Rv2090 Resolved · high auto-curated
H37Rv Rv2090 · MTBC0 - ·
393 aa · 2347373–2348554 (+) ·
RefSeq NP_216606.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 5'-3' exonuclease |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 5'-3' exonuclease. Pfam: 5_3_exonuc_N (PF02739.23), 5_3_exonuc (PF01367.26). |
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 |
P9WNU3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 5'-3' exonuclease |
| EC (curated) |
EC 3.1.11.-
|
| Curated function | 5'-3' exonuclease acting preferentially on double-stranded DNA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| Preferred name | polA_1 |
| eggNOG description | 5'-3' exonuclease |
| Orthologous group | COG0258 |
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.841 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 11 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 |
|---|---|---|---|---|
5_3_exonuc_N | PF02739.23 | 3.1e-45 | 80–260 | 5'-3' exonuclease, N-terminal resolvase-like domain |
5_3_exonuc | PF01367.26 | 2.0e-19 | 269–353 | 5'-3' exonuclease, C-terminal SAM fold |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: recA (recombinase A), high confidence from genomic context alone (score 926 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2116 lppK |
lipoprotein LppK | 948 | 944 | experimental:772 database:630 |
Rv0002 dnaN |
DNA polymerase III subunit beta | 948 | 944 | experimental:772 database:630 |
Rv1277 hyp |
hypothetical protein | 937 | 930 | experimental:777 database:652 |
Rv2737c recA |
recombinase A | 952 | 926 ctx | cooccurence:537 experimental:455 database:585 |
Rv2529 hyp |
hypothetical protein | 891 | 876 | experimental:662 database:622 |
Rv3731 ligC |
DNA ligase C | 858 | 849 | experimental:429 database:569 |
Rv0938 ligD |
multifunctional non-homologous end joining DNA repair protein/ATP dependent DNA ligase LigD | 877 | 828 | experimental:429 database:569 |
Rv3062 ligB |
DNA ligase | 834 | 823 | experimental:429 database:569 |
Rv2101 helZ |
helicase HelZ | 830 | 810 | experimental:447 database:660 |
Rv1278 hyp |
hypothetical protein | 829 | 807 | experimental:432 database:652 |
Rv2089c pepE |
dipeptidase PepE | 807 | 799 ctx | neighborhood:788 |
Rv1329c dinG |
ATP-dependent helicase DinG | 819 | 796 | experimental:469 database:621 |
Rv1179c hyp |
hypothetical protein | 766 | 753 | experimental:430 database:580 |
Rv1947 hyp |
hypothetical protein | 766 | 753 | experimental:430 database:580 |
Rv1961 hyp |
hypothetical protein | 766 | 752 | experimental:430 database:580 |
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): 5'-3' exonuclease
- Pfam (hmmscan --cut_ga): 5_3_exonuc_N PF02739.23 (E=3e-45), 5_3_exonuc PF01367.26 (E=2e-19)
- (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_216606.1)
- Domains: Pfam-A via hmmscan --cut_ga — 5_3_exonuc_N (PF02739.23), 5_3_exonuc (PF01367.26)
- 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
COG0258 - Curated reference: UniProt P9WNU3 (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 —
110 functional partner(s); context anchor
recA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2090| MPAPDPMRGDPPHPAPPRLRSPLDPTSGDPLHPAPPRLRSPLDPTSGDPLHPAPPRLRSPLDPTSGDPLHPAPPRLRSPLVLLDGASMWFRSFFGVPSSITAPDGRPVNAVRGFIDSMAVVITQQRPNRLAVCLDLDWRPQFRVDLIPSYKAHRVAEPEPNGQPDVEEVPDELTPQVDMIMELLDAFGIAMAGAPGFEADDVLGTLATRERRDPVIVVSGDRDLLQVVADDPVPVRVLYLGRGLAKATLFGPAEVAERYGLPAHRAGAAYAELALLRGDPSDGLPGVPGVGEKTAATLLARHGSLDQIMAAADDRKTTMAKGLRTKLLAASAYIKAADRVVRVATDAPVTLSTPTDRFPLVAADPERTAELATRFGVESSIARLQKALDTLPG