Rv2310 Resolved · high auto-curated
H37Rv Rv2310 · MTBC0 - ·
114 aa · 2583435–2583779 (+) ·
RefSeq NP_216826.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | excisionase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Excisionase. Pfam: HTH_17 (PF12728.14). |
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 |
P9WLC3
SwissProt · reviewed
· Predicted
|
|---|---|
| UniProt name | Uncharacterized protein Rv2310 |
UniProt still lists this protein as Uncharacterized protein Rv2310; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Helix-turn-helix domain |
| Orthologous group | COG3311 |
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 | 1.054 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 |
|---|---|---|---|---|
HTH_17 | PF12728.14 | 3.8e-14 | 20–69 | Helix-turn-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3749c vapC50 hyp |
hypothetical protein | 800 | 801 ctx | cooccurence:774 |
Rv2311 hyp |
hypothetical protein | 589 | 581 ctx | neighborhood:576 |
Rv2309A hyp |
hypothetical protein | 540 | 540 ctx | neighborhood:530 |
Rv2807 hyp |
hypothetical protein | 438 | 438 | |
Rv2312 hyp |
hypothetical protein | 412 | 411 ctx | neighborhood:409 |
Rv0842 |
integral membrane protein | 661 | 55 | textmining:656 |
Rv1584c |
phage protein | 870 | 47 | textmining:870 |
Rv2657c |
prophage protein | 521 | 47 | textmining:518 |
Rv0061c hyp |
hypothetical protein | 803 | 41 | textmining:803 |
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): excisionase
- Pfam (hmmscan --cut_ga): HTH_17 PF12728.14 (E=4e-14)
- (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_216826.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_17 (PF12728.14)
- 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
COG3311 - Curated reference: UniProt P9WLC3 (SwissProt, reviewed; 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 — 9 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2310| MVAALHAGKAVTIAPQSMTLTTQQAADLLGVSRPTVVRLIKSGELAAERIGNRHRLVLDDVLAYREARRQRQYDALAESAMDIDADEDPEVICEQLREARRVVAARRRTERRRA