Rv3810 pirG |
cell surface protein | 675 | 675 ctx | cooccurence:670 |
Rv3707c hyp |
hypothetical protein | 662 | 663 ctx | cooccurence:661 |
Rv0479c |
membrane protein | 651 | 651 ctx | cooccurence:651 |
Rv3593 lpqF |
lipoprotein LpqF | 604 | 604 ctx | cooccurence:603 |
Rv2743c hyp |
hypothetical protein | 582 | 582 ctx | cooccurence:582 |
Rv2712c hyp |
hypothetical protein | 576 | 577 ctx | cooccurence:574 |
Rv2015c hyp |
hypothetical protein | 550 | 550 ctx | cooccurence:549 |
Rv0322 udgA |
UDP-glucose 6-dehydrogenase UdgA | 514 | 515 ctx | neighborhood:513 |
Rv2151c ftsQ |
cell division protein FtsQ | 517 | 513 ctx | cooccurence:510 |
Rv0318c |
integral membrane protein | 502 | 502 ctx | neighborhood:496 |
Rv3803c fbpD |
MPT51/MPB51 antigen | 502 | 502 ctx | cooccurence:500 |
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: hypothetical protein
- MTBC0 PGAP product: hypothetical protein
- Pfam (hmmscan --cut_ga): VldE PF26571.1 (E=3e-20)
- (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_214834.1)
- Domains: Pfam-A via hmmscan --cut_ga — VldE (PF26571.1)
- 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
COG3103 - Curated reference: UniProt O07246 (TrEMBL, unreviewed; Predicted)
- 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 —
41 functional partner(s); context anchor
pcp - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000341|Rv0320| MGRHELARDRRKSSAVLAAVLAPAAVFFATGGDVSTLAARADANPVLGDDAPCCVQIVPVAPLAFSSQISGGEIGTGLAASQFASASRWRIVSRYLPVGVAPEQGLQVKTVLTARSISAAFPEIREIGGVRPDALRWHPNGLALDVMVPNPGTAEGIALGNEIVAFVLKNATRFGMQDVIWRGAYYTPNGARTTGAGHYDHIHITTVGGGYPTGEELYIR