Rv0910 Family assigned · medium auto-curated
H37Rv Rv0910 · MTBC0 mtbc0_000965 ·
144 aa · 1018081–1018515 (+) ·
RefSeq NP_215425.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | toxin |
|---|---|
| MTBC0 PGAP re-annotation | SRPBCC family protein |
| Revised (this work) | SRPBCC family protein. Pfam: Polyketide_cyc2 (PF10604.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJ05
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Toxin Rv0910 |
| Curated function | Toxic component of a type II toxin-antitoxin (TA) system. Upon expression in M.smegmatis inhibits colony formation. Its toxic effect is neutralized by coexpression with cognate antitoxin Rv0909. Does not exert its toxic effect via translation. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | Polyketide cyclase / dehydrase and lipid transport |
| Orthologous group | COG3427 |
| Gene Ontology (6) |
GO:0008150, GO:0040008, GO:0045926, GO:0048519, GO:0050789, GO:0065007
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 1 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 |
|---|---|---|---|---|
Polyketide_cyc2 | PF10604.16 | 5.1e-25 | 1–142 | Polyketide cyclase / dehydrase and lipid transport |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0909 (antitoxin), high confidence from genomic context alone (score 887 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0909 |
antitoxin | 978 | 887 ctx | neighborhood:882 textmining:814 |
Rv0513 |
transmembrane protein | 715 | 716 ctx | cooccurence:713 |
Rv3584 lpqE |
lipoprotein LpqE | 709 | 710 ctx | cooccurence:707 |
Rv0826 hyp |
hypothetical protein | 661 | 661 ctx | cooccurence:660 |
Rv1645c hyp |
hypothetical protein | 653 | 654 ctx | cooccurence:650 |
Rv3346c |
transmembrane protein | 630 | 630 ctx | cooccurence:629 |
Rv0911 hyp |
hypothetical protein | 619 | 620 ctx | neighborhood:614 |
Rv3391 acrA1 |
acyl-CoA-reductase AcrA | 589 | 589 ctx | cooccurence:579 |
Rv0466 hyp |
hypothetical protein | 557 | 557 ctx | cooccurence:553 |
Rv0383c ttfA hyp |
hypothetical protein | 551 | 552 ctx | cooccurence:537 |
Rv3527 hyp |
hypothetical protein | 544 | 545 ctx | cooccurence:542 |
Rv2991 hyp |
hypothetical protein | 543 | 544 ctx | cooccurence:541 |
Rv2743c hyp |
hypothetical protein | 543 | 543 ctx | cooccurence:543 |
Rv3415c hyp |
hypothetical protein | 542 | 543 ctx | cooccurence:541 |
Rv3906c hyp |
hypothetical protein | 530 | 530 ctx | cooccurence:526 |
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: toxin
- MTBC0 PGAP product: SRPBCC family protein
- Pfam (hmmscan --cut_ga): Polyketide_cyc2 PF10604.16 (E=5e-25)
- (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_215425.1)
- Domains: Pfam-A via hmmscan --cut_ga — Polyketide_cyc2 (PF10604.16)
- 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
COG3427 - Curated reference: UniProt P9WJ05 (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 —
53 functional partner(s); context anchor
Rv0909 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000965|Rv0910| MAKLSGSIDVPLPPEEAWMHASDLTRYREWLTIHKVWRSKLPEVLEKGTVVESYVEVKGMPNRIKWTIVRYKPPEGMTLNGDGVGGVKVKLIAKVAPKEHGSVVSFDVHLGGPALLGPIGMIVAAALRADIRESLQNFVTVFAG