Rv1870c Family assigned · low auto-curated · to review
H37Rv Rv1870c · MTBC0 - ·
211 aa · 2120795–2121430 (-) ·
RefSeq NP_216386.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | No Pfam domain above threshold; Foldseek indicates a fold similar to 4uob-assembly1_A Crystal structure of Deinococcus radiodurans Endonuclease III-3 (prob 1.00, TM 0.56). Structure-based, putative. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed (flagged for human review).
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 |
P95145
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Endonuclease |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
L Replication, recombination and repair
|
|---|---|
| eggNOG description | DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N- glycosidic bond, leaving an AP (apurinic apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate |
| Orthologous group | COG0177 |
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 | 1.834 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 5 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.42% of strains (615) · clonal |
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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Structural neighbours (Foldseek on the ESMFold model, exploratory)
ESMFold model confidence: mean pLDDT 95.2 (very high). A confident model makes the fold comparison meaningful.
Best matches against the PDB, ranked by Foldseek homology probability. A high probability / TM-score suggests a shared fold; unless flagged sig (E < 0.01) these are fold hypotheses, not assignments.
| Target | Prob | TM | E-value | Description |
|---|---|---|---|---|
4uob-assembly1_A |
1.00 | 0.56 | 3.6e-03 sig | 4uob-assembly1_A Crystal structure of Deinococcus radiodurans Endonuclease III-3 |
8a5g-assembly1_A |
1.00 | 0.57 | 8.2e-03 sig | 8a5g-assembly1_A Crystal structure of Deinococcus radiodurans Endonuclease III-3 double mutant |
7ulc-assembly1_A |
1.00 | 0.55 | 1.5e-02 | 7ulc-assembly1_A Crystal structure of queuine salvage enzyme DUF2419 mutant D231N, in complex with queuosine-5'-monophosphate |
7u5a-assembly2_B |
1.00 | 0.54 | 1.1e-02 | 7u5a-assembly2_B Crystal structure of queuine salvage enzyme DUF2419 mutant K199C, complexed with queuosine |
7u1o-assembly1_A |
1.00 | 0.54 | 2.1e-02 | 7u1o-assembly1_A Crystal structure of queuine salvage enzyme DUF2419 complexed with queuosine |
7ayy-assembly4_DDD |
1.00 | 0.47 | 1.0e-02 | 7ayy-assembly4_DDD Structure of the human 8-oxoguanine DNA Glycosylase hOGG1 in complex with activator TH10785 |
7ugk-assembly1_A |
1.00 | 0.51 | 4.1e-02 | 7ugk-assembly1_A Crystal structure of the human queuine salvage enzyme DUF2419, wild-type apo form |
4aia-assembly4_D |
1.00 | 0.61 | 1.7e-01 | 4aia-assembly4_D The structural basis of 3-methyladenine recognition by 3- methyladenine DNA glycosylase I (TAG) from Staphylococcus aureus |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1869c (reductase), high confidence from genomic context alone (score 783 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) |
|---|---|---|---|---|
Rv1297 rho |
transcription termination factor Rho | 820 | 821 | coexpression:796 |
Rv1871c hyp |
hypothetical protein | 814 | 815 ctx | neighborhood:799 |
Rv1631 coaE |
dephospho-CoA kinase CoaE | 811 | 812 | coexpression:801 |
Rv0427c xthA |
exodeoxyribonuclease III protein XthA | 818 | 799 | experimental:403 database:641 |
Rv3921c yidC |
membrane protein insertase YidC | 788 | 789 | coexpression:788 |
Rv1869c |
reductase | 783 | 783 ctx | neighborhood:773 |
Rv3920c hyp |
hypothetical protein | 732 | 732 | coexpression:732 |
Rv1872c lldD2 |
L-lactate dehydrogenase | 611 | 611 ctx | neighborhood:595 |
Rv1613 trpA |
tryptophan synthase subunit alpha | 558 | 559 | coexpression:554 |
Rv0670 end |
endonuclease IV | 530 | 480 | experimental:441 |
Rv2902c rnhB |
ribonuclease HII | 512 | 467 | coexpression:459 |
Rv1614 lgt |
prolipoprotein diacylglyceryl transferase | 459 | 460 | coexpression:441 |
Rv1873 hyp |
hypothetical protein | 443 | 443 ctx | neighborhood:441 |
Rv0797 |
insertion sequence element IS1547 transposase | 441 | 442 ctx | cooccurence:425 |
Rv0188 |
transmembrane protein | 432 | 432 ctx | cooccurence:432 |
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): hypothetical protein
- Foldseek best: 4uob-assembly1_A Crystal structure of Deinococcus radiodurans Endonuclease III-3 (prob 1.00, E=4e-03, TM=0.56)
- (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_216386.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG0177 - Curated reference: UniProt P95145 (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)
- Model confidence: ESMFold per-residue pLDDT (mean 95.2, very high)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
30 functional partner(s); context anchor
Rv1869c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1870c| MPPRIAGMRLLVIKPEPLARRLLKLAGTTYAAEAGIRIRDKPMPLFQLLVLCMLASKPIGAATAARAARELFCSGLRTPKAVLSAERQTMISAFGRAHYVRYDESSATRLTAIAHRVRDEYSGDLRELAQRTRPDVSAAKRMLKTFNGIGDTGADIFLREVQDVWIWVRPYFDDRATAAAKQLGLPTDPKKLASVAPSSNALLAAALVRVA