Rv2179c Resolved · high auto-curated
H37Rv Rv2179c · MTBC0 mtbc0_002314 ·
168 aa · 2467818–2468324 (-) ·
RefSeq NP_216695.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 3'-5' exoribonuclease |
|---|---|
| MTBC0 PGAP re-annotation | polyadenylate-specific 3'-exoribonuclease AS |
| Revised (this work) | Polyadenylate-specific 3'-exoribonuclease AS. Pfam: Rv2179c-like (PF16473.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJ73
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 3'-5' exoribonuclease Rv2179c |
| EC (curated) |
EC 3.1.13.-
|
| Curated function | Exonuclease that cleaves single-stranded 3' overhangs of double-stranded RNA. Has no activity with 5' overhangs. Has negligible endonuclease activity. Can bind ATP, dATP and AMP (in vitro); the nucleotide occupies the predicted substrate binding site. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolism
|
|---|---|
| eggNOG description | Exonuclease that cleaves single-stranded 3' overhangs of double-stranded RNA |
| Orthologous group | 2CPKU |
| Gene Ontology (6) |
GO:0003674, GO:0005488, GO:0005515, GO:0008150, GO:0040007, GO:0042802
|
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 | 0.334 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Rv2179c-like | PF16473.12 | 6.4e-12 | 2–154 | 3'-5' exoribonuclease Rv2179c-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2180c (integral membrane protein), high confidence from genomic context alone (score 884 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2180c |
integral membrane protein | 884 | 884 ctx | neighborhood:882 |
Rv2178c aroG |
phospho-2-dehydro-3-deoxyheptonate aldolase AroG | 789 | 779 ctx | neighborhood:779 |
Rv2181 |
alpha-(1-2)-phosphatidylinositol mannoside mannosyltransferase | 805 | 776 ctx | neighborhood:775 |
Rv2744c 35kd_ag hyp |
hypothetical protein | 773 | 774 ctx | cooccurence:773 |
Rv0948c |
chorismate mutase | 773 | 774 ctx | cooccurence:773 |
Rv2468c hyp |
hypothetical protein | 764 | 764 ctx | cooccurence:764 |
Rv3605c hyp |
hypothetical protein | 746 | 746 ctx | cooccurence:746 |
Rv3412 hyp |
hypothetical protein | 728 | 728 ctx | cooccurence:728 |
Rv2520c |
membrane protein | 721 | 721 ctx | cooccurence:720 |
Rv2170 |
GCN5-like N-acetyltransferase | 715 | 716 ctx | cooccurence:714 |
Rv2754c thyX |
thymidylate synthase ThyX | 713 | 713 ctx | cooccurence:711 |
Rv1209 hyp |
hypothetical protein | 702 | 702 ctx | cooccurence:702 |
Rv3311 hyp |
hypothetical protein | 700 | 700 ctx | cooccurence:700 |
Rv1638A hyp |
hypothetical protein | 682 | 682 ctx | cooccurence:681 |
Rv3915 cwlM |
peptidoglycan hydrolase | 670 | 670 ctx | cooccurence:670 |
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: 3'-5' exoribonuclease
- MTBC0 PGAP product: polyadenylate-specific 3'-exoribonuclease AS
- Pfam (hmmscan --cut_ga): Rv2179c-like PF16473.12 (E=6e-12)
- (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_216695.1)
- Domains: Pfam-A via hmmscan --cut_ga — Rv2179c-like (PF16473.12)
- 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
2CPKU - Curated reference: UniProt P9WJ73 (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 —
46 functional partner(s); context anchor
Rv2180c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002314|Rv2179c| MRYFYDTEFIEDGHTIELISIGVVAEDGREYYAVSTEFDPERAGSWVRTHVLPKLPPPASQLWRSRQQIRLDLEEFLRIDGTDSIELWAWVGAYDHVALCQLWGPMTALPPTVPRFTRELRQLWEDRGCPRMPPRPRDVHDALVDARDQLRRFRLITSTDDAGRGAAR